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Hidden Disturbance in Regional Vegetation Dynamics from Road Paving in a Coupled Natural and Human System

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Title:
Hidden Disturbance in Regional Vegetation Dynamics from Road Paving in a Coupled Natural and Human System A Case Study from the Southwest Amazon
Creator:
Klarenberg, Geraldine
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[Gainesville, Fla.]
Florida
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University of Florida
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english
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1 online resource (287 p.)

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Degree:
Doctorate ( Ph.D.)
Degree Grantor:
University of Florida
Degree Disciplines:
Agricultural and Biological Engineering
Committee Chair:
MUNOZ-CARPENA,RAFAEL
Committee Co-Chair:
KIKER,GREGORY A
Committee Members:
BROWN,MARK T
CROPPER,WENDELL P,JR
PERZ,STEPHEN GEORGE

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Subjects / Keywords:
amazon -- roads -- timeseries -- vegetation
Agricultural and Biological Engineering -- Dissertations, Academic -- UF
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bibliography ( marcgt )
theses ( marcgt )
government publication (state, provincial, terriorial, dependent) ( marcgt )
born-digital ( sobekcm )
Electronic Thesis or Dissertation
Agricultural and Biological Engineering thesis, Ph.D.

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Abstract:
Infrastructure development, specifically road construction, contributes socio-economic benefits to society worldwide. However, detrimental environmental effects of road construction have been documented, most notably increased deforestation. Beyond deforestation, this study hypothesized that road construction introduces degradation, "unseen" regional effects on forests, over time. This potentially leads to changes in ecosystem services a forest provides. In coupled natural-human (CNH) systems this has implications for both nature and humans. At a regional scale, such changes would be visible in vegetation dynamics: as species composition shifts or vegetation structure changes, the phenology patterns, or vegetation dynamics, change. To test this hypothesis, we use a long-term remotely sensed vegetation index, EVI2, as a proxy for vegetation dynamics, combined with field-based socio-ecological data and biophysical data from global data sets, for a transboundary region in the southwestern Amazon that has been subject to construction of the Inter-Oceanic Highway (IOH) during our study period of (1987 to 2009). These data were available for 99 communities that experienced road paving at different times. Specialized time series analysis techniques were applied, designed to uncover underlying structure of vegetation dynamics and find linkages with other localized variables. First, we found 4 areas of common vegetation dynamics associated with the average extent of road construction, Vegetation Dynamics Clusters (VDCs). We analyzed the importance of shared trends and explanatory variables within and across VDCs with a multivariate time series reduction technique, Dynamic Factor Analysis. We found that human-related covariates become more important in explaining forest structure dynamics as road construction intensity increases. Trends, indicators of underlying unexplained effects, become relatively less important as construction increases and are dominated by lower frequency signals; potentially influenced by climate indices. By applying novel causality analyses, we identified increased feedback in causal relationships from vegetation dynamics to biophysical variables from the unpaved to the paved state. This potentially indicates less stability, and more opportunity for vegetation changes to affect the local and global climate. This study indicates the need for a focus on regional degradation as part of road infrastructure development projects in forest-rich countries. ( en )
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In the series University of Florida Digital Collections.
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Includes vita.
Bibliography:
Includes bibliographical references.
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Description based on online resource; title from PDF title page.
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This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Thesis:
Thesis (Ph.D.)--University of Florida, 2017.
Local:
Adviser: MUNOZ-CARPENA,RAFAEL.
Local:
Co-adviser: KIKER,GREGORY A.
Electronic Access:
RESTRICTED TO UF STUDENTS, STAFF, FACULTY, AND ON-CAMPUS USE UNTIL 2018-06-30
Statement of Responsibility:
by Geraldine Klarenberg.

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6/30/2018
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HIDDEN DISTURBANCE IN REGIONAL VEGETATION DYNAMICS FROM ROAD PAVING IN A COUPLED NATURAL AND HUMAN SYSTEM: A CASE STUDY FROM THE SOUTHWEST AMAZON By GERALDINE KLARENBERG A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2017

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2017 Geraldine Klarenberg

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To my children and my parents

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4 ACKNOWLEDGMENTS I would like to thank my advisor, Dr Rafa el Muoz Carpena for his unwavering support throughout the years. His enthusiasm for science, passion for learning new things and his willingness to discuss ideas and methods have been invaluable to my development as a scientist I would also like to thank my Co Chair Dr. Greg Kiker and my committee, Dr. Stephen Perz, Dr. Wendell Cropper and Dr. Mark Brown for their guidance and feedback I am grateful for the time they have made available to provide support and input into this research. The diversity of their viewpoints a nd backgrounds have been important in increasing my understanding of various disciplines I am indebted to the N ational S cience F oundation for the funding provided for the first part of my research. From the UF Department of A gricultural and B iological Eng ineering, I am grateful to Dr. Ray Huffaker, Dr. Miguel Campo Bescos, Dr. Matteo Convertino Dr. Galia Selaya Miles Medina and from the UF Department of Geography Dr. Jane Southworth, Dr Matt Marsik, Dr Erin Bunting and Dr Likai Zhu. Without their help with data collection, guidance on methods and discussions on topics of interest, this study would have surely not come to be Staff at t he UF High Performance Computing Center, specifically Matt Gitzendanner Max Prokopenko, Alex Moska lenko and Yin g Zhang, have been tremendously helpful and I than k them for all their assistance There are so many friends who took this journey with me; some on the same journey, others on a completely different path, but always understanding and caring. have buoyed me these past years

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5 Last but not least I would like to thank my family from the bottom of my heart First and foremost, my kids Sebastiaan and Amara who never asked for their mom to do a PhD, but who ha d to deal with my absences, long work hours and forgetfulness. They put up with it, loved me more than anything anyway and were my indefatigable cheerleaders during that last push to finish. My husband Chris and his kids Charlotte and Jack for the love, s upport and understanding during these long years. Chris support was invaluable as he provided a listening ear (for both my excitement as well as my griping ) helpe d me with computer problems, always kept me grounded and gave me a place of love to come h ome to every day F inally, my parents Richard and Marga they raised me to have grit and to believe in myself. Without those two things, this dissertation would not have come to fruition While far away, they are always in my thoughts and my heart We have had to miss each other for too long and I am looking forward to more visits home.

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6 TABLE OF CONTENTS page ACKNOWLEDGMENTS ................................ ................................ ................................ ...... 4 LIST OF TABLES ................................ ................................ ................................ ................ 9 LIST OF FIGURES ................................ ................................ ................................ ............ 11 LIST OF ABBREVIATIONS ................................ ................................ ............................... 13 ABSTRACT ................................ ................................ ................................ ........................ 15 CHAPTER 1 INTRODUCTION ................................ ................................ ................................ ........ 17 Coupled Human Natural Systems, Complexity and Change ................................ ..... 17 Stability, Regime Shifts and Resilience ................................ ............................... 18 Road Infrastructure Development and Forest Degradation ................................ 20 Ecosystem Services and Ecosystem Function ................................ ................... 21 Ecosystem Function and Vegetation Dynamics ................................ .................. 23 The Study Area ................................ ................................ ................................ .... 25 Hypothesis and Sub Hypotheses ................................ ................................ ............... 31 Hypothesis ................................ ................................ ................................ ............ 31 Expected Significance ................................ ................................ .......................... 31 Sub Hypotheses ................................ ................................ ................................ ... 32 2 A SPATIAL TE MPORAL DATABASE TO EVALUATE ROAD DEVELOPMENT IMPACTS IN A COUPLED NATURAL HUMAN SYSTEM IN A TRI NATIONAL FRONTIER IN THE AMAZON ................................ ................................ .................... 41 Background and Summary ................................ ................................ ......................... 41 Methods ................................ ................................ ................................ ....................... 44 Data Collection and Compilation ................................ ................................ ......... 44 Human Variables ................................ ................................ ................................ .. 44 Environmental Variables ................................ ................................ ...................... 47 Stationary Variables ................................ ................................ ............................. 53 Data Records ................................ ................................ ................................ .............. 56 Technical Valida tion ................................ ................................ ............................. 57 Usage Notes ................................ ................................ ................................ ......... 59 3 CLUSTER ANALYSIS OF VEGETATION DYNAMICS AND ASSOCIATION WITH ROAD PAVING ................................ ................................ ................................ 65 Background ................................ ................................ ................................ ................. 65 Methods ................................ ................................ ................................ ....................... 68

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7 Data ................................ ................................ ................................ ...................... 68 Ti me Series Clustering Based on an Adaptive Dissimilarity Index ..................... 69 Clustering Validation Measures ................................ ................................ ........... 71 Number of States and Breakpoint Analysis ................................ ......................... 73 Data Availability ................................ ................................ ................................ .... 74 Results ................................ ................................ ................................ ........................ 74 Four EVI2 Clusters Along a Road Paving Gradient ................................ ............ 74 Additional Cluster Analysis on Biophysical Variables ................................ ......... 75 States and Breakpoint A nalysis ................................ ................................ ........... 76 Discussion ................................ ................................ ................................ ................... 76 Assessment of Final Clusters ................................ ................................ .............. 76 Comparison of States Changes ................................ ................................ ........... 77 Methodological Findings: Cluster Selection and State Changes ........................ 78 4 CHANGING LANES: HIGHWAY PAVING IN THE SOUTHWESTERN AMAZON ALTERS LONG TERM TRENDS AND DRIVERS OF REGIONAL VEGETATION DYNAMICS ................................ ................................ ........................ 88 Background ................................ ................................ ................................ ................. 88 Results ................................ ................................ ................................ ........................ 93 Identification of Clusters Vegetation Dynamics and their Association with Road Paving Extent ................................ ................................ .......................... 93 Common Trends Explain the Shared Variability of Each VDC ........................... 94 In a D isturbed System State, Covariates Explain More of the Variance In Vegetation Dynamics Than in an Undisturbed System State .......................... 95 Variables Associated with Anthropogenic Activity Increase in Importance in Explaining Vegetation Dynamics in the Disturbed System State .................... 96 Among Natural Covariates, Temperature is the Main Direct Driver of Vegetation Dynamics ................................ ................................ ........................ 98 Low Frequency Signals Explain Trend Behavior Across the Study Area as a Whole, but Dominate Particularly in the Paved State ................................ .... 101 Unpaved to Paved Conditions Repr esent Two Stable System States with a Transition State in Between Them ................................ ................................ 103 Discussion ................................ ................................ ................................ ................. 104 Main Findings ................................ ................................ ................................ ..... 104 Broader Impact s ................................ ................................ ................................ 105 Limitations and Further Research ................................ ................................ ..... 106 Methods ................................ ................................ ................................ ..................... 107 Study Area ................................ ................................ ................................ .......... 107 Response Covaria te: Vegetation Dynamics, EVI2 ................................ ............ 108 Candidate Covariates Related to Human Activity ................................ ............. 109 Candidate Covariates Associated with Biophysical Processes ........................ 110 Clustering ................................ ................................ ................................ ........... 111 Lagging and Reduction of Covariate Data Set ................................ .................. 112 Dynamic Factor Analysis ................................ ................................ ................... 113 Importance of Trends and Covariates ................................ ............................... 114 Spectral Analysis of Trends ................................ ................................ ............... 115

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8 Software Used ................................ ................................ ................................ .... 115 Data Availability ................................ ................................ ................................ .. 116 5 CAUSALITY ANALYSIS OF REGIONAL BIOPHYSICAL AND VEGETATION VARIABLES REVEALS INCREASED FEEDBACK ALONG A ROAD PAVING GRADIENT IN THE SW AMAZON ................................ ................................ ........... 128 Background ................................ ................................ ................................ ............... 128 Materials and Methods ................................ ................................ ............................. 135 Study Site and Data ................................ ................................ ........................... 135 Methods ................................ ................................ ................................ .............. 138 Data Availability ................................ ................................ ................................ .. 145 Results ................................ ................................ ................................ ...................... 145 Identification of Four Vegetation Dynamics Clusters along a Road Paving Gradient ................................ ................................ ................................ ........... 145 Signal separation reveals different signals for vegetation in each VDC ........... 146 Causality testing of signals for three VDCs indicates an increase in causal relationships for EVI ................................ ................................ ........................ 148 Discussion ................................ ................................ ................................ ................. 150 Vegetation Dynamics Clusters and Signals ................................ ...................... 150 Application of Causality Analyses on Complex Systems: Implications of Findings and Methods ................................ ................................ .................... 151 Concluding Remarks ................................ ................................ ................................ 155 6 CONCLUSIONS ................................ ................................ ................................ ........ 169 Main Findings ................................ ................................ ................................ ............ 169 Scientific Findings ................................ ................................ .............................. 169 Methodol ogical Findings ................................ ................................ .................... 176 Limitations And Future Research ................................ ................................ ............. 177 Broader Impacts ................................ ................................ ................................ ........ 181 APPENDIX A SUPPLEMENTARY MATERIALS FOR CHAPTER 4 ................................ .............. 184 B SUPPLEMENTARY MATERIALS FOR CHAPTER 5 ................................ .............. 212 C ADDITIONAL NOTES ON GRANGER CAUSALITY ANALYSIS ............................ 243 Granger Prediction ................................ ................................ ................................ .... 243 Results for Granger Prediction ................................ ................................ ................. 245 Discussion ................................ ................................ ................................ ................. 246 LIST OF REFERENCES ................................ ................................ ................................ 266 BIOGRAPHICAL SKETCH ................................ ................................ .............................. 287

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9 LIST OF TABLES Table page 2 1 Overview of dynamic variables collected and compiled for the area in Madre de Dios (Peru), Acre (Brazil) and Pando (Bolivia), the MAP area. ....................... 60 2 2 Overview of stationary data collected and compiled for the area in Madre de Dios (Peru), Acre (Brazil) and Pando (Bolivia), the MAP area. ............................ 63 3 1 Dunn Index and Silhouette Width results from all clustering options for EVI2 ..... 79 3 2 Values of the validation measures indicating the best number of VDCs after a hierarchical cluster analysis. ................................ ................................ .................. 80 4 1 List of variables used in the analysis, their unit of measure, and source. .......... 117 4 2 Results of dynamic factor analyses of Enhanced Vegetation Index (EVI2) for 4 Vegetation Dynamics Areas (VDCs). ................................ ................................ 119 5 1 Periodicities that were selected to create reconstructed signals of time series and the contribution of each signal to the decomposition ................................ ... 157 5 2 Surrogate data test results ................................ ................................ ................... 160 5 3 Significant cross skill mapping after applying extended CCM ............................ 163 A 1 Overview of communities included in the study. ................................ ................. 184 A 2 Statistical characteristics of mon thly EVI2 time series (1982 2010) per VDC 187 A 3 Statistical properties of the monthly area weighted time series of C andidate Explanatory Variables ................................ ................................ .......................... 188 A 4 Lags applied to time series of candidate explanatory variables. ........................ 190 A 5 Results of Variation Inflation Factor (VIF) analysis for explanatory variables included in dynamic factor analyses per VDC. ................................ .................... 191 A 6 Dynamic Factor Model (Model I, trends only) goodness of fit results of selected (best) models for individual communities. ................................ ............. 192 A 7 Average relative importance of trends and explanatory variables in dynamic factor analyses (Model II, trends and explanatory variables) simulating EVI2 ... 195 A 8 Dynamic Factor Model (Model II, trends and explanatory variables) goodness of fit results of selected (best) models for in dividual communities. ... 199

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10 A 9 Dynamic Factor Model s II (trends and explanatory variables). ........................... 202 A 10 M odels II (trends and explanatory variables), for each community. ................... 206 A 11 Frequencies, cycle lengths and spectral power density values for the Pacific Decadal Oscillation (PDO) ................................ ................................ ................... 210 B 1 Cycle lengths (months) used to set the window length in Singular Spectrum Analysis (based on spectral de nsity results). ................................ ...................... 212 B 2 Weighted adjacency matrices ................................ ................................ .............. 213 B 3 Relevant lags identified with extended CCM ................................ ....................... 214 C 1 Results of Granger causality analysis for VDC 4 ................................ ................ 247 C 2 VAR models with p value for the Ljung Box test > 0.05 ................................ ...... 248 C 3 Granger causality test results for all v ariables (at selected AR order) ............... 256

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11 LIST OF FIGURES Figure page 1 1 Schematic representation of the relationships between ecosystem services and fun ctions, and the human system, including the role of vegetation dynamics. ................................ ................................ ................................ ................ 39 1 2 The MAP area in Peru, Brazil and Bolivia, with the Inter Oceanic Highway, other roads, protected areas major cities and communities ................................ 40 2 1 Comparison of monthly values per communi ty polygon for AVHRR derived EVI (1982 2010) ................................ ........................ 64 3 1 Average values of EVI2 and biophysical variables p er community for the period 1987 2009 ................................ ................................ ................................ ... 81 3 2 Analysis framework for clustering analysis ................................ ............................ 83 3 3 Selection criteria for determination of the appropriate number of clusters ........... 84 3 4 Dendrogram of EVI2 time series clusters, with 4 clusters selected. ..................... 85 3 5 Characteristics of the study area ................................ ................................ ........... 86 4 1 Characteristics of the study area after clustering analysis ................................ .. 121 4 2 Contributions of model components of the final VDC DFMs II for each community to explaining variance in vegetation dynamics ................................ 122 4 3 Proportion of variance explained by each covariate for each community .......... 123 4 4 Lagged time series of the covariates used in the final Dynamic Factor Models (DFMs) II for each VDC ................................ ................................ ........................ 124 4 5 coefficients of the covariates used in the final Dynamic Factor Models (DFMs) II for each VDC ................................ ................................ ........................ 125 4 6 Characteristics of the trends (unknown explained variance) in the selected Dynamic Factor Models II ................................ ................................ .................... 126 4 7 Flow chart o f methods ................................ ................................ .......................... 127 5 1 Analysis framework for causality analysis ................................ ........................... 164 5 2 Characteristics of the study area after clustering analysis ................................ 165 5 3 Reconstructed time series, the signals, after Singular Spectrum Analysis ........ 166

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12 5 4 Heat maps for the observed EVI2, reconstructed EVI2 and line plots for the observed a nd reconstructed EVI2 ................................ ................................ ........ 167 5 5 Networks of cross mapping skill ( ) of deterministic signals of EVI ( ) per VDC, after testing for false positives due to synchronicity ............................ 168 A 1 Simulated and observed monthly Enhanced Vegetation Index (EVI2) time series ................................ ................................ ................................ .................... 211 B 1 Observed, area weighted time series for each VDC ................................ ........... 216 B 2 Results of Singular Value Decomposition (VDC) of time series of VDC 1 ......... 217 B 3 Results of Singular Value Decomposition (VDC) of time series o f VDC 2 ......... 221 B 4 Results of Singular Value Decomposition (VDC) of time series of VDC 3 ......... 225 B 5 Results of Singular Value Decomposition (VDC) of time series of VDC 4 ......... 229 B 6 Results of Singular Value Decomposition (VDC) of time series of climate indices ................................ ................................ ................................ ................... 233 B 7 Line plots and heatmaps of original and reconstructed time series of all variables for all 4 VDCs ................................ ................................ ........................ 234 B 8 Nonlinear cross prediction s kill to determine stationarity of signals, per VDC ... 241 B 9 Networks of cross mapping skill ( ) of deterministic signals ( ) per VDC, after testing for false positives due to synchronicity ................................ .. 242 C 1 Conditional Granger causality ( p <0.05) results for VDC 1 and VDC 4 ............... 265

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13 LIST OF ABBREVIATIONS AAFT Amplitude Adjusted Fourier Transform AIC AMO Atlantic Multidecadal Oscillation AVHRR Advanced Very High Resolution Radiometer BEF Biodiversity Ecosystem Functioning BIC Bayesian Information Criterion CCM Convergent Cross Mapping CNH Coupled Natural Human CPC Climate Prediction Center (NOAA) CRU Climate Research Center (University of East Anglia) DBH Diameter at breast height DEM Digital Elevation Map DFA Dynamic Factor Analysis DFM Dynamic Factor Model ENSO El Nio / Southern Oscillation EVI Enhanced Vegetation Index EVI2 Enhanced Vegetation Index 2 fPAR Fraction of Photosynthetically Active Radiation GC Granger Causality IIRSA Initiative for the Integration of the Regional Infrastructure of South America IOH Inter Oceanic Highway IQR Interquartile Range LAI Leaf Area Index

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14 MAP Madre de Dios / Acre / Pando MASL M eters above sea level MEI Multivariate ENSO Index MODIS Moderate Resolution Imaging Spectroradiometer NDVI Normalized Difference Vegetation Index NFTP Non Forest Timber Product NOAA National Oceanic and Atmospheric Administration NPP Net primary Production NSE Nash Sutcliffe Coefficient of Efficiency PDO Pacific Decadal Oscillation PET Potential Evapotranspiration PFT Plant Functional Type PPS Pseudo Phase Space SSA Singular Spectrum Analysis SVD Singular Value Decomposition UN REDD United Nations Programme on Reducing Emissions from Deforestation and Forest Degradation VDC Vegetation Dynamics Cluster VIF Variance Inflation Factor VIP Vegetation Index and Phenology (research group at the University of Arizona)

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15 Abstract of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy HIDDEN DISTURBANCE IN REGIONAL VEGETATION DYNAMICS FROM ROAD PAVING IN A COUPLE D NATURAL AND HUMAN SYSTEM: A CASE STUDY FROM THE SOUTHWEST AMAZON By Geraldine Klarenberg December 2017 Chair: Rafael Muoz Carpena Cochair: Greg Kiker Major: Agricultural and Biological Engineering Infrastructure development, specifically road constru ction, contributes socio economic benefits to society worldwide. However, detrimental environmental effects of road construction have been documented most notably increased deforestation. Beyond deforestation, this study hypothesize d that road constructio n introduces degradation, regional effects on forests over time. This potentially leads to changes in ecosystem services a forest provides. In coupled natural human (CNH) systems this has implications for both nature and humans. At a regional scale, s uch changes would be visible in vegetation dynamics: as species composition shifts or vegetation structure changes, the phenology patterns or vegetation dynamics change To test this hypothesis, w e use a long term remotely sensed vegetation index EVI2, as a proxy for vegetation dynamics, combined with field based socio ecological data and biophysical data from global data set s, f or a transboundary region in the southwestern Amazon that has been subject to cons truction of the Inter Oceanic Highway (IOH) during our study period of (1987 2009 ) These data were available for 99 communities that experienced road paving at different times S pecialized time series

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16 analysis techniques were applied, designed to uncover underlying structure of vegetation dy namics and find linkages with other l ocalized variables. First, we fou nd 4 areas of common vegetation dynamics associated with the average extent of road construction Vegetation Dynamics Clusters (VDCs). We analyzed the importance of shared trends and exp lanatory variables within and across VDCs with a multivariate time series reduction technique, Dynamic Factor Analysis. W e fou nd that human related covariates become more important in explaining forest structure dynamics as road construction intensity incr eases Trends, indicator s of underlying unexplained effects, become relatively less important as construction increases and are dominated by lower frequenc y signals; potentially influenced by climate indices By applying novel causality analyses, we identified increased feedback in causal relationships from vegetation dynamics to biophysical variables from the unpaved to the paved state. This potentially indicates less stability, and more opportunity for vegetation changes to affect the local and glob al climate This study indicates the need for a focus on regional degradation as part of road infrastructure development projects in forest rich countries.

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17 CHAPTER 1 INTRODUCTION Coupled Human Natural Systems, Compl exity and Change (J. Liu et al., 2007) Further than that though, it provides a framework for scientific understanding in which processes and complex interactions between human and natural systems are integrated (Chen and Y. Liu, 2014) Dynamics in one system affect dynamics in the other, and when changes occur in one, this is often carried over to the other in a nonlinear fashion. As many natural and human systems become more interwoven due to increased exploitation, expansion of human living space, increased population and climate change, research on understanding these systems is i mportant. Gaining insight into issues of ecological deterioration and sustainable development are paramount, and researching only one or the other system will be unlikely to paint a complete picture of the challenges and potential solutions. As Liu et al. (2007) point out, many systems are unique and will need unique research and solutions. All of them have characteristics of complex systems though: feedback loops, nonlinear dynamics, thresholds, time lags, heterogeneity, legacy effects, emergent properties essence, this can be summarized as spatial, temporal and organizational complexity (Pickett et al., 2005) Spatial complexity refers to spatial heterogeneity and configurations of components of the system. Temporal complexity considers the effects of past states and legacies, and organizational complexity encompasses connectivity between components. Emergent properties are an imp ortant aspect of understanding complex systems: they refer to properties that emerge as a result of complex

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18 interaction, i.e. they are not based on linear relationships and thus not easily predicted. When research ing change in complex systems, it becomes i mportan t to define change, stability and (especially) resilience in the context of the system under consideration. Stability Regime Shifts a nd Resilience It has been posited that systems can be subject to critical transitions, which involves a drastic ch ange of one state to another, due to a small change in a variable or a small stochastic disturbance. This otherwise insignificant event causes a shift in system state because the system has become increasingly fragile due to various earlier disturbances (Gu nderson and Holling, 2002; Hirota et al., 2011; Scheffer, 2009; Scheffer et al., 2009 ; 2001 ) This current thinking has evolved from classical catastrophe theory (Zeeman, 1976) a branch of bifurcation theory which particularly regards hysteresis (a fold catastrophe) and cusp bifurcati ons ( Scheffer et al., 2001 ) Hysteresis occurs in situations where the value of a physical property lags behind changes in the effect causing i t An example is algae outbreaks in surface water caused by high nutrient loads; there is usually a particular value of nutrient loading at which the system shifts from clear to an algae outbreak. However, to return the system to its original clear state, nutrient loads need to be reduced far lower than the value at which the system shifted in the first place. So, besides the catastrophical shift itself in the system, it is also more difficult to return to the original system. Zeeman (1976) provided applied examples of catastrophe theory in biology and behavioral sciences, and applications of the theory and identification of phenomena such as multimodality (the existence of multiple stable states, associated with hysteresis) have since expanded to ecology (Frelich and Reich, 1999; Gunderson and Holling, 2002; Scheffer et al., 2001 ; Wissel, 1984)

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19 Importantly Scheffer (2009) or CNH systems clear that a stable system is not necessarily in only one state: cyclical, chaotic and oscillates, or the (strange) attractor around or toward which it moves, are stable. This comp licates the identification of alternative stable regime s or change points ; and in addition, ecological systems generally display an amount of noise due to stochastic events and processes. (Holling, 1973; Scheffer et al., 2001 ) that is, the boundary of the area of the domain of an attractor. It is hypothesized that this domain chan ges over time due to hysteresis If a basin of attraction has been identified and delineated for the identity of a particular system, the mo st pressing question for practical purposes is where t he system is positioned within the basin of attraction at a particular point in time. If it is close to the edge, the outer boundary, less change or disturbance is required to cause a regime shift, a cr itical transition. A more practical and persistence of relationships within a system and [it] is a measure of the ability of these systems to absorb changes of state variables, driving variables, and p arameters, and (Holling, 1973) This description has been further refined by Cumming et al. (2005) who no te that relationships within a system often change, but in order for a

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20 its identity, and the attributes that define it. Recent studies have indicated that the Amazon system in general is possibly heading for a transition to a regime dominated by disturbances, with associated changes in water and energy cycles ( Davidson et al., 2012 ) or even that the system is cha nges (Nepstad et al., 2008; Nobre and Borma, 2009 ) Numerous studies have simulated land cover changes taking place in the Amazon due to human induced climate change, anthropogenic disturbances and positive feedback cycles (Almeyda Zambrano et al., 2010; Keller, 2009; Marsik et al., 2011 ) Road Infrastructure Development and Forest Degradation For forest ecosystems, road construction and paving are the main drivers of deforestation (Laurance et al., 2002a; Marsik et al., 2011 ) There are also signs that road paving contributes to degradation of forest systems. Previous research found that even limited logging disturbances had a permanent local effect on forest structure in Madagascar (Brown and Gurevitch, 2004) D ifferences in vegetation structure and phenology between natural and anthropogenic treefall gaps 1 to 4 years after logging we re also identified in a Bolivian forest, despite almost identical forest cover percentages (mean 88% for the anthropogenic gaps, and 91% for the natural gaps), with lower mean number of flowering and fruiting plants in anthropogenic gaps, as well as more r egeneration of non commercial pioneer species in these gaps (Felton et al., 2006) A review study concluded that in Neotropical secondary forest s, the recovery trajectory of vegetation and its characteristics is uncertain in anthropogenic settings, and dependent on site specific factors and land use (Guariguata and Ostertag, 2001)

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21 C hange s in forest structure will in turn impact components of the system : changes in tropical forest structure have been linked to modifi cations in wildlife populations in Panama (DeWalt et al., 2003) and ecosyste m productivity was found to be driven by canopy phenology in the Amazon (Restrepo Coupe et al., 2013) A forest inventory study (Baraloto et al., 2015) found differences in forest value (based on biodiversity, carbon stocks and timber and non timber forest products), and highlighted that deforestation and degra dation do not always respond similarly to road paving. Considering these findings and the need for better understanding of CNH systems, there is a need to do more research on the complexity of road paving and forest degradation. Road paving increases conne ctivity within an area and a CNH system, making it important that research considers this issue regionally. F or research purposes, f orest degradation needs a clear er meaning than this broad collection of processes and changes. In this study, the definiti on of Putz and Redford (2010) is adopted: forests that lose their defining attributes (e.g., ancient trees, fauna, and coarse woody debris) through logging, market hunting, wildfires, or invasion by exotic species, become degraded forest with the earlier definition of resilience and allows us to consider degradation in an comprehensive and systematic manner. To streamline the approach further, ecosystem services can be considered as one of these attributes, especially for CNH systems. Eco system Services a nd Ecosystem Function It has long been acknowledged in both science and society that nature provides essential services goods and cultural services to humankind the past, the focus has mainly been on tangible or direct benefits, such as materials

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22 defined in the Millennium Ecosystem Assessment ( 2005) The latter was initiated in 2001 with support of the United set out to assess the consequences of ecosystem change for human well being and to establish the scienti fic basis for actions needed to enhance the conservation and sustainable use of ecosystems and their contributions to human well The Millennium Ecosystem Assessment gives a (non exhaustive) list of various services that fall under the 4 earlier men tioned categories of ecosystem services. Using this broad approach, the ecosystem services of the Amazon as a whole have been found to be under great pressure (Foley et al., 2007) Also at smaller scales, since CNH systems consist of ecological as well as anthropogenic com ponents and influences, it is reasonable to evaluate a system from the point of view of ecosystem services. Then, i n order to evaluate CNH systems in terms of resilience and, possibly, tipping points, a decision needs to be made what identity em to consider. For this research, we propose that vegetation dynamics and structure are suitable when considering forest degradation due to their linkages with ecosystem services (Figure 1 1). This will be explained in the following sections. The concept of e cosystem services is generally regarded as a subjective metric since what is regarded as a service by one might not necessarily constitute as a service hardly ever straightforw ard and hinders measurability Instead, the associated notion of ecosystem function is more objective and more measurable E cosystem functions are defined as and services that

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23 satisfy human (De Groot et al., 2002) Hence, services are obtained from functioning of the ecosystem (Baraloto et al., 2014) Three generally recognized ecosystem functions are the carbon, the hydrological and the nutrient cycle. Each ecosystem function is a product of the natural processes that define its ecological str ucture and processes, and the natural processes are a result of interactions of biotic and abiotic components of the system (Figure 1 1). This is in line with the definition of system processes such as primary production, total plant biomass, or nutrien t, gain, loss, or concentration (Tilman, 2001) Ecosystem Function and Vegetation Dynamics Ecosystem functions that are of importance in forest areas in general are carbon storage, and diversity. Specific species can provide very specifi c and local ecosystem services (such as timber or non timber products), whereas carbon storage provides a more regional and global ecosystem service. The regional and global relevance in diversity lies mostly in functional diversity (diversity of traits), which in turn supports other functions and services such as carbon storage, hydrology and nitrogen cycles. Forests that experience a reduction in their functioning (and thus services), while still classified as a forest can be regarded as a degraded fores t, or a forest of lesser quality, from an ecosystem services point of view. The proposal to evaluate vegetation dynamics to assess forest degradation in a CNH system stems from the notion that vegetation dynamics drive ecosystem functioning, which in turn drives ecosystem services Vegetation dynamics, also termed phenology, play an important role in timing of ecosystem functions such the water and carbon cycle, or primary productivity. Phenology e.g. growth and senescence is

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24 affected by biophysical v ariables such as temperature and precipitation, and has been used extensively to evaluate impacts of climate change (Donn elly and Yu, 2017; Menzel et al., 2006) However, it also differs per species, so phenological signatures are also an expression of species composition or vegetation structure. Recent controlled experiments on the timing of flowering showed that increas es or decreases in diversity changed the timing of flowering (Wolf et al., 2017) Hence, different phenology patterns or vegetation dynamics can imply differences in species composition, vegetation structure or diversity. Vegetation dynamics are unique and a change in these dynamics implies a change in vegetation stru cture and species composition, as well as a change in subsequent ecosystem functions and services. To analyze vegetation dynamics at a regional level and a longer time period, time series of vegetation indices can be used. These remote sensing products have been used in many studies to monitor and evaluate phenology (Asner et al., 2000; Morton et al., 2014; Reed et al., 1994) The Enhanced Vegetation I ndex (EVI) is one of these products. It is calculated from surface reflectances measured by the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite in a way that it reduces the influence of aerosols and soil back scatter and decouples these influences from the vegetation signal (Huete et al., 2010) The advantage of EVI over other indexes such as the Normalized Difference Vegetation Index (NDVI) is its increased sensitivity in areas with high biomass, i.e. it does not saturate at high values (Weng, 2011) Since EVI is a measure of the contrast between absorption of blue and red wavelengths (by chlorophyll in leaves) and scatter of near infrared radiation (dependent on canopy properties such as Leaf Area Index (LAI), leaf angle d istribution, leaf morphology), it is

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25 an expression of physiological and structural properties of the canopy (Huete et al., 2010) It is sometimes also referred to as greenness mposite optical property of (Huete et al., 2002) Though it does not give exact information in terms of species composition, it can provide indications of structural change in a forest. T he relationships b etween EVI and biophysical vegetation properties such as Leaf Area Index (LAI), biomass or Gross absorbed photosynthetically active radiation) have been summarized in previo us work (Huete et al., 20 02) The link with fPAR, or chlorophyll content, is cleare st as is the link with gross primary production (though the latter was only established for temperate regions (Huete et al., 20 10) The Study Area This study focuses o n the construction of the Inter O ceanic Highway (IOH) which connect s ports on the Pacific coast of Peru with the Atlantic ports in Sout hern Brazil, and run s through the so Amazon covers an area where three nations meet: Peru, Bolivia and Brazil (Figure 1 1) The acronym MAP refers to the departments of these three countries that comprise the area: Madre de D ios (Peru), Acre (Brazil) and Pando (Bolivia). The area lies between Mountains and in the headwaters of the Amazon River. The climate is tropical, classified as Awi (K ppen) with an average daily temperature of 25 C and mean annual precipitation of approximately 2000 mm. The dry season runs from June to September, in which monthl y rainfall averages < 100 mm ( Marsik et al., 2011 )

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26 The types of forest in the area are dense tropical forest, open tropical forest with palm trees, and open forests dominated by bamboo with many locations containing a mix of these forest types (Carvalho et al., 2013 ; Rockwell et al., 2014; Salimon et al., 2011) The area is of significance for tropical conservation (Killeen and Solorzano, 2008; Myers et al., 2000; Phillips et al., 2006) with high diversity in biota in terms of tree species, birds and i nsects (Phillips et al., 2006) The large Chi co Mendes Extractive Reserve forms part of the study area (in Brazil), as well as the Manuripi National Wildlife Reserve (in Bolivia) Figure 1 2 The natural vegetation generally has a faster turnover than forests further north and east ; on average the we stern Amazon has a turnover rate of 2.6% a 1 as opposed to 1.4% a 1 ( Quesada et al., 2012 ) which is attributed to both soil fertility and climate. Above ground biomass and stand level wood density are also lower in the region compared to the rest of the Amazon (Nogueira et al., 2008; Quesada et al., 2012 ) Quesada et al. (2012) posit that feedback mechanisms associated with soil physical quality is primarily responsible for this phenomenon: higher soil fertility favors fast growing sp ecies, which generally have shorter lifespans. This in turn creates higher mortality, more gap formation and higher light levels lower in the forest: taken together with the high availability in nutrients, this again promotes the growth of species with hig her increments of diameter which invest less in structure (wood density) and thus live shorter. Another study (Keeling et al., 2008) also observed this negative relationship between wood density (representing shade tolerance) and annual diameter increment, ind icating that species that thrive under high light conditions allocate more carbon to diameter increase than to wood density. In combination with the low wood densities

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27 recorded in the area, this indicates that the area experiences a naturally high disturba nce regime. The study area has historical economic and social importance due to its role in the rubber boom in the late nineteenth and early twentieth century (establishing e.g. Rio Branco, Xapuri and Cobija). Most communities outside the urban areas still have extractivist livelihoods, though there has been a shift to cattle in for instance Acre. In this state, the main forest product is timber, contributing 43% to its exports (Duchelle et al., 2014) In Pando the primary industry is Brazil nuts ( Bertholletia excelsa ), also known as castaa Regionally, it plays an important role, with the estimated production for the year 2000 was 10,000 metric tons by Bolivia, 7,800 metric tons by Brazil and 2,200 metric tons by Peru (Collinson et al., 2000) Only 3% of the harvest is used domestically, the majority is exported. To illustrate the importance of the industry: it is estimated that in 2000 in Madre de Dios alone, 38% of the population (27,000 people) depended directly or indirectly on brazil n ut trade, and that it generates on average 67% of their gross annual income (Collinson et al., 2000) Being an internationally traded commodity, it has significant impac ts on forest management policies: it is for instance illegal to cut down Brazil nut trees in all three countries (Rockwell et al., 2015) Another study conducted in th e region found that higher agricultural income is positively correlated with more deforested area, but higher income from Brazil nuts is associated with less deforestation (Duchelle et al., 2010) Concerns have been raised about current harvest levels being unsustainable to maintain populati ons in the long term (Peres et al., 2003) Other nontimber forest products (NTFP) that are of importance in the area are aai ( Euterpe precatoria ) and natural rubber ( Hevea brasiliensis ) to some extent

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28 (Duchelle et al., 2014) High value timber products in the area are mah ogany ( Switenia macrophila sp.), cedro (also referred to as Spanish cedar, Cedrela odorota ) and cumuru ( Dipteriyx intermedia Ducke), and illegal logging has been cited as a problem, specifically in Madre de Dios (Mendoza et al., 2007) Gold mining is another problem in Madre de Dios, as much of it is artisanal and even illegal. It has been fou nd to cause deforestation and degradation, and is creating environmental and human health problems (Ashe, 2012; Scullion et al., 2014) The state capitals of Madre de Dios, Acre and Pando are respectively Puerto Maldonado (139,000 inhabitants), Rio Branco (320,000 inhabitants) and Cobija (56,000 inhabitants). Funding was made available in 1985 to connect Rio Branco to Cruzeiro do Sul in northern Acre and to the state of Rondnia by paving the BR 364 highway, but the work was only finalized in 2002. In the past, Puerto Maldonado was connected to Cusco through an unpaved roa d traversing the Andes. Cobija in Bolivia was connected to Riberalta in the east and Chive in the south, both via an unpaved road through Porvenir. Recent road paving (i.e. during the study period) involves finalization of the Inter Oceanic Highway (IOH) a s per the 2004 agreement between Brazil and Peru: the BR 317 runs from Rio Branco to Capixaba, past Xapuri, through Brasileia to Assis Brasil/Iapari at the border with Peru. From there, the 30C runs through Iberia to Puerto Maldonado, and from there to th e rest of Peru (Cusco and Arequipa), and 3 ports at the Pacific Ocean. The highway was officially finished and opened in 2011. Bridges were built at Brasileia and Cobija (2004 ) and at Assis Brasil and Iapari both crossing the Rio Acre (2006) and at Puer to Maldonado over the Rio Madre de Dios (2009 2010).

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29 There have been concerns about possible negative impacts of paving of the highway, specifically increases in illegal immigration, illegal mining, population, deforestation, threats to indigenous populations (Collyns and Phillips, 2011; Roberts, 2011) Concerns have been raised about the lack, or very limited, environmental impact assessment that has been conducted in relation to the construction of this highway (Almeyda Zambrano et al., 2010; Redwood, 2012) Several studies have been conducted in the MAP area, aiming to identify and quantify impacts of road paving in the area, and recommend mitigating measu res (Mendoza et al., 2007; Perz et al., 2011a; 2013a; 2013c; 2011b) These studies evaluated s ocio economic as well as ecological impacts. Other research focused exclusively, and more in depth, on regional ecological phenomena, such as deforestation and fragmentation (Broadbent et al., 2008; Marsik et al., 2011 ) Studies at a more local level focused on edge effects (Phillips et al., 2006) which suggested little effect from anthropogenic disturbances, which was attributed to the earlier mentioned faster growth rates in the area and hence adaptation. The 99 communities that this research specifically focuses on are resource dependent rural communities that were part of earlier studies (Perz et al., 2013c; 2011b) They are def by Perz et al. (2011). Population densities are low, with an average family density of 0.07 families/km 2 and a maximum of 3.17 families/km 2 for the study period. Land use is described by Phi l lips et al. (2006) as complex and shifting, and includes urban areas, subsistence agriculture, logging, selective harvesting, gold mining, conservation areas, secondary forest and old growth forest in which non timber forest products (NTFPs such as bra zil nuts and rubber) are harvested.

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30 (J. Liu et al., 2007) which are characterized by a variety of factors creating complexity. A similar description of the area, as a socio ecological system in line with a statement from the Stockholm Resilience Center (201 2) is also applicable it emphasizes the humans in the environment perspective; that earth foundation and ecosystems services But also that the ecosystems we observe h ave been shaped by human decision making throughout history and human actions directly and indirectly alter their capacity to Since social actors are an integral part of this approach, adaptive management is an important aspe ct. As Gunderson and Holling (2002) stress, rigid management of natural resources can actually have detrimental effects, often leading to a lack of resilience and the collapse, or transition, of ecosystems. This r esearch will focus on attributes and states associated with this identity of a CNH system in relation to highway development. Specifically, we question whether the vegetation dynamics and structure of the system is subject to change and possible with ecosystem services, making it closely related to the both the human and natural components of the system. Even though the eco CNH system might be compromised or altered in many ways whic h cannot be measured or quantified by looking at forest cover only.

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31 Hypothesis and Sub Hypotheses Hypothesis The identity vegetation dynamics of the coupled natural and human system in the SW Amazon in the MAP area is affected by road paving, beyond on ly deforestation, and different stable states exist. Expected Significance This research will contribute to understanding the stability dynamics of the system in question, and will help local stakeholders make decisions about policies and adaptive manageme nt. At a more general level, it is expected that this research will facilitate a deeper understanding of vegetation dynamics at a large regional scale, and over longer time periods. This will be an addition to the growing body of work on more applied resea rch on resilience, stability and critical transitions. REDD). In legal and policy ter ms, this program focuses on carbon sequestration and land cover by trees, but as has been pointed out in literature (Putz and Redford, 2010; Sasaki and Putz, 2009) in tho se terms without taking into account biodiversity or vegetation structure, would actually be a disservice. Hopefully outcomes of this research will prove informative for policy and decision makers faced with having to understand complex coupled natural and human systems. More specifically, this research hopes to assist Brazil, Peru and Bolivia in planning and implementing Work Area 4 of the UN REDD Programme 2011 2015 Strategy, which and

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32 In order to test the main hypothesis of this research, we developed a working premise, upon which sub hypotheses were based and tested: that EVI vegetation dynamics in the SW Amazon MAP area will reflect states, beyond tradition al forest/non forest alternative states. Sub H ypotheses H1: Within the vegetation dynamics there are distinct transitional states closely associated with road paving. In answering the first hypothesis we aimed to understand whether there was a commonality across vegetation dynamics that we could associate with road paving. We hypothesized that the longer roads had been paved, the more vegetation would be impacted in terms of species and structure, and this would show in altered dynamics (phenology). Communi construction varied across the area, so we hypothesized to find differences in vegetation dynamics accordingly. We used clustering to conduct this analysis, with a very specific focus on time series clustering. Cluste rs are created based on the (dis)similarity between time series. We were specifically interested in dynamics, or patterns of change, and the selected methodology for creating the dissimilarity matrix (Chouakria and Nagabhushan, 2007) The latter refers to directions of change between two points in time. This method has been applied in studies with large data set s, such as tree phylog eny (Bosela et al., 2016) fish abundance based on catch data (Ono et al., 2015) gene expression (Douzal Chouakria et al., 2009) and analysis of precipitation time series (Palizdan et al., 2016) There are a number of ways the ti me series can then be clustered hierarchically and all methods give all possible clusters, from all time series being their own cluster to all time series in one cluster. Since the best type of clustering

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33 and the optimum number of clusters is usually not i mmediately apparent, we base our final decision on the use of two clustering indices conjunctively. After clustering vegetation dynamics, we also extend the clustering analysis to other variables, and conduct an analysis to check for system states of veget ation dynamics (i.e. dominant values). This is done to evaluate and characterize differences between the clusters, since clustering is based largely on behavior of standardized values, so general statistics such as mean values and standard deviations are u nlikely to be informative. The number of states, based on the histogram of values, is associated with dynamics for instance, a perfectly sinusoidal time series generates a bimodal distribution, two dominant values. By doing this analysis using a moving w indow, we can check whether this changes over time per cluster. H2: The relative contribution of human factors to explaining vegetation dynamics increases with road paving. Here we aim to understand the dynamics in the area and the linkages between variabl es, based on statistical analysis. This is important in trying to understand what influences system state both temporally and spatially. We expect that forest dynamics respond to different drive rs as one moves along the paving gradient Specifically ant hropogenic covariates are expected to become more important under more advanced pav ing conditions Previous research has shown that increased regional disturbances are integral to driving and changing vegetation structure and dynamics (Sousa, 1984; Thonicke et al., 2001) and that anthropogen ic disturbances have different effects than natural disturbances (Brown and Gurevitch, 2004; Felton et al., 2006; Guariguata and Ostertag, 2001)

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34 Work conducted to test this hypothesis w ill be based on long term data sets (+20 years) for the MAP area, comprising a range of variables associated with either natural or human system. Vegetation dynamics are modeled as the response variable in this study. The method applied, Dynamic Factor Ana lysis (DFA) aims to increase understanding of relationships between state variables ( and the state of the system). It is spatially explicit, and can quantify the contribution of different drivers to the state of the system (Campo Bescs et al., 2013; Kaplan et al., 2010; Muoz Carpena et al., 2005; Zuur et al., 2007; 2003b) This is a multivariate time series reduction technique which aims at finding a (or more) common trend(s) across multiple spatially explicit state variable time series as linear combinations. The approach then proceeds to add explanatory variables (also time series) to the model, with the aim of reducing the importance of the trend and shifting explained variance to know variables. The general mathematical formula of a Dynamic Factor Model is: (1 1 ) (1 2) S n (t) is the value of the n th response variable at time t; a m (t) is the m th unknown trend at time t; represents the unknown factor loadings; is the n th constant level parameter for displacing each linear combination of common trends up and down; represents the unknown regression parameters for the K explanatory variables ; is the error component. Every location for which a time series of the response variable is available, will have unique coefficients for the shared trends and variables in model These express the importance of each at that location.

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35 Eventually the aim is to construct a multi linear regression model with explanatory variables and as few trends as possible to explain the variability in the response variable. Comparison of the mode led and the measured values will provide a Nash Sutcliffe coefficient of Efficiency (C eff Information Criterion (AIC) or Bayesian Information Criterion (BIC), these goodness of fit measures allow for evaluation of models with different combinations of explanatory variables. The model(s) with the lowest AIC or BIC, and an acceptable C eff are selected for the Okavango Delta, which explored the different factors driving vegetation (Campo Bescs et al., 2013) Th is study found various factors (rainfall, precipitation, ev a potranspiration, etc.) weighted differently along a rainfall gradient. This method thus adds an important spati al component to the analysis of the system; and by considering regression coefficients across a spatial gradient, the weight or importance of covariates (drivers) can be outlined (Campo Bescs et al., 2013) This analysis aims to add (spatial) insight into relationships between socio economic and natural drivers and system response. H3: The causal networks of natural and climate variables are disrupted and become sparser with road paving extent. After having looked at rela tionships between variables with DFA, the next step is to investigate whether any causal relationships exist. For this study, the selected methodology requires time series that are dynamic (signals), so it includes the vegetation dynamics, biophysical vari ables and some climate indices. We expect that undisturbed forests are more resilient and show strong relationships with all variables since climate/vegetation feedbacks have been reported in previous studies (Betts et al.,

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36 2004; Notaro et al., 2006; Q uesada et al., 2012 ) We anticipate that causal relationships between biophysical variables and vegetation dynamics change with more paving, with more emphasis on precipitation and soil moisture, and less on temperature influences. This stems from previ ous work that found that under fragmented or logged conditions, forest becomes more sensitive to drought and moisture related variables (Laurance and Williamson, 2001; Nepstad et al., 2001) The methodologies involved in testing this hypothesis are relatively new, and center around the consideration of the system as a deterministic system, specifically a nonlinear low dimensional deterministic system. This is the opposite of a stochastic linear system. Thus, there is no randomness involved and behavior is nonlinear. Low dimensionality refers to the number of variables involved in the system, i.e. dimensions. Since noise in data can obscure identification of this system, the first part of this study aims to find system attractors (also called signals) and determine whether these exhibit nonlinear determini sti c behavior and/or responses. Detect ion and reconstruction of signal s in each time series is done with Singular S pectrum A nalysis (SSA), which serves to separate (potentially determini sti c ) signals from unstructured noise (Golyandina et al., 2014; Golyandina and Z higljavsky, 2013) It then proceeds to test for statistical causality by applying a novel approach, Convergent Cross Mapping (Huffaker et al., 2017; Sugihara et al., 2012) The suitability of this analysis depends on the outcomes of the s ignal reconstruction and tests for stationary nonlinear deterministic behavior, as well as tests for low dimensionality. CCM is only suitable for stationary low dimensional systems. Since signals have to pass a number of tests to be found suitable

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37 for CCM, this study is also an exploration of whether or not the system can be expressed as a low dimensional deterministic system The basis for the methods is that for deterministic systems, time series that are causally related (e.g. x and y ) will form an attra ctor when plotted against each other in state space. However, if there is only one signal available ( x ), one can still form the attractor if lagged versions are created from the original with the appropriate time delay (the time delay of the causal effect) The methods applied here are based on, and are space with n dimensions, a so called shadow attractor. Hence this is not the real attractor (of x and y ), but if this is done for both x and y their shadow attractors map to the real attractor 1:1 (Sugihara et al., 2012) So if x and y are dynamically coupled, they will also map to each other. CCM thus aims at detecting causality by testing for correspondence between shadow attractors (Sugihara et al., 2012) These methods are more suitable than previous methodologies, such as Granger causality ( Granger, 1969 ; Guo et al., 2010) which are based on linear approaches. Considering the complexit y of the system, it is unlikely that relationships are linear. The requirements for Granger causality analysis is that time series are separable, meaning that drivers are separable from other factors (BozorgMagham et al., 2015) This is u nlikely in complex systems with (suspected) feedback dynamics. This research aims to find causal linkages across the research area between various variables CCM might be able to identify causal relationships between system components and allow us to build a causal network The method has been applied previously in a number of ecological and environmental studies (Huffaker et al., 2016b;

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38 Sugihara et al., 2012; Van Nes et al., 2015; Ye et al., 2015) Most of these had a limited number of variables involved, but we hope that in our approach we can build a comprehensive causal network.

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39 Figure 1 1. Schematic representation of the relationships between ecosystem services and functions, and the human system, in cluding the role of vegetation dynamics.

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40 Figure 1 2. The MAP area in Peru, Brazil and Bolivia, with the Inter Oceanic Highway, other roads, protected areas major cities and communities. State capitals are named in bold.

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41 CHAPTER 2 A SPATI AL TEMPORAL DATABASE TO EVALUATE ROAD DEVELOPMENT IMPACTS IN A COUPLED NAT URAL HUMAN SYSTEM IN A TRI NATIONAL FRONTIER IN THE AMAZON Background and Summary Road infrastructure development is on the rise, and is predicted to increase 60% in total length by 2050, compared to 2010 (Laurance et al., 2014) From a macro economic perspective, road infrastructure is described as a nece ssity, as the increase of trade and economic growth will require gateway and corridor infrastructure for imports and exports (OECD, 2011) Population growth a nd the increasing proportion of people living in cities is also indicated as a driver of increased mobility and thus driving the need for infrastructure. Having quality infrastructure is considered the key to competitiveness on a global level, as it integr ates national markets and provides access to international markets. Addition of new infrastructure is projected to predominantly take place in emerging economies (Dulac, 2013) and with that, many of these roads will be constructed in and through wilderness and pristine areas ( Laurance et al., 2009 ) Local negative impacts by roads and the associated effects from increased anthropogenic disturbance on forest ecosystems have been documented in many studies: defores tation, increased logging, increased fire, loss of biodiversity, decreased mobility and increased mortality of wild life, hydrological changes, increased human migration, violent conflicts and illegal (economic) activities (Almeyda Zambrano et al., 2010; Chazdon, 2003; Coffin, 2007; Foley et al., 2007; Forman, 2003; Laurance et al., 2009 ; 2001; Nepstad et al., 2001; Perz et a l., 2013c) Previous research predicts road impacts to be highest in areas high in biodiversity and carbon storage (Laurance e t al., 2014) i.e. tropical forest regions.

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42 The Amazon forest provides a number of locally, regionally and globally important provisioning, cultural, regulating and supporting ecosystem services (Foley et al., 2007; Millennium Ecosystem Assessment 2005) It contains hotspots for biodiversity (Killeen and Solorzano, 2008; Myers et al., 2000) provides timber and non timber forest products (NTFPs) and is home to a number of indigenous peoples and cultures. At the global level, carbon storage and nutrient cycling are important supporting ecosystem services, as well as hydrological regulation and climate regulation throu gh freshwater discharge and vegetation atmosphere feedbacks ( Davidson et al., 2012 ; Pereira et al., 2012) The total Amazonian area (including non protected areas) at risk from current or near ter m threats (transportation, mining, agriculture, timber, etc.) was found to be 53% (Walker et al., 2014) T he same study calculated that t his area cont ains 46% of Amazonian aboveground carbon; 39,743 MtC. This is a very conservative finding, as the study did not include the loss of forest associated with road infrastructure, or the increased access to the forest interior due to it (Walker et al., 2014) This illustrates the possible consequences of concerns that have been expressed in various studies about the Amazon potentially reaching a tipping poi nt, considering the multiple threats to the system (Cumming et al., 2012 ; Hirota et al., 2011; Nepstad et al., 2008; Nobre and Borma, 2 009 ; Pereira et al., 2012; Scheffer et al., 2001 ; Verbesselt et al., 2016) Many of these studies predict a shift in states, from a system dominated by tropical forest to a savannah dominated system, or large scale rainforest die back. As climate varia bility and human disturbances have become sources of major concern ( Davidson et al., 2012 ; Malhi et al., 2008) in these scenarios, there is a need to increasingly conduct long term studies that consider road development in the Amazon

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43 as part of a complex human natural system with specific spatio temporal characterist ics. Particularly in tropical forest areas where livelihoods are often closely associated with the natural environment, and ecosystem services extend to regional and global scales, integration of scales and sub systems is important. With this type of infor mation, we can conduct studies that take a comprehensive view of the system to evaluate trade offs, advantages and disadvantages of road development. From this perspective, data w ere collected and compiled for an area in the Amazon impacted by road deve lopment. The area in question is a tri national frontier area where the states of Madre de Dios (Peru), Acre (Brazil) and Pando (Bolivia) meet, also known as the MAP area. The Inter Oceanic Highway (IOH), which connects the ports in Peru and ports in Brazi l, was constructed in the MAP area between the 1980s and 2011, with increased construction activity from 2002 onwards. This database is unique as it covers the time period before, during and after highway construction, and contains data pertaining to the h uman sub system as well as the natural sub system. At a spatial level, a large part of the data is available for 100 municipal or state level, giving a more detailed and livelihoods focused perspective. Certain variables are no t available at community or state level, but at country level: this is due to the disparities in data availability between states in different countries. The focus was on data that are available across the area equally. Different components of this database have been used in studies that assessed either the human component of the system (Perz et al., 2013c; 2007) the biophysical component ( Cumming et al., 2012 ; 2012b; Mar sik et al., 2011 ) or a combination of both (Baraloto et al., 2015; 2014; Perz et al., 2011b; 2011a) We anticipate that these d ata can be used for more studies,

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44 particularly simulation and modelling studies, as well as studies focusing on improving environmental impact assessments conducted for road development projects. Methods Data Collection and C ompilation The database contain s information on natural and human sub systems as time series, with variables available at global, country, community and point level. A definition is a result of one o f the earlier survey studies in the MAP area see next section (Perz et al., 2011a) Data compilation was primarily focused on the time period 1980 2010 (the road construction period), though data availability varied (Tables 2 1 and 2 2). This database is a combination of data obtained from field work in the area, reanalysis (calculated) data from larger, often global, data set s, as well as remotely sensed data and information derived from remote sensing. Secondary data sources were accessed in the period 2 013 2014. There are also data records included in the database that are not dynamic that provide stationary spatial and qualitative information. Human V ariables The survey methods applied to collect data from 10 0 communities in the MAP area are extensivel y outlined in a previous study (Perz et al., 2011b; 2011a) In brief, community boundaries were identified in a GIS with the help of administrative data sources such as censuses, cadastral maps, zoning plans, etc. The focus was on areas around the IOH in the three states, Madre de Dios (Peru) and Acre (Brazil) and roads in Pando (Bolivia) that were deemed in the sphere of influence of the IOH. Systematic geographic sampling led to a selection of communities with varying distances to the IOH

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45 and regional capitals In addition to rec ording regional (state) capitals, the nearest markets to communities were identified. In 2007 and 2008, researchers and students from the University of Florida, the National Amazonian University of Madre de Dios, the Amazonian University of Pando and the F ederal University of Acre interviewed current and past community representatives, using a structured questionnaire with open ended questions. The questionnaire covered interviewee characteristics, general information about the community, and specific topic s: community population, community infrastructure, community assistance, community livelihood activities, change in the importance of those activities in the past 5 years, change in availability of forest resources in the past 5 years, marketing of key pro ducts, conflicts over natural resources, and community response to fires. GPS information was collected to calculate precise distances to nearest (local) markets and the nearest capitals. Information on population changes (as number of families) in the com munities includes the reported number of families in a community as of 2007 (from community leader survey s ; averaged among leader estimates), families considered community members but living elsewhere (usually a town), number of families joining the community in the last 5 years, number of families leaving the community in the last 5 years B ased on this information population changes we re extrapolated from 2007 to 2012 with an exponential growth rate. Using the rural growth rate pre 2002 (based on ru ral populations in censuses pre 2002), population growth rates were extrapolated back to 1987. Using surface area of the communities, family density over time was calculated Changes in population size in the state capitals and the nearest markets were obt ained from census data.

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46 Road paving is expressed as a value between 0 (no paving) and 1 (fully paved) and refers to the road segment closest to the community it is associated with Field notes and official documentation with the timing of the onset and con clusion of paving of segments provides the 0 and 1 values, and linear interpolation was applied to obtain a time series for paving proportion in the period in between. Connectivity between communities and the nearest market and the regional capital was exp ressed as travel time in minutes. These calculations are based on the distance to town, the paving status of different road segments travel speeds and road maintenance (especially for unpaved roads) Travel speeds were based on direct experience in the fi eld, hence this also takes topography related conditions into account such as curves and steepness. Information was collected on tenure rules and the (perceived) enforcement of these rules for each community. These were similarly based on fieldwork, which included workshops with stakeholders, and official rules for resource use given by community is allowed to cut down. Values vary between 0 and 1, representing 0 to 100% d eforestation allowed. Enforcement values reflect perceptions by experts as to the extent to which those use rules are actually enforced by government agencies responsible for oversight, which roughly corresponds to the probability of infractions being dete cted and punished. Here again, the values run from 0 to 1, with higher values indicating more likely enforcement. At country level, a number of socio economic indicators were collected from the World Bank DataBank ( http://databank.worldbank.org/data/home.aspx ), at annual resolution. These variables are: electricity from non renewable resources, electricity

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47 from renewable sources (excluding hydroelectric), foreign direct investment, profit from for ests, GDP growth, GDP per capita growth, profit from natural gas, life expectancy at birth, profit from minerals, total profit from natural resources, profit from crude oil, power consumption, and GDP per capita. Environmental V ariables Data for a number of biophysical variables were obtained from global reanalysis data set s and remote sensing products : minimum, mean and maximum temperature, precipitation, potential evapotranspiration, soil moisture, species richness, forest cover, vegetation dynamics (Enh anced Vegetation Index), fire occurrence, and Net Primary Productivity (NPP) Using GIS, these were area weighted to obtain monthly time series at community level. Data records for country level environmental variables were also gathered, as well as climat e indices (global level). At point level, two data set s were compiled: river flow, and precipitation at meteorological stations. Monthly data sets for the minimum, mean and maximum temperatures, precipitation and potential evapotranspiration were sourced f rom the Climatic Research Unit (CRU) at the University of East Anglia ( https://crudata.uea.ac.uk/cru/data/hrg/ ) The mean, minimum and maximum temperatures (in C) and precipitation (in mm) were obtai ned at a resolution of 0.5 x 0.5 (Harr is et al., 2013) and were assigned to each community polygon in an area weighted manner. Potential evapotranspiration (in mm) is also included in the CRU data set, and is calculated from a variant of the Penman Monteith formula, using mean, minimum and maximum temperature, vapor pressure and cloud cover (Harris et al., 2013) Soil moisture data come from the N ational O ceanic and A tmospheric Administration (NOAA) Climate Prediction Center (CPC) model at a resolution of 0.5 x

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48 0.5, which uses CPC precipitation data and temperature data fro m the NCEP/NCAR Reanalysis (Fan, 2004) It can be downloaded from the NOAA Earth Syst em Research Laboratory (ESRL) website ( https://www.esrl.noaa.gov/psd/data/gridded/data.cpcsoil.html ). The data are provided as average soil moisture in terms of water height equivalents (mm). As with the other data sets, the soil moisture data are calculated as an area weighted average time series for each community polygon. Inferred species richness of vegetation is calculated from diversity (within habitat diversity) of vegetation, computed from Landsat imagery by applying a method that is based on the Shannon entropy of pixel intensity (Convertino et al., 2012) at an annual scale Landsat imagery was collected for each year and the images were analyzed for each visible band (blue, green and red). A wavelet based texture retrieval method was used that applied wavelet analysis to decompose local (pixel) signals. The diversity is calculated as Sha entropy, the spectral heterogeneity measured by reflectance is used. Because different species have different reflectance levels in the visible bands, the range of reflectance is indicative of diversi ty. If the range of reflectivity is higher, the entropy is higher, hence the diversity is higher. The number of species is calculated from the diversity ; time series per community are calculated as i n area weighted manner. The data on area covered by f orest in each community (in km 2 and as a percentage) were generated with methods from a previous study in the Bolivian part of the MAP area ( Marsik et al., 2011 ) The method for forest nonforest (FNF) classification relied on Landsat images (4 and 5 TM and 7ETM+) of the area from 1986, 1991, 1996,

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49 2000, 2005 and 2010. Images were sourced for the dry season, to minimize the impact of cloud cover and smoke. Corrections for atmospheric and seasonal differences were applied to the images, and they were georeferenced to less than 15 m, with the Maryland Global Land Cov er Facility 2000 Geocover as base images. After mosaicking and removal of clouds, shadows and water with a PCA image differencing and thresholding method, derived image products for bands 4, 5 and 7 were generated to assist in classification. These product s were tasseled cap indices (producing three bands that represent brightness, greenness and wetness), a mid infrared index and a 3x3 moving variance window calculation of each pixel. The latter gives a measure of texture, which is helpful in classifying fo rest and non forest, and especially in cases where selective logging has resulted in small cleared areas in the forest matrix. The first two products, greenness and mid infrared bands, help in differentiating forest from other types of vegetation, and the brightness bands in detecting non forest areas. Training samples were obtained from Pando, Bolivia, in 2006, recording known locations of forest, pasture and bare or built land cover. The latter two were combined as the non forest class. The primary and se condary image products were used to get pixel values for these locations. Application of decision tree classification started with creating the decision rules with data mining software (Compumine, http://www.compum ine.com) using 85% of the data to train and create the decision tree, and 15% to test the tree. To create classifications the ERDAS Knowledge Engineer rule based classifier was used. Finally, more than 350 training sample points were collected in 2006 and 2007 with land cover type observations, which were used to evaluate classification of the 2005 images. In addition, Advanced Spaceborne Thermal Emission and Reflection Radiometer

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50 (ASTER) images were used for an additional accuracy assessment. Average accuracy of the classification for the 2005 images was 8 7.85% for the field samples, and 97.96% for the ASTER images. Subsequently the classification method was applied to all images. For the community polygons, forest area (km 2 ) and forest as proportion of the whole community area were calculated. Remotely sen sed d ata for the Enha nced Vegetation Index (EVI) and fire from the Moderate Resolution Imaging Spectroradiometer (MODIS) were downloaded from the Land Processes Distributed Active Archive Center (LP DAAC, https://lpdaac.usgs.gov/data_access/data_pool ) EVI is a reflectance based index, (Huete et al., 2010; 2002) The product used was MOD13Q1, providing EVI at 250 m spatial resolution and essentially 16 day temporal resolution (the algorithm uses the best pixel value from a 16 day period). Values of EVI range betwe en 1 and 1, with higher values reflecting higher levels of is sensitive to canopy structural changes, and does not saturate as easily as other vegetation indices unde r high biomass conditions, found in tropical areas. For data series per community and at a monthly time step, 16 daily data were averaged per month and GIS was used to extract area weighted averages. For fire (or thermal anomalies) time series, MOD14A2 dat a, also from MODIS, were downloaded with a temporal resolution of 8 days and a spatial resolution of 1 km. In this product, pixels have been assigned a classification of fire or no fire experiencing fire was calculated (for the 8 day data), which was then averaged over all fire masks in a month

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51 to obtain monthly values. The values thus represent the average area in a community that experienced fire in a particular month. N et P rimary P rodu ctivity ( NPP, in kg C/m 2 / year) is available from the NASA Earth Observations (NEO) website ( https://neo.sci.gsfc.nasa.gov/about/ftp.php ) and is the result of an algorithm that combines several fac tors Remotely sensed data; the Fraction of Photosynthetically Active R adiation ( f PAR), Leaf Area Index (LAI) and land cover classification from MODIS are used. Temperature, incoming solar radiation, and vapor pressure deficit from global reanalysis data set are included, as well as a Biome Parameter Lookup Table with conversion efficiency parameters for different types of vegetation. Running and Zhao (2015) describe the algorithm that produces MOD17A3 (annual NPP at 1 km resolution) in detail, and Running et al (Running et al., 1999) provide an in depth explanation of the development of monthly data All MODIS data are available from 2000 onwards. Longer time series for the Enhanced Vegetation Index (EVI2) were obtained from the University of Vegetation Index and Phenology lab (VIPLab, https://vip.ari zona.edu/ ), wh ich applies an algorithm to translate two band data from the Advanced Very High Resolution Radiometer (AVHRR) into MODIS EVI which uses 3 bands (Z. Jiang et al., 2008) to create longer EVI time series. AVHRR data have been collected since 1982. The conversion method involves a calculation that expresses EVI2 as a function of the ratio of red to blue reflectivity. Before this conversion, a number of pre processing steps, quality control, gap filling, and calculations to ensure continuity across sensors are taken. These processes are all outlined on the VIPLab website, in the DataExplorer ( https://vip.arizona.edu/vi plab_data_explorer.php ). The data were obtained in monthly

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52 time steps and at a 0.05 resolution for 1982 2010. Area weighted time series were extracted for each community polygon. A number of corrections were applied to ensure continuity between pre and p ost are differences between the earlier mentioned EVI records and these EVI2 records for 2000 2010 due to the different resolutions of the data, and the modifications applied at the VIPLab. At point l evel, monthly precipitation data (in mm) from stations were extracted from the Global Historical Climatology Network (GHCN) by NOAA ( https://www.ncdc.noaa.gov/ghcnm/v2.php ): 5 stations in Acre (Brazil) 1 in Madre de Dios (Peru) and 2 in Pando (Bolivia ). All these time series have gaps, ranging from a few months to a full year. Monthly minimum maximum and average stream flow data (in m 3 /s) for the three most important rivers in the area were also loca ted an d downloaded: for the Rio Acre and Rio Madre de Dios. The data were obtained from the Agncia Nacional de guas (ANA) in Brazil, through its Hidroweb ( http://www.snirh.gov.br/hidroweb/ or http://hidroweb.ana.gov.br/ ). Searches were conducted to find stations for two river basins; Rio Acre is in the sub basin numbered 13 by ANA (Solimes), and Rio Madre de Dios is in sub basin 15 (Madeira). Both are part of th e larger Amazon basin. The Rio Acre forms the border between Peru and Brazil, and for a part between Bolivia and Brazil (until Cobija/Brasilia). Then it turns north, with the Rio Xapuri and Rio Branco being tributaries before the river reaches the town of Rio Branco. From Cobija and Brasilia onwards part of the border is the the Rio Abua, which is a tributary to the Rio Madeira (in the state of Rondnia, Brazil). The Rio Madre de Dios originates in Peru,

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53 flows into Bolivia and eventually joins the Rio Be ni and the Rio Madeira. Most stations have gaps in the data in varying degrees, and for 3 stations on the Rio Acre enough data were available to apply a gap filling method based on linear regression between station data to create continuous time series. A t country level, annual indicators from the World Bank DataBank ( http://databank.worldbank.org/data/home.aspx ) were compiled for the natural sub system: agricultural land, arable land and protect ed areas, all as percentage of the land area in each country. At the global level, monthly time series for the Atlantic Multidecadal Oscillation (AMO), the Pacific Decadal Oscillation (PDO) and the Multivariate El Nio/Southern Oscillation Index (MEI) were obtained from the NOAA Earth System Research Laboratory ( https://www.esrl.noaa.gov/psd/data/climateindices/list/ ). For the AMO we obtained the unsmoothed version (Enfield et al., 2001) This time series is an index of surface temperature of the North Atlantic Ocean. The PDO consists of the first principal component of monthly anomalies of sea surface temperature of the North Pacific Ocean (Mantua et al., 1997; Zhang et al., 1997) The MEI is a composite index that is believed to better reflect the El Nio/Southern Oscillation (ENSO) phenomenon than simpl y sea surface temperatures (Wolter and Timlin, 2012) It incorporates sea level pressure, surface air temperature, sea surface temperature, cloudiness fraction, zonal and meridional components of surface wind over the tropical Pac ific Ocean. Stationary V ariables Stationary data for the communities covered in this database are provided as separate records. These records contain information on names, area, distances to and mean elevation ( meters above sea

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54 level, MASL). Mean elevation is extracted from a Digital Elevation Map (DEM) using the This DEM was sourced from the website of the United States Geological Society ( USGS, http://gdex.cr.usgs.gov/gdex) associated with LP DAAC. Most importantly, this record with community information contains community IDs that should be used to link the various files with country and community level data. Forest types were available for the Acre area (Brazil) from a previous study (Salimon et al., 2011) that used a combination of the Brazilian Forest Classification System and the Vegetation map of the Ecological and Economical Zoning for Acre for its classification. The latter vegetation map is based primar ily on the Radambrasil project ( Projeto Radar da Amaznia) the first large scale monitoring project in the Amazon. This classification takes soil, climate geological and geomorphological attributes into account. Using this classification, f orest types wer e generated for Madre de Dios (Peru) and Pando (Bolivia) with a Random Forest model that included the covariates EVI, soils, elevation, and slope. Where forest is absent, the land cover is rcentage of forest types and/or land cover is given. Botanical data w ere collected for a number o f sites in the area between 2007 and 2010 for studies on biomass (Baraloto et al., 2014) and forest value (Baraloto et al., 2015) These articles provide an in depth overview of methods used, a summary will be provided here. Study sites were selected to represent geographic variability, and community leaders were engaged to provide consent and identify a reas representative of the community area. Focus was on terra firme forests with the aim of being able to evaluate human impacts. Across the whole MAP area 67 sites were sampled with an

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55 adaptation of the Phillips et al (Phillips et al., 2003) modified Gentry plot method (Baraloto et al., 2011) in a paired design, with the purpose of measuring biodiversity and aboveground biomass. T here were 27 sites in Acre, 25 in Madre de Dios and 15 in Pando. Distance from roads varied, with generally one site closer to roads (< 2 km) and 1 further away (> 5 km) in each community. Each site consisted of a 100 x 190 m sampling grid, within which 10 subplots of 2 x 50 m were sampled. The subplots were situated perpendicular to a randomly chosen baseline, alternatively opposite of each other along this baseline. Woody plants with a diameter at breast height (DBH, at 1.3 m) 2.5 cm were measured for h eight and DBH. Then, each subplot was extended to 10 x 50 m, and all woody stems with DBH 20 cm were measured. Voucher specimens were collected for species that could not be identified in the field, and collections from each country are held at their loc al herbaria: t he National Amazonian University of Madre de Dios in Puerto Maldonado (Peru), the Center for Research on Amazon Protection of the Amazonian University of Pando in Cobija (Bolivia), and the Zoobotanical Park of the Federal University of Acre i n Rio Branco (Brazil). After extensive identification efforts, 93.5% of samples were identified to the genus level, 99.5% to the family level. In addition to detailed plant data, aboveground biomass and biomass in timber species w ere calculated per site. A boveground biomass was estimated with allometric equations based on size class as per Baraloto et al (Baraloto et al., 2011) To obtain soil information for the area, a gridded soil data set was downloaded from the International Soil Reference and Information Centre (ISR IC World Soil Information, http://www.isric.org/explore/soilgrids ). This data set has a resolution of 1

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56 km and provides soil organic carbon (g/kg), soil pH, sand, silt and clay fractions (%), bulk de nsity (tones/m 3 ), cation exchange capacity (cmol/kg), volumetric coarse fragments, soil organic carbon stock (tonnes/ha), depth to bedrock (m), World Reference Base soil groups and USDA Soil Taxonomy suborders at 6 depths covering 0 200 cm soil profiles (Hengl et al., 2014) For this database, we averaged the 6 values to obtain single values. Values for saturated hydraulic conductivity (10 6 m/s), saturated volumetric water content and residual volumetric water content (both cm 3 /cm 3 ) were calculated with pedotransfer functions listed in Marthews et al (Marthews et al., 2014) using those by Cosby et al (1984 in Marthews et al., 2014) for saturated hydr aulic conductivity and those by Tomasella and Hodnett (1998 in Marthews et al., 2014) for water content. Information for each community was extracted using GIS. Shapefiles are made available as well, these include: state boundaries, communities, roads, riv ers and protected areas. The metadata for the point data (flow and precipitation from stations) provide coordinates for the stations. Data Records All data set s and records are stored in a Figshare repository (Data Citation 1: 10.6084/m9.figshare.c.3933364 ). The main level of data organization is under the headers human variables, natural variables and stationary data (Table 2 1). Within ta are grouped at either community or country level. Table 2 1 lists the available data and their level, and files are named according to the listed abbreviation. All data are provided in comma delimited files (.csv), with either a country or community ide ntifier. Where necessary, metadata files are included to elaborate on data in the files. Environmental variables have a similar format and organization, and also contain data at global or point level.

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57 Data at global level (climate indices) are not linked t o any country or community. Point data files contain coordinates for their location in a metadata file, including station numbers. Separate files contain the data per station. For precipitation this is all contained in one file, but since flow data contain a number of time series (minimum, maximum and mean), it is separated per station. These files are also comma delimited files (.csv). Dynamic variables that have a temporal resolution of 1 month contain a column for months and a column for years to reduce issues with reading dates into data analysis programs. The time periods for which data are available varies, see Table 2 1. Stationary data are a mix of comma delimited files (.csv) and shapefiles (.shp and associated files). Data are grouped for community information, botanical data, forest type, shapefiles and soil type (Table 2 2). All metadata files are comma delimited as well. Technical Validation Data from reanalysis projects or larger global data set s were sourced from reputable sources (e.g. WorldBank data, data from NOAA, CRU, ISRIC) with internal data checks. Other local data were obtained from sources with documentation on measurements and calculations (e.g. ANA, GHCN). We double checked coordinat es for the stations to ensure that they were in the MAP area and along water ways (for the flow data). In addition, visual checks of data relating to dynamic variables was done to ensure there were no anomalous data. Where there were minor issues with comm unity data relating to human variables (e.g. travel times, family density), these were identified and resolved in an iterative manner due to several authors evaluating the data set s. Note that some station data (precipitation and stream flow) have gaps.

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58 Da ta correction was performed on EVI2 data to address outliers and discrepancies between AVHRR derived EVI (1982 1999) and MODIS EVI (2000 2010), because AVHRR derived EVI exhibited consistently lower values This is a ttributed to the lower quality of AVHRR data in areas with high cloud density (pers. comm. Dr. K. Didan). For this correction, data were divided into pre and post 2000 data. For each data group, outliers were defined as an uncharacteristically positive change from one month to the other, shaped as a peak. Negative changes were not scrutinized, since vegetation can be cut down, causing a large negative change in EVI. However, it would be unlikely for EVI to peak very quickly. Any change larger than 2 times the interquartile range of the data is f lagged and removed. The change value was purposefully kept large since the data had already undergone pre processing at the VIPLab. Removed values were replaced with long term averages on a month by month basis (i.e. a gap for January was filled with the l ong term average for January). Finally the pre 2000 data set was adjusted by moving the data up by the long term post 2000 average, again on a month by month basis for each community separately. This was done on a month by month basis because differences b etween the long term averages varied per month (Figure 2 1). The data repository contains an RMarkdown file with code and this explanation. We highly encourage users to consult the original sources, websites and publications for general data limitations an d caveats. While all reanalysis and calculated data comes from reputable sources, underpinned by peer reviewed publications, users should familiarize themselves with these and take these into account during and after analyses. All variables have been captu red and recorded in the International System of

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59 Units (SI). Note that Portuguese or Spanish names can include special characters that do not transfer well into coding or analysis applications. Usage Notes As the impact of human disturbances increases and intensifies in many areas due to road infrastructure development, it is important to be able to analyze systems as a broad as possible. Considering systems as coupled natural human systems that are dynamic over time and space allows researchers to fully ex plore what kinds of impacts to expect. We would like to encourage researchers to use these data in explicit spatio temporal approaches, integrating human and natural variables. While a number of studies have already been conducted with these data, each mos tly considered separate components of the data set Of particular interest for future research would be changes over time in the system associated with road infrastructure development. These data could also be used to investigate spatial variability and he terogeneity in relation to road infrastructure. With the available data, analyses can take place at the regional level, or at community level. Of interest could be: 1. Time series research on dynamic variables to understand the interplay between variables and find drivers or causality mechanisms; 2. Simulation and prediction studies to identify important variables, and the potential for system state changes. This type of research would be informative for other areas undergoing road infrastructure development in terms of types of models to use and data collection requirements; 3. Global Sensitivity and Uncertainty Analyses to understand the workings of these models. The data in this database can provide a baseline for the development of distributions required for mo del parameters.

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60 Table 2 1 Overview of dynamic variables collected and compiled for the area in Madre de Dios (Peru), Acre (Brazil) and Pando (Bolivia), the MAP area. Sub system Spatial resolution Dynamic Variables Temporal resolution Time period HUMAN Community ENF Enforcement of tenure rules (0 to 1: with 0=least, 1=most) Annual 1985 2010 Country ENR Electricity from non renewable sources (oil, gas and coal; % of total) Annual 1980 2010 Country ER Electricity from renewable sources, excluding hydroelectric (% of total) Annual 1980 2010 Community FAM Number of families in the community 5 yearly 1987 2012 Community FAMD Family density (families/km 2 ) 5 yearly 1987 2012 Country FI Foreign direct investment, net inflows (% of GDP) Annual 1980 2011 Country FR Profit from forests (% of GDP) a Annual 1980 2010 Country GDP GDP growth (annual %) Annual 1980 2011 Country GDPC GDP per capita growth (annual %) b Annual 1980 2011 Country GR Profit from natural gas (% of GDP) c Annual 1980 2010 Country LE Life expectancy at birth, total (years) Annual 1980 2011 Country MR Profit from minerals (% of GDP) d Annual 1980 2010 Country NRR Total profit from natural resources (% of GDP) e Annual 1980 2010 Country OR Profit from crude oil (% of GDP) f Annual 1980 2010 Country PC Power consumption (kWh per capita) Annual 1980 2010 Community PNC Population in (nearest) state capital Annual 1986 2010 Community PNM Population in nearest market Annual 1986 2010 Country PPP GDP per capita, PPP (current international $) = GDP converted to international dollars using purchasing power parity rates Annual 1980 2011 Community PAV Paving (0 to 1, with 0=no paving, 1=fully paved) Annual 1985 2012 Community TEN Percentage of deforestation allowed under tenure rules (0 to 1: e.g. 0.1=maximum of 10% deforestation allowed) Annual 1985 2010 Community TTC Travel time to capital (minutes) Annual 1986 2010 Community TTM Travel time to nearest market (minutes) Annual 1986 2010

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61 Table 2 1. Continued. Sub system Spatial resolution Dynamic Variables Temporal resolution Time period NATURAL Country AG Agricultural land (% of land area) g Annual 1980 2009 Global AMO Atlantic Multidecadal Oscillation Monthly 1987 2009 Country AR Arable land (% of land area) h Annual Community EVI Enhanced Vegetation Index (MODIS product) Monthly 2000 2010 Community EVI2 Enhanced Vegetation Index 2 (VIPLab product) Monthly 1982 2010 Community FIR Fire occurrence (average over a community area per month) Monthly 2000 2010 Point FLOW River flow at a number of stations Monthly* ~1967 2012* Community FOR Forest area as percentage of community area 5 yearly 1986 2010 Community MAXT Maximum temperature (C) Monthly 1982 2010 Community MEANT Mean temperature (C) Monthly 1982 2010 Global MEI Multivariate ENSO Index Monthly 1987 2009 Community MINT Minimum temperature (C) Monthly 1982 2010 Community NPP Net Primary Production (C/m 2 /year) Monthly 2000 2010 Community P Precipitation (mm) Monthly 1982 2010 Country PA Percentage Protected Areas (% of whole country) Annual 1980 2009 Global PDO Pacific Decadal Oscillation Monthly 1987 2009 Point PP Precipitation (mm) at a number of meteorological stations Monthly* ~1985 2011* Community PET Potential evapotranspiration (mm) Monthly 1982 2010 Community SM Soil moisture (mm) Monthly 1982 2010 Community SR Species richness (alpha diversity) i Annual 1984 2012 a and a region specific rental rate. b GDP per capita based on purchasing power parity (PPP) PPP GDP is gross domestic product converted to international dollars using purchasing power parity rates. An international dollar has the same purchasing power over GDP as the U.S. dollar has in the United States. GDP at purchaser's prices is the sum of gross value added by all resident producers in the economy plus any product taxes and minus any subsidies not included in the value of the products. It is calculated without making deductions for depreciation of fabricated assets or for depletion and degra dation of natural resources. Data are in current international dollars. c and total costs of production. d ce between the value of production for a stock of minerals at world prices and their total costs of production. Tin, gold, lead, zinc, iron, copper, nickel, silver, bauxite and phosphate are included. e the sum of oil rents, natural gas rents, coal rents, mineral rents and forest rents. f production.

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62 Table 2 1. Continued. g Agricultural land refers to the share of land area that is arable, under permanent crops, and under permanent pastures. Land under permanent crops is land cultivated with crops that occupy the land for long periods and need not be replanted after each har vest, such as cocoa, coffee, and rubber. This category includes land under flowering shrubs, fruit trees, nut trees, and vines, but excludes land under trees grown for wood or timber. Permanent pasture is land used for five or more years for forage, includ ing natural and cultivated crops. h Arable land includes land defined by the FAO as land under temporary crops (double cropped areas are counted once), temporary meadows for mowing or for pasture, land under market or kitchen gardens, and land temporarily fallow. Land abandoned as a result of shifting cultivation is excluded. i Alpha diversity translated into number of species per polygon, inferred from Landsat data by Convertino et al (2012) Some time series have gaps, for flow 3 stations have been gap in length for each station

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63 Table 2 2 Overview of stationary data collected and compiled for the area in Madre de Dios (Peru), Acre (Brazil) and Pand o (Bolivia), the MAP area. Sub system Spatial resolution Stationary Variables (units) HUMAN Community COM Community characteristics Community names Community ID Community area (km 2 ) Elevation (MASL) Distance to nearest market (km) Distance to (state) capital (km) NATURAL Community SOIL Soil types Soil organic carbon (g/kg) Soil pH Sand, silt and clay fractions (%) Bulk density (tones/m 3 ) Cation exchange capacity (cmol/kg) Volumetric coarse fragments Soil organic carbon stock (tonnes/ha) Depth to bedrock (m) World Reference Base soil groups USDA Soil Taxonomy suborders Saturated hydraulic conductivity (10 6 m/s) Saturated volumetric water content (cm 3 /cm 3 ) Residual volumetric water content (cm 3 /cm 3 ) Community FOR_TYPE Forest types Alluvial (%) Bamboo dominated (%) Palm dominated (%) Dense (%) Developed (%) Water (%) Wetlands (%) Submontane dense (%) Transects BOT Botanical data Family Genus Diameter at breast height (cm) Height (m) Aboveground biomass (kg/m 2 ) Timber volume OTHER Shapefiles State boundaries Community boundaries Roads Rivers Protected areas

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64 Figure 2 1. Comparison of monthly values per community polygon for AVHRR derived EVI (1982 2010) A) Monthly averages for 2 periods. B) Differences between the monthly averages for the 2 periods.

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65 CHAPTER 3 CLUSTER ANALYSIS OF VEGETATION DYNAMICS AND ASSOCIATION WITH ROAD PAVING Background The Amazon region in South America holds the largest areas of intact forest in the world and has be en proven to be of great importance to the global climate system and biodiversity (Foley et al., 2007; Keller, 2009) There is global concern about changes in land cover in the Amazon caused by anthropological disturbances and the consequences of such land cover changes; both globally and locally ( Davidson e t al., 2012 ; Keller, 2009; Nobre and Borma, 2009 ) Anthropological disturbances have an impact directly on forest cover by deforestation, but also on forest structure and composition, varying with the extent and frequency of the disturbances. Structural and phenological changes due to anthropological disturbances (logging, fire) are for instance changes in basal area, community composition (J. Zh u et al., 2007) understory composition and vine cover (Felton et al., 2006) Infrastructure development, such as road building, increases these disturbances and many studies have highlighted negative socio economic and biophysical effec ts that thes e developments have at local, regional and even larger scales. Road paving and construction has been found to be the main driver of deforestation ( Laurance et al., 2009 ; 2002c) Other effects include land degradation, impacts on abiotic processes (such as hydrology), disruption of movement of organisms and increased mortality, alteration of natural disturbance regimes (e.g. fi re), pollution, violent conflict over natural resources, and rural urban migration (Coffin, 2007; La urance et al., 2009 ; Marsik et al., 2011 ; Perz et al., 2011b; 2011a)

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66 The Inter Oceanic Highway (IOH) runs through the forested and highly biodiverse national area that includes parts of Peru, Brazil and Bolivia, for which we gathered a large multi disciplinary long term database. Paving of the highway has started at different times across the area, offering a valuable study site with data before, during and after anthropological disturbance. Considering the tight coupling of natural and human systems in this area, changes in ecosystem servi ces from the natural (forest) system would have far reaching consequences. This concern goes beyond deforestation or forest loss: even if forest cover is maintained, is this forest degraded or altered over time due to road paving? Degradation of the forest ecosystem has an effect on ecosystem services, and in order to evaluate degradation, we propose to look at vegetation dynamics in this study. Vegetation dynamics, or phenology, refer to the timing of biological processes, such as flowering, growth and sen escence. Vegetation structure and species composition have an effect on vegetation dynamics, and vegetation dynamics in turn affect ecosystem services such as primary productivity and nutrient cycling (Figure 1 1). If a change in vegetation dynamics is fou nd, we can deduct that ecosystem services broadly will also have changed. We use the extended Enhanced Vegetation Index (EVI2), a remote sensing product, as a proxy for vegetation dynamics. This product is an extended version of original EVI (which is ava ilable from 2000 onwards), with values as far back as 1982 obtained from a conversion of other remote sensing data (form the Advances Very High Resolution Radiometer). Previous research on vegetation dynamics in the Amazon using the Normalized Difference Vegetation Index (NDVI) within which phenology is similar (F. B. Silva et al., 2013) Similarly, this study aims at

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67 assess es these dyna mics at a smaller scale, particularly in the presence of road paving. Road paving introduces new and amplified perturbations to the system (Cumming et al., 2005) thus w e hypothesize that vegetation dynamics are affected by road paving over time. We expect that similar vegetation dynamics (in terms of values and timing) can be grouped together, and that they are associated with the extent of road paving Since the d ata cover areas with roads that were paved at the beginning of the study period (1987 2009), areas that had roads paved over the course of the study period and areas that never had paved roads, we expect to identify different (transitional) states of veg etation dynamics To answer this hypothesis, we use time series of EVI2 to explore potential clusters, and the characteristics of these clusters. Considering the size of our overall data set and further research, the additional advantage is the reduction o f complexity of the data set Cluster analysis is a useful method to deal with large data set s, to gain initial understanding of the structure and potential relationships, before proceeding to more complex analyses. Specific methods have been developed to cluster time series. Some of the best known are Dynamic Time Warping (DTW) and shape based distance (SBD). For the purpose of our research, a method was needed that clusters time series together based on timing of values specifically, not just frequencies. We wanted to ensure that vegetation dynamics that peak or fall in a particular month were clustered together: the focus is on similarity in phenological variation. Hence, for the creation of a dissimilarity matrix on which clustering is based this nee ds to be accounted for. In this study, we used a method that creates an adaptive dissimilarity index: this takes into (Chouakria and Nagabhushan,

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68 2007) After clustering the data with a number of hierarchical methods, we employed two validation measures that supply criteria for the optimum number of clusters and clustering method based on compactness and separation (Figure 3 2) In order to investigate if there were biophysical variables that had the potential explain the cluster results for EVI2, we applied cluster analysis to the data set s for minimum, maximum and mean temperature, precipitation, soil moisture, potential evapotranspiration and species richness. We also took into account values and behavior (similar to the EVI2 clustering), and evaluated if the results were similar to EVI2 clustering To investigate cluster differences, mean and median values for the EVI2 per cluster are not useful, since a) a ll analyses were and will be done on normalized data, to focus on the dynamics, and b) the dissimilarity index takes dynamics into account as well as actual values. Neither does comparing variance provide much information, since these values can be the sam e, but the timing can differ. We decided to look at the dominant values, i.e. peaks in the probability distribution of the values. By defining these using a moving windo w over the whole study period, we can see if the number of states change over time. We applied a breakpoint analysis to assess differences between the clusters. Methods Data For this analysis we primarily focused on time series for EVI2, the long term EVI data set with AVHRR converted EVI data for the period pre 2000. We used monthly time series for road paving, minimum, maximum and mean temperature, precipitation, PET, soil moisture and species richness to attempt to interpret the cluster results. These

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69 da ta set s are described in detail in Chapter 2. For these analyses, we used monthly data from January 1987 to December 2009, considering that this was the time frame for which data described in Chapter 2, and to be used in subsequent Chapters, overlaps. Figu re 3 1 shows average values over this time period for each community in the study area. It gives an indication of the differences in average values, but in this study we did not use absolute values. All data were normalized, since we are only interested in dynamics shape and relative magnitude of values not absolute values. Time Series Clustering Based on an Adaptive Dissimilarity Index All clustering methods start with developing a matrix that contains distances between points or objects (Figure 3 2) For clarification, in this text we refer to this matrix as the dissimilarity matrix (other terms are distance, similarity or proximity matrix). Each time series in the analysis is called an object. The dissimilarity measure we calculate is related to close ness of values and time series behavior (Chouakria and Nagabhushan, 2007) which is achieved by including an automatic adaptive tuning function in the conventional dissimilarity index: (3 1) with (3 2) in which S is an object (a time series) and a parameter that determines how much is taken into account, with being the temporal correlation coefficient ( see Equation 3 4). At a value of the dissimilarity matrix is based on values only. At higher measure for dissimilarity based on values is expressed in which is the

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70 summed Euclidian distance between series and at with respective values and for points in time: (3 3 ) The temporal correlation coefficient that is used in Equation 3 1 is: (3 4) where lies between 1 and 1. At 1, series and exhibit exactly the same behavior between and : increase or decrease with the same growth rate. At 0 their growth rates are stochastically linearly and independent, and at 1 their behavior is opposite. Parameter k determines how much proximity with respect to behavior or with respect to value contributes to the dissimilarity i ndex. After developing dissimilarity matrices for a range of values for ( hierarchical agglomerative clustering was applied. This method takes a bottom up approach, starting with each object as a singleton cluster. At each step, clusters merge b ased on certain distance metrics, until all objects are clustered in one cluster. The resulting cluster tree or dendrogram can then be evaluated to decide where to cut off the tree. We evaluated the results of four cluster methods: single linkage, complete the clusters with the smallest minimum pair wise distance (between objects in different clusters) are clustered together at each step. Complete linkage clustering is also based on pairwise distances, but it clusters those together that have the smallest maximum distance. This method is more sensitive to outliers. Average linkage clustering calculates the average distance between all objects in one cluster and all objects in

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71 different approach than these three methods: instead of using distance metrics, it analyzes variance. For each possible combination of clusters at a step, the error sum of sq uares (ESS) is calculated, and whichever pair yields the smallest ESS is clustered together. The ESS thus compares individual objects against cluster means. With objects with dissimilarity values in cluster it is calculated as: (3 5) This implies that the initial cluster distance (between singleton clusters) is the Euclidean squared distance between objects. For each cluster method, we evaluated the results of 2 to 10 clusters, for dissimilarity matrices with ranging from 0 to 5 for each (a total of 216 cluster options) Figure 3 2 Clustering Validation Measures The Dunn Index (Dunn, 2008) and the Silhouette Width (Rousseeuw, 1987) were used as met rics to determine the suitability of the clusters. These are widely used metrics that focus on compactness and separation of clusters. They are known as internal validation measures: evaluation of the clusters is based on the data and clustering only and n The number of clusters with the highest Dunn index (DI) indicates this the optimum number of clusters; i.e. the highest separation between clusters, and the least spread of data within clusters. The index is the ratio of the minimum distance between observations not in the same cluster, and the maximum distance between observations within a cluster. This can be written as (3 6)

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72 where is the di stance between clusters and and is the within cluster distance (the diameter) for a cluster with objects. The Silhouette width (SW) ranges from 1 to 1, with higher values meaning that the clusters are cohesive and well separated. This meas ure takes the lowest average dissimilarity of a series with other clusters (Euclidean distance) and subtracts the of this number to whichever average dissimilarity is the highest: if the average dissimilarity with the neighboring cluster is larger than the average dissimilarity within cluster, this yields a positive number The average silhouette is the final metric. For instance, for a system with cluster and a number of clusters (for which ), the calculation of silhouette for object in is (Rousseeuw, 1987) : (3 7) (3 8) After calculating this for all clusters we find the smallest value: (3 9) and calculate silhouette : (3 10) this can then be average for all objects in (3 11) and eventually be averaged for all clusters. code so th ey could use the previously described adaptive dissimilarity matrix.

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73 Number of States and Breakpoint Analysis After cluster analysis, EVI2 time series were grouped together in their respective cluster. They were then averaged in an area weighted manner for each cluster for this analysis, based on the area of the community the EVI2 time series is associated with. We developed histograms and calculated the probability distribution functions over a moving window of 5 years (60 months) for each area weighted ti me series. The number Moving the window one month at a time, all states were recorded for the full period of record. This method has been applied in the past theoretic al systems such as Lorenz curves (Huffaker et al., 2017) from which the code has been derived and a simi lar approach has been used on climate systems (Livina et al., 2010) Since the number of states appeared to vary over time, we applied a break point analysis (Andersen et al., 2009; Zeileis et al., 2003; 2002) to determine the point where there was a statistically significant difference in number of states between two periods. This is termed a (Zeileis et al., 2002) was used to perform the breakpoint analysis. The method we implemented relies on F test statistics, and tests for a single breakpoint across the whole time period of interest, for each potential change point. This test is also known as a Chow test: for a particular point in time two linear models are fitted one for the d ata before this point and one for data after that point. The resulting residuals are then compared to the residuals from a linear model fitted for the complete time series. If n is the number of observations and k the number of regressors in the model,

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74 (3 12) with RSS the restricted sum of squares (residuals from one model for all observations) and ESS the error sum of squares (residuals from a model with two components). In our analyses the linear model was a model without a slope, hence the mean of the time series. The implemented approach uses moving breakpoints, thus generating sequential F tests. The year for which the F statistic is highest (and above the critical F level), is regarded as the breakpoin t (Andersen et al., 2009; Zeileis et al., 2003) To determine whether a breakpoint is statistically significant (above the critical F level), p values are calculated which are adjust ed for asymptotic p value approximations (Hansen, 1997) Data Availability The data set s generated during and/or analysed for this study as well as code, are available in a Figshare repository, 10.6084/m9.figshare.c.3933367 Results Four EVI2 Clusters Along a Road Paving Gradient The validation measures that were calculated for all possible clusters, indicated that all options were valid clusters, i.e. their values were larger than zero. DI and SW are low overall, indicating that the clustering is weak to moderate. In determining the appropriate number of clusters, we first looked for results where the optimum number of clusters recommended by the DI and SW were the same (Table 3 1 and Figure 3 3 ). While a number of clustering methods indicated that two clusters gave the highest DI and SW, we decided to cluster the data into four clusters the result from clustering 3 and 3 4 ). Since we are interested in finding and

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75 analyzing heterogeneity in the study area, having more clus ters essentially allows us to analyze the data at a higher resolution. We opted to use the results from the analysis that used in the adaptive dissimilarity index calculations. While the SW is lower than for the option with the DI is almost twic e as large. Since the DI seems to take into account outliers more (since it takes the maximum within cluster distance), we preferred this value to be higher. At the contribution of the behavior component to the dissimilarity index is 76.2% and the val ue component contributes 23.8% (Chouakria and Nagabhushan, 2007) After deciding on the appropriate number of clusters, t he results were mapped (Figures 3 5a and 3 5b ). The resulting clusters showed spatial cohesi on and will be referred to as Vegetation Dynamics Clusters (VDCs). We calculated the mean road paving extent per community (one value per community Figures 3 5c and 3 5e ), and area weighted average paving extent per VDC (a time series per cluster Figure 3 5d ). We then ordered the VDCs accordingly: there was an increasing tendency in me di an pav ing extent across VDCs (Figure 3 5e ). There were also distinct differences in area weighted average paving extent per VDC (Figure 3 5d ) in terms of start and end tim e of paving. Road paving extent is indicated by values between 0 and 1, with 0 indicating an unpaved road, 1 a fully paved road, and anything in between indicating road paving in progress. Based on these distinctions VDC 1 represents the unpaved system st ate, VDC 2 and VDC 3 transition states, and VDC 4 the mostly paved system state. Additional Cluster Analysis on Biophysical Variables To test whether there were biophysical variables that could be associated with the clustering found for EVI2, these were a lso clustered with the same methods and

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76 evaluation metrics. We applied the same cluster analysis (with for the adaptive dissimilarity index calculation) to the time series for minimum, maximum and mean temperature, precipitation, PET, soil moisture an d species richness. The optimum number of clusters suggested by the DI and SW were not identical to EVI2 (Table 3 2). States and Breakpoint A nalysis The number of states was variable fo r each VDC over time (Figure 3 6 ). For VDCs 1, 2 and 3 the number of st ates is generally lower (2 to 3) at the end of the study period. The breakpoint analysis found statistically significant breakpoints for each VDC, which were all located between 1997 and 2001. We added the point in time where average area weighted pavin g w as at 0.1 (10%) to Figure 3 6 to compare it with the timing of the breakpoint. Discussion Assessment of Final Clusters The DI and SW values indicate that overall, clustering is weak to moderate. This is a result of the noisiness of the EVI2 data, something that is a problem with much remote sensing data in the tropics (Huete et al., 2002) However, all cluster results are valid in the sense that the DI and SW are positive values. Negative values would indicate that clusters are overlapping, and that assignment of an object to a cluster is probably misspecified. The moderate clustering stre ngth is something to take into account with further analyses. There might be outliers for each cluster that could complicate analyses or interpretation of results. Spatially, one such outlier is potentially the community in Bolivia (without paving) that ha s been clustered together with the communities in Brazil (VDC 4). Still, from field work it appears that this community is closely associated with the Brazilian communities, so even though it has no road paving

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77 officially, the EVI2 similarities could be du e to proximity to paved communities. Overall though, the final clusters show spatial coherence, with clusters identified in Brazil, Peru, Bolivia and one covering the tri national border area. Biophysical variables showed higher values for the cluster val idation measures DI and SW, but we need to keep in mind that this data comes from reanalysis data, so potentially less noisy, and is available at a lower resolution than the EVI2 data. The latter makes it likely that certain communities have more similar t ime series. Eventually, the biophysical variables did not cluster to a similar number of clusters as EVI2 did. We take this as an indication that there is not one single variable that potentially drives the EVI2 clustering for the whole region. Comparison of States Changes The method we applied, finds statistically significant breakpoints in the number of states of EVI2 over the study period. There could potentially be a relationship with road paving: the breakpoint is some time after paving starts for VDC 4, but happens sooner after road paving starts in VDC 3. In VDC 2 and 1, the breakpoint even happens before road paving starts. We could potentially attribute this to the spill over effect of neighboring clusters being paved already. However, the nature o f the EVI2 data means we should proceed with caution with drawing conclusio ns. The data from before 2000 are AVHRR adjusted data and are expected to suffer from noisiness and uncertainty associated with remote sensing difficulties in tropical regions (e.g. cloudiness and aerosol interference). The fact that all breakpoints are located around that time suggests that this is potentially a contributing factor to breakpoint identification. The existence of multiple states indicates that the data are probably no isier. We would therefore advise not to use methods that do

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78 comparisons on EVI2 data of pre and post paving periods. Since VDCs also cluster along an average road paving gradient (Figure 3 5 ), an appropriate approach would be to interpret the VDCs as area s increasingly impacted by road paving. This research confirmed the hypothesis, that there are states associated with road paving but we do not have complete certainty about transitions. The state changes and breakpoint analysis suggest an ordering along the road paving gradient, but the noisiness of the EVI2 data requires that we interpret these results carefully. Methodological Findings: Cluster Selection and State Changes Selection of clustering is seldom straightforward, and we used two well known met hods to evaluate clusters based on compactness and distance from other clusters. While these methods should help in making the decision on the number of clusters less subjective, choosing evaluation or validation measures is in itself also subjective sin ce many exist. Using two methods, however, is a good safeguard against subjectivity. We expected that the two measures would be more in agreement though, since they purport to evaluate similar things; compactness and separation. The type of calculations ap plied for each measure appear to result in differences though. Hence, in choosing the appropriate number of clusters, it is also important to evaluate the validation measure that is used by applying more than one measure and comparing results. The method o f finding state changes is a useful tool to better understand dynamic data. In this study, however, the nature of the EVI2 data limits the interpretation of the results with much certainty. The method could be expanded by also evaluating the values associa ted with the states, and the height of the peaks in the histograms. This could provide information on stability of the states and allow for an even deeper understanding of potential changes.

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79 Table 3 1. Dunn Index and Silhouette Width results from al l clustering options for EVI2 Optimum umber of clusters Test values Clustering method k Dunn Index Silhouette Width Dunn Index Silhouette Width 0 3 8 0.53 0.09 1 8 4 0.41 0.15 2 4 4 0.30 0.22 3 4 4 0.16 0.28 4 7 4 0.14 0.32 5 7 6 0.09 0.37 Single linkage 0 2 2 0.78 0.18 (minimum) 1 2 2 0.59 0.21 2 2 2 0.40 0.24 3 2 2 0.26 0.26 4 2 2 0.17 0.28 5 2 2 0.11 0.29 Average 0 2 2 0.78 0.18 1 2 2 0.50 0.18 2 2 2 0.30 0.23 3 2 2 0.17 0.28 4 3 7 0.12 0.32 5 2 6 0.09 0.38 Complete 0 2 2 0.67 0.13 (maximum) 1 6 2 0.42 0.18 2 10 4 0.26 0.20 3 7 4 0.22 0.26 4 10 6 0.12 0.28 5 10 4 0.06 0.37

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80 Table 3 2. Values of the validation measures indicating the best number of VDCs after a dissimilarity index (Chouakria and Nagabhushan, 2007). The validation measures are the Dunn index (DI ) and the Silhouette width (S W). Both need to be maximized. Two to ten clusters were tested. Variable Measure Score Clusters EVI2 DI 0.30 4 SW 0.22 4 Mean temperature DI 0.17 9 SW 0.59 2 Minimum temperature DI 0. 15 9 SW 0. 61 2 Maximum temperature DI 0.17 2 SW 0. 66 2 Potential evapotranspiration (PET) DI 0.17 5 SW 0.65 2 Precipitation DI 0.14 7 SW 0.61 4 Soil moisture DI 0. 31 2 SW 0.58 2 Species Richness DI 0. 19 8 SW 0.18 9

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81 Figure 3 1. Average values of EVI2 and biophysical variables per community for the period 1987 2009. a) EVI2, b) potential evapotranspiration, c) species richness, d) average temperature, e) minimum temperature, f) maximum temperature, g) precipitation and h) soi l moisture.

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82 Figure 3 1. Continued.

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83 Figure 3 2. Analysis framework for clustering analysis

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84 Figure 3 3 Selection criteria for determination of the appropriate number of clusters. in the calculation of the dissimilarity matrix. A) Results from the Dunn Index. B) Results from the Silhouette Width

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85 Figure 3 4 Dendrogram of EVI2 time series clusters, with 4 clusters selected.

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86 Figure 3 5 Characteristics of the study area after clustering analysis. a) The study area with 4 VDCs. b) Minimum, median, maximum monthly Enhanced Vegetation Index (EVI2) time series per VDC. c) Map of the study area, with 99 communities and their average paving extent for the period 1987 2009. d) Area weighted average paving extent per Vegetation Dynamics Cluster (0=road section associated with the community i s unpaved,1=road section associated with the community is fully paved). VDCs are based on the adaptive dissimilarity index of EVI2. e) Average paving extent of the communities in each VDC, with an upward non linear tendency from VDC 1 to 4. The tendency is a loess curve based on the median paving values per cluster.

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87 Figure 3 6 Results from the breakpoint analysis of EVI2 per cluster. Panels on the left show the states over a moving window of 5 years. States are peaks in the probability distribution of values. Panels on the right show the F statistic for the test of different means before and after a moving breakpoint, as well as the critical F value, the breakpoint (black) and the point where road paving was at 10% in the cluster.

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88 CHAPTER 4 CHANGING LANES : HIGHWAY PAVING IN THE SOUTHWESTERN AMAZON ALTERS LONG TERM TRENDS AND DRIVERS OF REGIONAL VEGETATION DYNAMICS Background The Amazon region in South America holds the largest areas of intact forest in the world (Killeen and Solorzano, 2008) ; (Keller, 2009) which is of great importance to the global and regional climate system, biodiversity and carbon sequestration (Foley et al., 2007; Myers et al., 2000) There is great concern about changes in land cover in the Amazon, and the global and local consequences of such changes (Foley et al., 2007) ; ( D avidson et al., 2012 ; Nobre and Borma, 2009 ) Anthropogenic disturbances have direct impacts on forest cover by deforestation, and on forest structure and composition that vary with the extent and frequency of the disturbances. For example, logging and f ire result in structural and phenological changes like reduction in basal area, vegetation composition (J. Zhu et al., 2007) understory composition and vine cover (Felton et al., 2006) Degradation of healthy forest reduces local, regional a nd global ecosystem services (Foley et al., 2007) Road construction and paving have been found to be a main driver of deforestation ( Laurance et al., 2009 ; 2002a; Marsik et al., 2011 ; Nepstad et al., 20 01) Large infrastructure projects also cause land degradation, impacts on abiotic processes (such as hydrology), disruption of movement of organisms and increased mortality, alteration of natural disturbance regimes (e.g. fire), and pollution. While in frastructure has been demonstrated to bring socio economic benefits, it can also lead to violent conflict over natural resources, and rural urban migration (Coffin, 2007; Laurance et al., 2009 ; 2002b; Perz et al., 2011b; 2011a) Increasing interest in the relationships

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89 between infrastructure development and the environment has given rise to the field of (Forman, 2003) mostly focused on effects in the vicinity of roads. Most studies have considered straightforward direct impacts such as deforestation (Laurance et al., 2002a; Marsik et al., 2011 ) and localized impacts such as edge effects on vegetation (Coffin, 2007; Lugo and Gucinski, 2000; Mesquita et al., 1999) ; ( Laurance et al., 2009 ) For example, environmental impact assessments conducted for Amazonian highway construction in Brazil only considere d very limited areas of impact along the roads, neglecting the potential regional impacts of road construction ( Laurance et al., 2009 ) such as forest degradation and changing vegetation dynamics in larger areas. Vegetation dynamics refer to temporal fluctuations and spatial variability in vegetation structure associated with disturbance regimes resulting from natural and anthropogenic drivers. Changes in vegetation dynamics are indicative of the shifting forest structure and the corresponding ecosystem services, which have social as well as ecologica l impacts (Foley et a l., 2007) It is therefore important to study changes beyond forest cover changes, and to do an analysis that addresses both natural and human processes, thus considering the system from a socio ecological perspective. The tri national area in the southwestern Amazon (the so called MAP area after the provinces of Madre de Dios (Peru), Acre (Brazil) and Pando (Bolivia)) has been (Killeen and Solorzano, 2008; Myers et al., 2000; Perz et al., 2011a) where livelihoods are closely associated with natural resources. The area is thus a useful example of a complex socio ecological or coupled natural human system (Perz et al., 2011b; 2011a; 2013b) This means that disturbances to the system can result from natural and anthropogenic drivers and their interactions

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90 (Chazdon, 2003; Cumming et al., 2012 ; Davidson et al., 2012 ; Phillips et al., 2008) One very specific anthropogenic disturbance in MAP is the development of roads, w hich has been an important part of regional economic integration and development in recent decades (Perz et al., 2008; 2011a ; 2007) In particular, the Inter Oceanic Highway (IOH), connecting the Atlantic and Pacific Oceans and traversing the MAP region, is one of the key infrastructure projects of the Peru Brazil Bolivia axis of integrati on (Rapp, 2005) The road is a major part of the Initiative for the Integration of Regional Infrastructure in South America ( IIRSA) that targeted infrastructure investments for (Perz et al., 2011 b ) Previous research found that even limited logging disturbances, without significant forest cover loss, had a permanent local effect on forest structure in Madagascar (Brown and Gurevitch, 2004) Differences in vegetation structure and phenology between natural and anthropogenic treefall gaps 1 to 4 years after logging were also identified in a Bolivian forest, despite almost identical forest cover perc entages (mean 88% for the anthropogenic gaps, and 91% for the natural gaps), with lower mean number of flowering and fruiting plants in anthropogenic gaps, as well as more regeneration of non commercial pioneer species in these gaps (Felton et al., 2006) A review study concluded that in Neotropical secondary forests, the recovery trajectory of vegetation and its characteristics is uncertain in anthropogenic settings, and dependent on site specific factors and land use (G uariguata and Ostertag, 2001) Changes in forest structure will in turn impact ecosystem service provision: changes in tropical forest structure have been linked to modifications in wildlife populations in Panama (DeWalt et al., 2003) and ecosystem productivity was found to be driven by

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91 canopy phenology in the Amazon (R estrepo Coupe et al., 2013) A forest inventory study in the MAP region (Baraloto et al., 2015) found differences in forest value (based on biodiversity, carbon stocks and timber and non timber forest products) across the frontier, and highlighted that deforestation and degradation do not always respond similarly to road paving. Unfortunately, in si tu vegetation structure assessments, while extremely valuable for purposes of biodiversity valuation, are time intensive, limited to discrete locations and usually have a limited time dimension (synaptic), making it difficult to assess changes in vegetatio n dynamics over time and space for a large area. There is a need to comprehensively assess spatially distributed changes in vegetation dynamics due to road paving to gain a better understanding of the system wide effects of infrastructure development. Base d on this evidence, we formulate a hypothesis that even if forest cover is maintained, the structure of the forest will be regionally impacted in the presence of advancing road paving. Our hypothesis asserts that there are different forest structures and d ynamics across a gradient of road paving, from dirt road to fully paved. Further we suggest that forest change responds to different drivers as one moves along the paving gradient. Specifically, anthropogenic covariates are expected to become more importan t under more advanced paving conditions associated with increased regional disturbances which are integral to driving and changing vegetation structure (Sousa, 1984; Thonicke et al., 2001) To test this hypothesis, we require a long term time series of vegetation index values in order to stu dy changes in vegetation structure and dynamics. The long term monthly Enhanced Vegetation Index (EVI), a remote sensing product from the Moderate

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92 Resolution Imaging Spectroradiometer (MODIS), has been found to indicate vegetation phenology and structure (Asner et al., 2000; Huete et al., 2002) It has been used in previo us studies to evaluate phenology, structure and ecosystem functioning (Bradley and Fleishman, 2008; Cabello et al., 2012; Reed et al., 1994; Volante et al., 2012) EVI2, used in this study, is a relatively new product (Z. Ji ang et al., 2008 ) consisting of EVI extended back in time from two band Advanced Very High Resolution Radiometer (AVHRR) data (1982 1999) and three band MODIS EVI (2000 and after). We combine the EVI2 data on forest vegetation with field based socioec onomic and biophysical data, which serve as indicators of drivers of vegetation change. Socio ecological survey da ta for the period 1987 2009 are available for 99 areas defined as communities in the MAP region (Perz et al., 2011b; 2011a ) as well as biophysical covariates (see M ethods). Paving of the IOH started at different times in different countries across the MAP frontier, offering a valuable long term study site with a paving gradient (before, during and after) for road construction. The objective of this paper is to test our hypotheses by applying advanced statistical time series analyses to explore the structural and phenological changes of forests at a regional scale, and how they are associated with the progression of road paving and natural and human drivers and intera ctions. The time and resource intensive methods that we apply allow us to analyse 99 unique long term time series of vegetation dynamics, without having to resort to simplification techniques. They focus on finding shared variance and common trends across large numbers of time series. We first identify areas of shared spatio temporal vegetation dynamics along a road paving gradient by means of cluster analysis. To identify common drivers for these

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93 vegetation dynamics, we separate and attribute the relative importance of latent effects (unexplained shared variance or trends) and explanatory natural and human covariates (explained variance or direct effects) by means of Dynamic Factor Analysis (DFA), a specialized dimension reduction time series analysis tech nique (Campo Bescs et al., 2013; Kaplan et al., 2010; Kuo and Lin, 2010; Ritter and Muoz Carpe na, 2013a) The results are twofold: identification of common trends and covariates across a larger region, while also specifying their importance at local level. The objectives are twofold: identification of common trends and covariates across a larger region, while also specifying their importance at local level. Our innovative approach provides a way for systematic and continuous assessment of forest degradation, represented by the shift in the importance of trends and human and natural covariates und er increased highway paving. Results Identification of Clusters Vegetation Dynamics and their Association w ith Road Paving Extent The socioeconomic survey includes 99 distinct communities in the MAP area in the Southwestern Amazon ( Figure 4 1a and Table A 1). Monthly time series of the vegetation index, EVI2 (Z. Jiang et al., 2008 ) ) for these communities were available, with bi ophysical and socio economic data (see Table 4 1 ). Hierarchical cluster analysis on an adaptive dissimilarity index (Chouakria and Nagabhushan, 2007) of normalized monthly EVI2 time series (1987 2009) permitted or ganization of the communities into 4 distinct clusters, based on identical Silhouette width and Dunn index results (Brock et al., 2008) see Figure s 3 3 and 3 4 These will be referred to as Vegetation Dynamics Clusters (VDCs) in this study ( Figure 4 1 d). Characteristics of the EVI2 time series of

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94 each VDC are given in Figure 4 1 e and Table 4 1 Normalized values were used in this study to retain the focus on the time series dynamics, and facilitate interpretation of model results. A distinct relationship was identified between VDCs ( Figure 4 1 c) and median area weighted average paving extent per VDC ( Figure 4 1 b). Road paving extent is indicated by values between 0 and 1, with 0 indicating an unpaved road, 1 a fully paved road, and anything in between indicating road paving in progre ss. An average was taken for each community for the period January 1987 to December 2009, and is an expression of when paving started and the length of the construction period ( Figure 4 1 c). Thus VDC 1 represents the unpaved system state, VDC 2 and VDC 3 transition states, and VDC 4 the mostly paved system state. Subsequent models and analyses were conducted for each VDC. Common Trends Explain t he Shared Va riability o f Each VDC Dynamic Factor Models (DFMs) for VDCs 1 through 4 simulated EVI2 with common trends only (DFMs I) identified 4, 7, 6 and 3 trends, respectively ( Table 4 2 ), based on their lowest Bayesian Information Criterion (BIC). The median goodness of fit (Nash Sutcliffe coefficient, C eff ) ranged between 0.67 and 0.76, indicating that the mode ls captured the shared variability within regions well. Respectively, 83%, 75%, 81% and 71% of VDC 1 through 4 models for each community had an acceptable (Ritter and Muoz Carpena, 2013a) C eff >0.60 (See Table A 6 for details and Figure A 1 for examples of fitted time series ) Overall, 98% of C eff were higher than 0.50 (97 out of 99), which is considered a good overall fit considering the typical noisiness of ecological data. The analysis identified regional, shared variance common trends underlying the vegetation dynamics for each VDC. Based on this result, we developed DFMs with

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95 both trends and area weighted averaged covariates to attempt to explain the shared variance in each VDC (see Methods and Figure 4 7 ). In a Disturbed System State, Covariate s Explain More of t he Variance In Vegetation Dynamics Than in a n Undisturbed S ystem State backward elimination of covariates or trends until the lowest BIC was reached. We started with all covariates and the number of trends from DFMs I. Elimination was based on the average importance of each model component per VDC, which was determined with a computationally intensive method (Grmping, 2006) that calculates semi partial R 2 of model components, averaged over all possible model orders (see Methods for a detailed explanation of this measure of importance of regression components). This produces an index of importance for each covariate for each community, which are then averag ed over the whole VDC to select the least important model component which will be eliminated from the model. Some covariates were lagged before DFA application, based on their cross correlation with average area weighted EVI2, to account for delayed respon ses of vegetation dynamics to covariates (Table A 4). Table 4 2 lists results for DFMs II with covariates ordered according to average importance for each model (see Table A 7 for more detailed results). We found that each final DFM II (bold in Table 4 2 ) based on the same number of trends as DFM I, with 6 to 8 covariates each Each DFM II contained both natural and human covariates. eff stayed the same or inc reased: thus, while the number of trends remained the same, their importance became sm aller A portion of the explained variance was shifted to the covariates, while maintaining model fit. Again, for 98% of DFMs II, C eff 0.50. Figure 4 2 a plots the total explained variance (R 2 ), and Figure 4 2 b shows the cumulative

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96 importance of all trends and covariates compared to average paving extent in communities. Importance is expressed as the average explained variance. While total R 2 stays fairly constant across all average paving extent ( Figure 4 2 a), the Loess curves in Figure 4 2 b show that once average paving extent passes 0.50 (50%), the importance of trends and covariates shifts Specifically, covariates explained approximately 25% of variance under unpaved conditions, and 50% under paved conditions, while trends exhibit a decrease their explan atory power. This implies that for communities where paving started longer ago, much of the vegetation dynamics can be explained with covariates directly. Tables A 8 to A 11 contain details on covariate time series, model fits and weighting and loading coe fficients for each community. Variables Associated w ith A nthropogenic Activity Increase in Importance i n Explaining Vegetation Dynamics in t he Disturbed System State In Figure 4 2 c, the explained variance is subdivided into that associated with natural covariates and with human covariates ( Table 4 1 ). Communities with more recent road paving (low average road paving extent, 0.10) showed an increase in variance explained by human covariates compared to communities with no road paving at all, but this decr eased for communities with higher average road paving (0.25), potentially due to adaptation of the system to a different disturbance regime. Eventually though, there was an inversion of importance of natural and human covariates that occurred after paving extent reached the 0.50 point. Figure 4 3 shows that travel time to market, family density and enforcement of tenure rules were the most important (highest average semi partial R 2 ) human covariates in the DFMs II. The covariate time series used in the DFM IIs for each VDC are shown in Figure 4 4 The standardized regression coefficients ( ) of the DFMs give

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97 additional information beyond the explained variance as its sign indicates an inverse or reinforcing effect of the covariates on vegetation dynamics. F or interpretation of the coefficients of this study, we need to keep in mind that covariates were added to the models with lags ( Figure 4 5 ). The inverse effect of family density is intuitive: increasing family density ( Figure 4 4 ) leading to decreasing EV I2 could be linked to increased pressure on vegetation and forest exploitation. For travel time to market, we need to take into account the average paving extent of communities in each VDC to understand its effect: for later paved communities (low average paving extent, VDC 2), the decrease in travel time is associated with decreased EVI2 (positive ), again due to increased pressure and exploitation associated with better access to markets for locals and better access to forest products by outsiders. Howe ver, for communities that had paved roads earlier in the study period (higher average paving extent, VDC 4), the sign of reverses to negative values. The change in travel time is less pronounced and occurs over a longer time period ( Figure 4 4 ), so it is possible that over time communities shift their focus to more urban sources of income rather than forest based ones, prompting higher EVI2 over time. Enforcement of tenure rules on deforestation also had a positive effect on EVI2 in communities that had u npaved roads during the study period (VDC 1), as expected. While enforcement also increased for the communities that had paving longer, in VDC 4 ( Figure 4 4 ) its effects appeared negative (i.e. lower EVI2). A possible explanation for this seemingly counter intuitive result is the 13 month lag applied to this covariate (in Figure 4 5 the lags are given above each covariate plot), relevant mostly to Acre, Brazil ( Figure 4 1 d). Most of the enforcement change occurs in the early years (1990 1991,

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98 Figure 4 4 ), af ter which enforcement stays fairly constant. Extraction of forest resources and conversion to agriculture had been going on for many decades in this area, and in the 1980s several groups (ranchers, rubber tappers, colonists) clashed over land use and defor estation (Hoelle, 2011) Subsequent i ncreased enforcement might have been too late to affect vegetation positively Among Natural Covariates, Temperature is the Main Direct Driver o f Vegetation Dynamics Temperature time series were important factors in all VDCs. Normalized minimum, maximum a nd average temperature had different temporal patterns ( Figure 4 4 ) and combined appeared relevant in simulating vegetation dynamics (Figure 4 3): on average, across all communities, the variance explained by the three temperature time series (average semi partial R 2 ) is 32% of all variance explained by natural covariates. This is probably due to their effect on photosynthesis, which affects phenological signatures. Figure 4 3 shows that with increased average paving, maximum temperature becomes relatively more important than minimum and average temperature. Minimum temperature is used unlagged in the models, indicating an immediate effect of this covariate in the simulation; average and maximum temperatures are lagged respectively 12 13 and 13 14 months ( Fi gure 4 5 ). Maximum and average temperature have an effect on germination, flowering or other reproductive processes, which would explain the longer lag in its effect. The positive coefficients for temperature shows that temperature and vegetation dynamic s are similar (increased temperature simulates increased EVI2 and vice versa), which is expected in this study area. Climate change is projected to affect maximum temperatures significantly in the

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99 future, including its anomalies (Pachauri et al., 2015) indicating that areas under the influence of road paving disturbances will be sensitive to these changes. In terms of hydrological controls, precipitation itself is less important than potential evapotranspiration and soil moisture in the models ( Figure 4 3 ). Their importance decreases in areas with higher average road paving extent. The importance of soil moisture for VD C 1, VDC 2 and VDC 3 is supported by previous research ( Quesada et al., 2012 ) which pointed to the relevance of the hydrologic cycle in combination with soil properties in these areas with mostly natural disturbances and limited anthropogenic disturbances. In te rms of the effect of soil moisture (the coefficient), it is mixed when there is less road paving ( Figure 4 5 ). As road paving increases, it becomes more distinctly negative ( 0.40 < < 0.0), meaning lower soil moisture leads to a higher EVI2. A key comp onent in interpreting this result is the lag of 3 4 months applied to this covariate. While soil moisture usually peaks at the beginning of the year during the later portion of the wet season (March April), EVI2 generally reaches its lowest points around t he middle of the year during the dry season (June September). By implementing the soil moisture with a lag, EVI2 and soil moisture essentially display opposite dynamics, and the timing of soil moisture peaks and lows become a factor in simulating EVI2 lows and peaks for most communities. However, some communities with lower average paving extent have a positive coefficient (0.0 < < 0.3): for VDC 1, for which soil moisture was also lagged 3 months, this implies that EVI2 in these areas have later peaks a nd dips than the other areas probably because of different vegetation types and/or structure. For VDC 2, the lag of 10 months plays a role in coefficient s being positive: soil moisture peaks are now aligned with EVI2

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100 peaks in December January. Overall, soil moisture dynamics appear to be an important control in vegetation dynamics, but this relevance disappears when average road paving increases While the importance of potential evapotranspiration is fairly constant across communities ( Figure 4 3 ), th e coefficient is negative for a number of communities in a transition paving state ( Figure 4 5 ) until the most paved state, where potential evapotranspiration has a positive effect on EVI2 The early negative effect indicates that higher evapotranspirati on results in lower EVI2. This is counterintuitive since we would expect a positive effect: higher evapotranspiration signifies more photosynthetic activity and thus higher EVI2 values. A component to consider is that potential evapotranspiration is lagged The lag is 14 months, meaning the PET peak of August/September is aligned with October/November EVI2 values, and the lowest PET values for July with September EVI2 values. EVI2 generally rises after the dry winter period (May September, Supplementary Fig S1), but the timing of this rise varies across the study area between September and November, and sometimes even December or January. There is similar variation in the beginning of the year, when potential evapotranspiration starts dropping (it is based mostly on temperature, see Methods), but EVI2 can still stay high. These differences in phenological signature could contribute to negative coefficients. Since PET dyna mics are fairly consistent (Figure 4 4), this points to mixed vegetation dynamics during the (early) transition state The negative coefficients for species richness ( Figure 4 5 ) for some communities are similar to earlier findings (Baraloto et al., 2014) which established that there are trade offs be tween plant diversity and forest structure covariate s in the region.

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101 Increased forest structure (in terms of aboveground biomass) was associated with less diversity. The species richness time series included in the models show ed no clear positive or negati ve trend for these areas. The percentage of a community under forest cover predictably has a positive coefficient ( Figure 4 5 ), but only plays a role in VDC 1 ( Figure 4 3 and 4 5), the communities with no paving Low Frequency Signals Explain Trend Behav ior Across the Study Area as a Whole, but Dominate Particularly in the Paved State While the number of common trends stays the same for each VDC for Models I and II (Table 4 1) their importance in explaining variance is diminished for all VDCs once covariates are added in Models II, compared to Models I None of the R 2 values for the Models II has decreased in comparison with Model I (Figure 4 2a), but the covariates now also explain variance in all communities (Figure 4 2c). This is a sign that the effects of certain covariates on vegetation dynamics were present in those trends, and were now removed from the trends The remaining trends still explain a fair amount of the variance across all VDCs (25 50%). These could represent covariate s missing from the models (e.g. fire occurrence, actual evapotranspiration, climate indices), or non linear interactions between covariates that are not modeled explicitly with DFA The variance explained by the trends for each community (expressed as average semi p artial R 2 ) is plotted in Figure 4 6 a, with the trends over time shown in Figure 4 6 b. It is of interest to note that even for communities with a similar paving history (x axis for Figure 4 6a), there is a range in the amount variance explained by each tren d across communities. In Figure 4 6a, it is easiest to see for the first trend in each VDC due to the color scheme, but the other trends also vary in the variance they explain This is a

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102 clear sign that there is information contained in the trends that is spatially variable and not included elsewhere If time series of physical processes are (partially) a result of the sum of various frequencies (Koopmans, 1995) spectral analysis can help disentangle them. Frequencies (i.e. cycle lengths) with the highest power spectral density contribute most to explain ing variance in relative terms ( this method does not quantif y absolute contribution ) The spectral power density of signals contained in the trends was determined (see Methods) and for each trend the three signals with the highest density are visualized in Figure 4 6 c. Certain low frequency signals long cycle le ngths show up consistently in each region, and we attribute these to solar and climatic influences. and its variation is acknowledged as a natural climate forcing (Pachauri et al., 2015) The solar cycle has an 11 to 22 year frequency, and a 5.6 year periodicity has been shown to be significantly present too (Ramanuja Rao, 1973) F requencies of 22.5, 11.25 and 5.625 years are pres ent in the trends in this study The Pacific Decadal Oscillation (PDO), a pattern of ocean atmosphere variability, has been found to play a role in the Amazon in previous studies (Arias et al., 2010; Herzog et al., 2011; G. A. M. D. Silva et al., 2011) The PDO contains a 4.8 and 8 year frequency (Table A 1 1 ), close to the 4.5 and 7.5 year frequencies also found in a number of the DFM trends There is a decrease in higher frequency signals ( cycle lengths < 18 months) across the VDCs with increased paving extent ( Figure 4 6 c). Especially for VDC 4 more of the variance of the trends is captured in the low frequency signals. Since the trends

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103 explain relatively little of the overall EVI2 variance for this VDC (Figure 4 6a) we deduc e that the covariates included in the model that offer high frequency variations (temperature, precipitation, PET) have more explanatory power on vegetation dynamics in this VDC. Unpaved t o Paved Conditions Repr esent Two Stable System States with a Transition State i n Between Them A transition state between paved and unpaved conditions can be clearly identified in Fig ure s 4 2b and 4 2c There is a shift in the importance of trends and covaria tes explaining EVI2 dynamics, as well as a shift in importance between natural and human covariates, as was noted above Both these shifts happen around an average paving extent of 0.75. This is an interesting finding as it shows that this system took more or less 16 17 years (0.75 of the 22 year study period) to go through an assumed full transition after road paving. The number of trends in the paved and unpaved state is similar and low ( Figures 4 6 a and 4 6b ). This points to the uniformity of vegetation dynamics in the communities across these regions possibly because the dynamics reached a stable state considering the duration they were unpaved or partially paved. The transition states, with 6 and 7 trends, have more heterogeneity in paving and impact s across the communities in their regions and a variety of vegetation responses. This highlights that while paving is ongoing, changes and system states at a regional level are more heterogeneous and more difficult to predict. Once the system stabilizes ag ain, the system state is different than before the disturbance: this is visible, in addition to DFM specification in terms of covariates in the frequencies contained in the trends. That

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104 VDC4 is stable is an assumption: re analysis of longer time series in the future would have to confirm this. Discussion Main Findings This research offers support for the hypothesis that there are areas that have distinct forest structures and phenologies along a road paving gradient, and provides support for the second par t of the hypothesis, that different covariates and mechanisms drive vegetation dynamics across the road paving gradient. We have found distinct areas with common temporal vegetation dynamics (VDCs), associated with road paving progression in the SW Amazon, confirming our hypothesis that vegetation structure is altered with increased road paving. With a time series dimension reduction technique, Dynamic Factor Analysis (DFA), we uncovered common trends and a number of (lagged) socio economic and biophysical covariates that explain shared variance of EVI2 for each VDC. We found differences in the Dynamic Factor Models (DFMs) between VDCs in terms of covariates and trends included, their importance in explaining variance, and coefficients (negative or positive effects). There are two stable system states identified with unpaved and paved conditions (VDC 1 and VDC 4). These two stable states have distinct differences in human and natural driving factors of vegetation dynamics. Human covariates are relatively more important in the paved state (family density and travel time to markets); similarly, the natural covariate for temperature is important in the paved state. In the unpaved state and the transition states, there is consid erable influence from natural variables like potential evapotranspiration, soil moisture, and minimum and average temperatures. Lastly, results show there is a change in trends from the unpaved to the

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105 paved system state, with trends losing both importance and overall number of signals, notably high frequency signals. The latter is associated with covariates explaining more variance in the paved state directly. Within VDCs, for communities with similar average paving extent, trends vary in their contribution to explained variance. This suggests that there are covariates with spatial variation that have not been included in this study, but that these are less important for the paved state (VDC 4). Broader Impacts This study has shown the power of Dynamic Fact or Analysis when applied to a complex data set where time series are subject to change over an extended period of time and space. This offered a continuous overview of the dynamics in the importance of the effects of different covariates, as opposed to sna pshots in time. DFA provides a systematic framework to study how forest degradation evolves over time as a process like road paving unfolds. Other areas in which this method could prove useful are experimental interventions in biological and health fields, to assess how complex systems respond, or governmental regulations affect the outcome. The results of the study will benefit local and regional planners, as well as conservation initiatives at a practical level. The findings shed light on which covariat es are relevant at different phases of the road paving process as they impact regional vegetation structure. The results thus point to management options by identifying important covariates that can also be managed, such as enforcement of tenure rules and migration. The analysis also provides insights into which biophysical covariates affected by climate change will have the most impact and where. With temperature anomalies projected to change in the future (Pachauri et al., 2015) the effect on areas in a paved state will be stronger. Most importantly though, the study indicates that

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106 vegetation dynamics and their effects on ecosy stem services will differ across regions associated with different levels of road paving. Future research on specific ecosystem services changes with change in forest dynamics is relevant for both conservation as well as future economic opportunities in the study area. Many livelihoods are strongly dependent on the natural environment, and infrastructure planning initiatives should anticipate these effects. Provisions should be made in the planning stages of a road project to monitor vegetation dynamics a fter project completion, beyond only deforestation. More detailed and localized technologies, such as Light Detection And Ranging (LiDAR) or products from the Fluorescence Explorer (FLEX), will provide useful. Governments and research institutes should inv est in these technologies for ongoing monitoring. Lastly, this study adds a regional, up scaled analysis to the field of road ecology. will undoubtedly continue into many forested areas such as the Amazon, Central Africa and Southeast Asia with unparalleled ecosystem services provision (Laurance et al., 2014) Limitations a nd Further Research While remote sensing products are increasingly available and useful for doing larger scale regional analyses, inherent noise in the data should be carefully evaluated. This is especially true in humid tropica l regions, which exhibit extended periods of cloud cover contributing to observation error. While the models exhibit an acceptable goodness of fit for most communities, their performance is low in some areas partly due to observation error. Further researc h on signals and frequencies in EVI2 data would be beneficial to quantify differing vegetation dynamics in more detail and assess errors, as

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107 well as field studies that measure biomass and vegetation structure, or more detailed remote sensing studies (e.g. with LiDAR). While DFA is efficient at capturing variance in ecological time series because of its autoregressive approach to modeling trends, if the variance is not accounted for among the covariates in expanded models and instead remains captured in the trends, it stays unknown. This requires more detailed investigations into issues such as logging, the role of fire, and species composition in terms of functional groups. It is however challenging to obtain reliable data on these concepts for sufficiently long periods of time. Dynamic Factor Models add covariates linearly, and while possible lagged responses have been accounted for, interactions are not explicitly accounted for. Future research should focus on untangling interactions between both human and natural covariates, in particular with mechanistic models. This would also assist in identifying causal relationships, since DFA does not account for this. Methods Study Area The 99 communities included in this study lie within the states of Madre de Dios of the Andes Mountains and in the headwaters of tributaries of the Amazo n River. The climate is tropical, classified as Awi (Kppen climate classification), with an average daily temperature of 25 C and mean annual precipitation of approximately 2000 mm. The dry season runs from June to October, in which monthly rainfall aver ages < 100 mm. The types of forest in the area are dense tropical forest, open tropical forest with palm trees, and open forests dominated by bamboo with many locations containing a

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108 mix of these forest types (Carvalho et al., 2013 ; Rockwell et al., 2014; Salimon et al., 2011) The Inter Oceanic Highway was paved between approximately 1992 (Rio Branco) and 2010 (Peru). Communities in Bolivia still had unpaved roads during the time period studied since road paving had not progressed much further than Cobija ( Figure 4 1 a). These are resource dependent rural communities that were part of earlier studies (Perz et al., 2013b; 2011b; 2011a ) tenure units and/or population c ( Perz et al., 2011a ) Population densities are low, with an average family density of 0.07 families/km 2 and a maximum of 3.17 families/km 2 for the study period. Land use is described as complex and shifting, and includes urban areas, subsistence ag riculture, logging, gold mining, conservation areas, secondary forest and old growth forest in which non timber forest products (NTFPs such as brazil nuts and rubber) are harvested ( Phillips et al., 2006 ) The methodologies that were applied to clean and analyze data are depicted in Figure 4 7 Response Covariate: Vegetation Dynamics, EVI2 Data for the enhanced vegetation index (EVI2) used in this analysis were which applies an algorithm to translate two band dat a from the Advanced Very High Resolution Radiometer (AVHRR) into MODIS EVI (Z. Jiang et al., 2008 ) AVHRR data have been coll ected since 1982. The data used in this analysis (1987 2009) were obtained from the VIP lab in October 2013 in monthly time steps and at a 0.05 resolution. Area weighted time series were extracted for each community polygon.

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109 Data correction was performed to address outliers and discrepancies between AVHRR derived EVI (1982 1999) and MODIS EVI (2000 2010), because AVHRR derived EVI exhibited consistently lower values (an overall average of 0.387 vs. 0.513). This is attributed to the lower quality of AVHRR data in areas with high cloud density (pers. comm. Dr. K. Didan). The final data set generally has the lowest EVI2 occurring in the driest months (June, July and August). EVI2 peaks during the wet season, in November, December and January. Variations in m onthly medians across communities are larger during the wet season than the dry season ( Figure 2 1 ). Candidate Covariates Related t o Human Activity Annual data sets for a variety of covariates associated with human activity in the study area are available from previous studies (Perz et al., 2013b) Variables uses in this study are: number of families in a community (FAM), family density (FAMD, number of families / km 2 ), p opulation in the nearest capital (PNC), population in the nearest market (PNM), paving (PAV), deforestation allowed under tenure rules (TEN), enforcement of tenure rules (ENF), travel time to the nearest capital (TTC) and travel time to the nearest market (TTM). See Table A 2. Data sets were linearly interpolated to create monthly time series. PAV is a value between 0 and 1 representing proportion of a road segment paved, and is derived from field work. The year when paving of the road segment along which a community sits is finalized is taken as the starting point to estimate increments in the proportion paved. If a community is along a highway segment between two towns year s). Proportions paved in the years prior are derived from field notes with the timing

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110 of the onset and conclusion of paving of that segment, with a linear interpolation of paving proportions during the intervening time period. Travel times, representing c onnectivity, are in minutes and based on the distance to the nearest capital or market, and average travel speeds taking into account paved and non paved segments. For some communities, the nearest market is also the capital, rendering the same time series for these covariates ( Figure 4 1 a). TEN and ENF are similarly based on fieldwork, which included workshops with stakeholders, and official rules for resource use given by governments. TEN is simply the percentage of forest a community is allowed to cut do wn. Values vary between 0 and 1, representing 0 to 100% deforestation allowed. ENF are perceptions by experts as to the extent to which those use rules are actually enforced by government agencies responsible for oversight, which roughly corresponds to the probability of infractions being detected and punished. Here again, the values run from 0 to 1, with higher values indicating more likely enforcement. Candidate Covariates Associated w ith Biophysical Processes Monthly data sets were sourced in June 2013 f rom the Climatic Research Unit (CRU) at the University of East Anglia. Covariates include the mean, minimum and maximum temperatures, precipitation and potential evapotranspiration (AVET, MINT, MAXT, P, PET). For more details, see Table A 2. The mean, mini mum and maximum temperatures (in C) and precipitation (in mm) were obtained at a resolution of 0.5 x 0.5 (Harris et al., 2013) and were assigned to each community polygon in an area weighted manner. Potential evapotranspiration (in mm) is also included in the CRU data set, and is calculat ed from a variant of the Penman Monteith formula, using mean,

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111 minimum and maximum temperature, vapor pressure and cloud cover (Harris et al., 2013) Soil moisture (SM) comes from the NOAA Climate Prediction Center (CPC) model at a resolution of 0.5 x 0.5, which uses CPC precipitation data and temperature data from the NCEP/NCAR Reanalysis (Fan, 2004) The data are provided as average soil moisture in terms of water height equivalents (mm). As with the other data sets, the soil moisture data are calculated as an area weighted time series for each community polygon. Forest area as a percentage of community polygon area (FOR) is sourced from a deforestation study conducted in the area ( Marsik et al., 2011 ) Forest and non forest percentages for each polygon are available fo r the years 1986, 1991, 1996, 2000, 2005 and 2010, and were interpolated to obtain monthly values. Inferred species richness (SR) is alpha diversity computed from Landsat imagery by applying a method that is based on the Shannon entropy of pixel intensity (Convertino et al., 2012) Clustering 3) calculation of the Dunn index and S ilhouette width as measures of compactness and separation of the clusters. The EVI2 (1982 2010) was normalized and a time series based dissimilarity matrix D was established (Chouakria and Nagabhushan, 2007) D c ontains aspects of Euclidian distance between time series, as well as a temporal correlation measure. Therefore, the proximity measure is related to similarity of values and time series

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112 behavior. Behavior is defined as the increase or decrease of values be tween points in time, as well as the rate of this change. An automatic adaptive tuning function is included in the conventional dissimilarity index calculations, with a parameter k that determines how much behavior and value proximity contribute to D At k =0, D is only based on values, and at k max = 5 behavior contributes most. D to group communities sum of squares if th ey are merged. All series start out with the value zero, as they are all regarded as their own cluster, and series or clusters are merged for those that have the smallest distance increase. The Dunn index and Silhouette width are calculated for 2 to 10 clu sters to determine the appropriate k and number of clusters. For k = 2 and 4 clusters, the Dunn index was highest (0.085) as well as the Silhouette width (0.36). All candidate covariate time series were clustered according to the regions that resulted from the EVI2 clustering analysis, to use in further analyses. Lagging and Reduction o f Covariate Data Set All candidate covariate time series (1987 2009) were reduced to a single time series for each VDC as an area weighted average. Based on the highest stati stically significant cross correlation with area weighted EVI2 of its region, each regional candidate covariate was lagged anywhere from 0 to 19 time steps (months); for more details, see Table A 4. A Variation Inflation Factor (VIF) analysis was applied t o detect collinearity (VIF > 10) (Neter et al., 1996; Zuur et al., 2007) with covariates with the highest VIF excluded from the data set in an iter ative manner until a covariate data set remained with all VIFs < 10 (see Table A 5).

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113 Dynamic Factor Analysis Dynamic Factor Analysis (DFA) is a dimension reducing statistical analysis that is applied to explore relationships between response covariates and common (shared) covariates in dynamic systems over time. It aims to explain shared variation of observed time series using a set of common trends, with the number of trends being substantially smaller than the number of observed time series. These common trends across all time series model temporal variation across the response covariates as linear combinations, and represent driving factors across all time series. The coefficient associated with a trend in a time series gives an indication of the importan ce of that trend for that time series. The trends are estimated using an Expectation Maximization (EM) algorithm, which allows maximum likelihood estimation in situations where there are latent random covariates in a model (Holmes et al., 2014; Zuur et al., 2007; 2003a) Covariates can be added to the model in a linear fashion. The Dynamic Factor Model being estimated is (4 1 ) (4 2) is the value of the n th response covariate at time t ; is the m th unknown trend at time t ; represents the unknown factor loadings; is the n th constant level parameter for displacing each linear combination of common trends up and down; represen ts the unknown regression parameters for the K covariate time series ; and m (t) are the error components. can be interpreted as the process errors of the hidden trends, and as the observation errors, which are independent Gaus sian noise with zero mean and a variance covariance matrix that can take different forms. For this analysis, the variance covariance matrices are implemented as

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114 symmetric (diagonal) matrices. The constant level parameter ( ) is set to zero since norma lized data are used. The Dynamic Factor Models (DFMs) were assessed based on their goodness of fit (Nash Sutcliffe coefficient of efficiency, C eff ) and parsimony (Bayesian Information Criterion, BIC). The aim throughout model development was to add enough covariates to explain most of the shared variance across all response covariate time series, so that reliance on the trends in minimized, without lowering the goodness of fit or worsening model parsimony (Campo Bescs et al., 2013; Kaplan et al., 2010; Kaplan and Muoz Carpena, 2011; Kuo and Lin, 2010; Muoz Carpena et al., 2005; Ritter et al., 2009) Whereas Models I contained only trends, Models II contained trends and covariates. Models with lowest BICs were considered the best models. To find the best contained the number of common trends from the best Model I and all covariates. The covariate or trend least important to explaining variance in the model was dropped, and a new Model II was then developed with a reduced set of trends and covariates. This step was iterated until the BI C hit its lowest point; covariate elimination was halted when BIC started rising again. Importance of Trends a nd Covariates The importance of trends and covariates in the models was examined by variance partitioning (Cheva n and Sutherland, 1991; Johnson and Lebreton, 2004; Zuur et al., 2007) This was implemented as the average semi partial R 2 over all possible (Grmping, 2 006; Lindeman et al., 1980) The latter is relative to the total coefficient of determination (R 2 ), is non negative and the values for all model components add up to 1, or 100% of R 2

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115 (also known as the Lindeman, Merenda and Gold (LMG) method (Grmping, 2006) ). Since DFA estimated a unique DFM for each community, based on common trends and covariates, we averaged the relative importance of each trend and covariate acros s the VDC, to then eliminate the factor with the lowest average value. This approach of taking the average semi partial R 2 over all possible orders of model components is driven by the fact that the order in which non orthogonal regressors appear in the re gression determines the amount of variance they explain which could lead to biased results if not all orders are taken into account. Spectral Analysis o f Trends To gain insight in the periodic components of the trends, spectral analysis was performed. D ominant periods or frequencies were identified by spectral density estimation: higher values indicate relatively more importance of a particular frequency in explaining oscillations in the trend. For each trend, the spectral density is estimated using a fa st Fourier transform with a modified Daniell kernel with dimension 2 as a smoother, and the 3 frequencies with the highest density were selected for display in Figure 4 6 Software Used All data cleaning was done in R (3.2.4) and Python. Maps were rendered in ArcMap. R was used for all subsequent analyses and figures. The following packages were used: TSclust (adaptive dissimilarity index), clValid (cluster validation, adjusted to be able to work with the adaptive dissimilarity index as input), fmsb (VIF), MARSS (DFA), relaimpo (relative importance in linear regressions), hydroGOF (Nash Sutcliffe coefficient), ggplot2, reshape2, zoo, grid, gridExtra, cowplot and gtable (figures).

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116 Data Availability The data set s generated during and/or analysed for this stud y are available in the Figshare repository, 10.6084/m9.figshare.c.3858064

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117 Table 4 1. List of variables used in the analysis, their unit of measure, and source Variable Units Source Response variable EVI2 Enhanced Vegetation Index 0 to 1 University of Arizona Vegetation Index and Phenology lab, https://vip.arizona.edu/viplab_data_explorer.php Human covariates ENF Enforcement of tenure rules 0 to 1: with 0=least, 1=most University of Florida, Department of Sociology FAM Number of families in the community (polygon) Count University of Florida, Department of Sociology FAMD Family Density families/km 2 University of Florida, Department of Sociology PAV Paving 0 to 1, with 0=no paving, 1=fully paved University of Florida, Department of Sociology PNC Population at nearest state capital Count University of Florida, Department of Sociology PNM Population at nearest market Count University of Florida, Department of Sociology TEN Tenure rules: fraction of deforestation allowed of community area 0 to 1 University of Florida, Department of Sociology TTC Travel time to capital Minutes University of Florida, Department of Sociology TTM Travel time to nearest market Minutes University of Florida, Department of Sociology

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118 Table 4 1. Continued. Variable Units Source Natural covariates AVET Mean temperature C University of East Anglia, Climate Research Unit, https://crudata.uea.ac.uk/cru/data/hrg/ FOR Forest area as fraction community area University of Florida, Department of Geography MAXT Maximum temperature C University of East Anglia, Climate Research Unit, https://crudata.uea.ac.uk/cru/data/hrg/ MINT Minimum temperature C University of East Anglia, Climate Research Unit, https://crudata.uea.ac.uk/cru/data/hrg/ P Precipitation mm University of East Anglia, Climate Research Unit, https://crudata.uea.ac.uk/cru/data/hrg/ PET Potential evapotranspiration mm University of East Anglia, Climate Research Unit, https://crudata.uea.ac.uk/cru/data/hrg/ SM Soil moisture mm NOAA Climate Prediction Center (PCP), https://www.esrl.noaa.gov/psd/data/gridded/data.cpcsoil.html SR Species richness Alpha diversity University of Florida, Department of Agricultural and Biological Engineering

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119 Table 4 2 Results of dynamic factor analyses of Enhanced Vegetation Index (EVI 2) for 4 Vegetation Dynamics Areas (VDC s). Model I : only trends are fitted no explanatory var iables. Model II: both trends and explanatory variables (EV) are fitted. EVs are listed according to their relative importance (LMG) in each model. BIC is the Bayesian Information Criterion, C eff is the Nash Sutcliffe coefficient of efficiency. Model resul ts in bold are the selected models for further discussion. VDC Model Number of trends Explanatory variables (EV) BIC Median C eff (95 % confidence interval) 1 I 1 10205 0.54 (0.27 0.81) unpaved I 2 10011 0.62 (0.30 0.85) ( n =18) I 3 9876 0.71 (0.32 0.87) I 4 9789 0.74 (0.49 0.87) I 5 9796 0.75 (0.50 0.89) II 4 ENF AVET MINT PET FOR SR SM FAMD MAXT P 9994 0.75 (0.52 0.87) II 4 ENF AVET MINT PET SR SM FOR MAXT FAMD 9958 0.75 (0.52 0.88) II 4 FOR ENF AVET MINT PET SR SM MAXT 9923 0.75 (0.51 0.87) II 4 FOR AVET MINT ENF PET SM SR 9896 0.75 (0.50 0.87) II 3 FOR AVET MINT SR PET ENF SM 9939 0.73 (0.40 0.86) 2 I 1 14379 0.41 (0.14 0.84) transition I 2 10915 0.49 (0.18 1.00) ( n =24) I 3 10305 0.60 (0.24 1.00) I 4 10144 0.72 (0.29 1.00) I 5 10055 0.77 (0.39 1.00) I 6 10043 0.80 (0.48 1.00) I 7 10007 0.80 (0.51 1.00) I 8 10034 0.82 (0.53 1.00) II 7 TTM PAV PET SM MAXT P MINT AVET SR TEN 10390 0.83 (0.54 1.00) II 7 PAV TTM PET SR MAXT SM P MINT AVET 10323 0.83 (0.54 1.00) II 7 PAV TTM SR PET SM MAXT P MINT 10266 0.83 (0.54 1.00) II 7 PAV TTM PET SM MAXT P SR 10244 0.82 (0.53 1.00) II 7 PAV TTM PET SM MAXT SR 10262 0.83 (0.46 1.00)

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120 Table 4 2. Continued VDC Model Number of trends Explanatory variables (EV) BIC Median C eff (95 % confidence interval) 3 I 1 23129 0.63 (0.40 0.76) transition I 2 22261 0.66 (0.41 0.82) ( n =43) I 3 21573 0.71 (0.48 0.85) I 4 21223 0.74 (0.55 0.90) I 5 18230 0.74 (0.55 1.00) I 6 18082 0.77 (0.56 1.00) I 7 18134 0.78 (0.56 1.00) II 6 PET SM MINT FAMD AVET MAXT P TEN SR ENF 19010 0.79 (0.59 1.00) II 6 PET MINT SM MAXT AVET FAMD P TEN SR 18900 0.79 (0.59 1.00) II 6 PET MINT SM MAXT AVET FAMD P TEN 18817 0.79 (0.59 1.00) II 6 FAMD PET MINT SM MAXT AVET P 18695 0.79 (0.59 1.00) II 6 FAMD PET SM MINT AVET MAXT 18590 0.78 (0.58 1.00) II 5 FAMD PET SM MINT AVET MAXT 18664 0.77 (0.58 1.00) 4 I 1 8224 0.59 (0.35 0.77) paved I 2 7992 0.66 (0.35 0.89) ( n =14) I 3 7986 0.68 (0.36 0.89) I 4 8007 0.70 (0.39 0.91) II 3 FAMD TTM PET MINT AVET MAXT P ENF SM TEN 8100 0.69 (0.38 0.90) II 3 FAMD TTM PET MINT AVET MAXT ENF P SM 8076 0.68 (0.38 0.90) II 3 FAMD TTM PET MINT AVET MAXT ENF P 8054 0.69 (0.38 0.90) II 3 FAMD PET MINT TTM AVET MAXT ENF 8056 0.69 (0.38 0.90)

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121 Figure 4 1 Characteristics of the study area after clustering analysis. a) Map of the study area, with 99 communities and their average paving extent for the period 1987 2009 b) Area weighted average paving extent per Vegetation Dynamics Cluster (0=road section associated with the community is unpaved,1=road section associated with the community is fully paved). VDCs are based on the adaptive dissimilarity index of EVI2. c) Averag e paving extent of the communities in each VDC, with an upward non linear tendency from VDC 1 to 4. The tendency is a loess curve based on all average paving values. d) The study area with 4 VDCs. e) Minimum, median, maximum monthly Enhanced Vegetation Ind ex (EVI2) time series per VDC

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122 Figure 4 2. Contributions of model components of the final VDC DFMs II for each community to explaining variance in vegetation dynamics. Average paving extent of each community is plotted along the x axis, colors indicate the VDC. a). Proportion of explained variance, R 2 of the DF Ms I and II, with a linear fit b) Average proportion of explained variance over all possible orders of the model components, average semi partial R 2 for trends and covariates. Loess curves indicate respectively a downward and upward tendency with increase d paving extent, with a transition identified between a paving extent of 0.50 and 0.90. c) Average proportion of explained variance over all possible orders of the model components, average semi partial R 2 for natural and human covariates. Loess curves in dicate resp. a downward and upward trend with increased paving extent, with a transition identified between a paving extent of 0.50 and 0.90.

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123 Figure 4 3 Proportion of variance explained by each covariate for each community. Average paving extent of each community is plotted along the x axis, colors indicate the VDC. Covariates are grouped in columns according to the extent (maximum) of variance explained: low (left column) and high (middle and right column)

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124 Figure 4 4 Lagged time series of the covariates used in the final Dynamic Factor Models (DFMs) II for each VDC. The applied lags are specified Figure 4 5 and in Table A 5. Colors are associated with VDCs. Not every covariate is used for each VDC, selection is based on Variation Inflation Factor (VIF) analysis

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125 Figure 4 5 coefficients of the covariates used in the final Dynamic Factor Models (DFMs) II for each VDC. The applied lags are specified in the grey bar above the plots, and in Ta ble A 5. Negative covariates (in the grey area in the plot) imply that the covariate has an opposing effect on EVI2. Colors are associated with VDCs. Grouping in columns is according to the extent of explained variance of the covariates from Figure 4 3 : no te the differences in y axis scaling for the columns.

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126 Figure 4 6 Characteristics of the trends (unknown explained variance) in the selected Dynamic Factor Models II. a) Average semi partial R 2 of trends for each community indicates trends c ontribute differently to explaining variance per community and across paving extent (x axis). b) Monthly values of trends over time. c) The three strongest frequencies for each trend in each VDC, identified with spectral density estimation, are depicted by large, medium and small circles. Where trends have signals of the same frequency in common, not all n trends x 3 signals are visible due to overlap. Trends with the same number for different VDCs are not the same, since trend estimation was done independe ntly for each VDC.

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127 Figure 4 7 Flow chart of methods

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128 CHAPTER 5 CAUSALITY ANALYSIS OF REGIONAL BIOPHYSICAL AND VEGETATION VARIABLES REVEALS INCREASED FEEDBACK ALONG A ROAD PAVING GRADIENT IN THE SW AMAZON Background Infrastructu re development is an essential component of economic development for many countries, but socio economic benefits are often accompanied by negative impacts. Rural urban migration, conflicts over natural resources, land degradation, changes in natural distur bance regimes, impacts on abiotic processes, pollution and the disruption of animal movement have been documented ( Laurance et al., 2009 ; Nepstad et al., 2001) For forest ecosystems, road construction and paving are the main drivers of deforestation (Laurance et al., 2002a; M arsik et al., 2011 ) Besides such land cover conversion from forest to non forest, studies have also highlighted potential impacts on vegetation dynamics. Vegetation dynamics in the simplest interpretation refer to the growth and senescence of vegetatio n over time, however on a broader level they convey the influence of biotic and abiotic processes, climate, and natural and anthropogenic disturbance regimes on vegetation structure and productivity. On localized scales, indications have been found that v egetation dynamics can indeed differ after anthropogenic disturbances, while forest cover did not change. In a Bolivian forest, regeneration after either natural or anthropogenic disturbances was dissimilar, with differences in vegetation structure and phe nology (Felton et al., 2006) Specifically, there were less flow e ring and fruiting plants in anthropogenic gaps, and more non commercial pioneer species. Similarly, in Madagascar limited logging disturbance had a permanent effect on forest structure (Brown and Gurevitch, 2004) These changes in vegetation dynamics can have an effect on ecosystem goods and

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129 services, ranging from local to global level, and from carbon storage to river flow regulation (Foley et al., 2007) For instance, at local level, differences in tropical forest structure limit certain wildlife populations in Panama (DeWalt et al., 2003) bat diversity is affected by vegetation structure (Santos et al., 2016) and other research found that productivity in the Amazon is mostly driven by canop y phenology, not radiation (Restrepo Coupe et al., 2013) Considering that vegetation dynamics play a role in ecosystem services provision ( Millennium Ecosystem Assessment 2005) they are p articularly important in coupled natural and human (CNH) systems. The Southwestern Amazon has been subject to highway paving since the 1980s. The so called MAP area, where the states of Madre de Dios (Peru), Acre (Brazil) and Pando (Bolivia) meet is an are a through which the Inter Oceanic Highway (IOH) has been built in recent years. This highway, connecting the Atlantic coast in Brazil and the Pacific coast in Peru, was finalized in 2011. The area has been recognized as a (Killeen and Solorzano, 2008; Myers et al., 2000; Perz et al., 2011a) and livelihoods have been and still are closely linked to natural resources (Almeyda Zambrano et al., 2010; Perz et al., 2013c) : the area is a typical example of a CNH system. As expected, deforestation in the area is associated with roads and urban centers (Southworth et al., 2011) though it is not clear how much deforestation accelerates with increased access ( Marsik et al., 2011 ) Previous field research in the area concluded that deforestation and degradation can experie nce different impacts, with forest plots experiencing slightly more effect on forest value by the proximity to the IOH, than to urban centers (Baraloto et al., 2015) Overall, we do not have a long term view of what the system wide effects of road construction in the area are on vegetation

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130 dynamics, and if and how these have evolved over time. Differences in vegetation dynamics would imply changes in structure and composition of vegetation, which in turn means al tered ecosystem services and a potential for impacts on livelihoods and the environment. Changes in vegetation dynamics are hard to evaluate at a regional scale because they involve structural changes in vegetation that are time consuming and costly to capture through local field studies, especially over time. Further, drawing conclusions at a larger scale from field plots has been shown to be challenging (Fisher et al., 2008) t assess regional vegetation dynamics. I n addition to this spatial scale, the temporal component is important since road construction is an incremental process itself, and impacts from the presence of roads can increase or decrease over time, they are rare ly once off events, and they can lag behind actual road construction (Findlay and Bourdages, 2000; Laurance et al., 2009 ) Considering the importance of vegetation dynamics in the MAP area and probable impacts of highway paving, there is a need for a spatio temporal analysis of long term vegetation dynamics to determine whether or not there has been an alteration in vegetation dynamics, and if so, whether the drivers of these dynamics have changed. The latter would imply there has been a shift in system state and a change in connectivity. In this study, we hypothesized that the causal network of long term vegetation dynamics and biophysical variables (and climate indices) differs across a gradient of road paving extent. We expected that, for the time period we studied, undisturbed forests are more resilient and show stro ng relationships with all variables since

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131 climate/vegetation feedbacks have been reported in previous studies (Betts et al., 2004; Notaro et al., 2006; Quesada et al., 2012 ) We anticipated that causal relationships between biophysical variables and vegetation dynamics would change with more paving with more emphasis on precipitation and soil moisture, and less on temperature influences. This stems from previous work that found that under fragmented or logged conditions, forest becomes more sensitiv e to drought and moisture related variables (Laurance and Williamson, 2001; Nepstad et al., 2001) In order to evaluate changes to vegetation dynamics over longer periods and larger areas, we can use remotely sensed vegetation indices (such as the Normalized Difference Vegetation Index, NDVI or the Enhanced Vegetation Index, EVI) as a proxy for vegetation dynamics (Asner et al., 2000; Bradley and Fleishman, 2008; Cabello et al., 2012; Chambers et al., 2007; Huete et al., 2002; Reed et al., 1994; F. B. Silva et al., 2013; Volante et al., 2012) We te sted our hypothesis by analyzing remotely sensed regional vegetation indices for clusters of communities along the IOH, and mapping potential causality between vegetation dynamics and other biophysical variables, using a combination of novel and traditiona l approaches. We did this at a relatively high temporal resolution of one month, with the objective of specifically capturing changes in vegetation dynamics within years, an indication of phenology and productivity (Chambers et al., 2007; F. B. Silva et al., 2013) The methods applied to construct causality networks are a combination of relatively new and innovative approaches, Singular Spectrum Analysis (SSA) and Convergent Cross Mapping (CCM). While there is no conclusive method causality with mathematical methods from the perspective of science philosophy, these

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132 techniques come closest to causality as it has been defined and employed by Wiener and Granger (Granger, 1980; 1969 ; 1963) ; analyses based on (statistically significant) predictability. The remainder of this paper uses the te rm causality in the same vein. The traditional approach has been Granger Causality (GC) analysis, which relies on the comparison of vector autoregressive models to establish w h ether or not a variable is significant in improving predictions of another vari able. The method has been used in various fields with or without modifications (Guo et al., 2010; 2008) such as neuroscience (Bressler and Seth, 2011) cognitive processing (Zhou et al., 2009) development studies (Weinhold and Reis, 2001) and ecological and environmental studies. (Damos, 2016; Detto et al., 2012; B. Jiang et al., 2015; Kaufmann et al., 2004 ; 2003; Tuttle and Salvucci, 2016) However, GC relies on the system dynamics being separable and linear, and complex natural systems are generally assumed to contain nonlinear deterministic components (Sugihara et al., 2012) Determinism means that the system is not stochastic, and that that there are theoretically identifiable (fix ed) relationships between variables or components in a system. In cases such as these, signals are not separable linearly since each will contain information associated with delayed embedding and state space reconstruction and can identify nonlinear signals reliably (this will be explained later in this Chapter). In noisy time series, which are common in environmental sciences, this is an important step. Finding signals and removing n oise is essential for the causality analyses. The systems within which these signals occur, can be weakly or strongly coupled. This coupling strength refers to synchronization of signals: strongly coupled systems have signals (i.e. dynamics) that are more

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133 synchronized. This makes it harder to identify the direction of causality in these systems. CCM analysis identifies causality and driving variables in low dimensional weakly coupled systems using these signals (BozorgMagham et al., 2015; Mnster et al., 2016) an d for systems where there are stronger coupled dynamics, extended CCM can distinguish between true bidirectionality or strong unidirectional forcing (Ye et al., 2015) involved in explaining the system, generally less than 6. This is another reason why the id entification of signals is important before causality testing: some high dimensional (more complex) systems can still be partly explained with low dimensional representations of it. We follow the approach by Huffaker et al. (2016b; 2017) to separate signa ls from the original time series, and extensively test signals for stationarity, determinism and eventually causal relationships. Stationarity and determinism are important for the causality analysis as it requires a certain degree of stability in the sign als to obtain reliable results. Since these conditions have to met before it is justified to test for are potentially high dimensional or linear stochastic, and we need to turn to other methods (Figure 5 1). We can apply GC analysis in these cases, and we can use Multivariate SSA (MSSA) first to remove shared seasonality across time series. Removal of shared seasonality, as advocated but also cautioned for by Gran ger (1979), is generally done to avoid that synchronized seasonality overpowers the GC analysis. It has been in done in several ways in the past (Papagiannopoulou et al., 2017; Tuttle and Salvucci, 2016) usually involving some form of model building to simulate seasonality.

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134 MSSA is an extension of SSA and is ideally suited for removal of seasonality, since it does not require (subjective) models and can identify a number of frequenc ies across various time series. Explanation and results of tests with GC causality are not discussed in this Chapter, but can be found in Appendix C. We apply SSA and CCM to a data set for the MAP area for a 23 year period (1987 2009), for communities alon g the IOH that experienced highway construction at different points in time. For 99 communities we obtained a long term Enhanced Vegetation Index (EVI2), maximum temperature, minimum temperature, potential evapotranspiration, precipitation, soil moisture, all from re analysis data sets. These variables have been highlighted in numerous Amazon wide studies as potential driving factors (Betts et al., 2004; Glo or et al., 2015; Phillips et al., 2009; Quesada et al., 2012 ) and are available at sufficient resolution. We also included the Multivariate ENSO Index (MEI), Atlantic Multidecadal Oscillation (AMO) and the Pacific Decadal Oscillation (PDO) since previo us research found them strongly correlated with global, hemispherical and continental carbon fluxes and climatic variables (Z. Zhu et al., 2017) We applied time series based cluster analysis to cluster the communities according to similar vegetation dynamics and associated these with road paving extent. All analyses were implemented per cluster, on area weighted average time series, and results were compared. The objective of this Chapter is multi faceted: first, to determine whether there are differ ences in vegetation dynamics between areas, and characterize them. This will be done with clustering and signal extraction. Second, to identify and compare driving forces in each area which will be achieved by mapping causal networks. Finally, all of

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135 these components combined give us a comprehensive overview of vegetation dynamics along a road paving gradient and enable us to identify differences and similarities. Materials and Methods Study Site and Data Study site The 99 communities included in this stu dy lie within the states of Madre de Dios (Peru), of the Andes Mountains and in the h eadwaters of tributaries of the Amazon River. The climate is tropical, classified as Awi (Kppen climate classification), with an average daily temperature of 25 C and mean annual precipitation of approximately 2000 mm. The dry season runs from June to Oc tober, in which monthly rainfall averages < 100 mm. The types of forest in the area are dense tropical forest, open tropical forest with palm trees, and open forests dominated by bamboo with many locations containing a mix of these forest types (Carvalho et al., 2013 ; Rockwell et al., 2014; Salimon et al., 2011) The Inter Oceanic Highway was paved between ap proximately 1992 (Rio Branco) and 2011 (Peru). Communities in Bolivia still had unpaved roads during the time period studied since road paving had not progresse d much further than Cobija. These are resource dependent rural communities that were part of ear lier studies (Perz et al., 2013b; 2013a; 2011b) They are defined in these units and/or population centers This ensures that any effects o n vegetation within a community results from the same land tenure arrangements and management decisions.

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136 Highway paving Highway paving histories w ere provided from previous studies (Perz et al., 2013b) It is a value between 0 and 1 representing proportion of a road segment paved, and is derived from field work. The year when paving of the road seg ment along which a community sits is finalized is taken as the starting point to estimate increments in the proportion paved. If a community is along a highway segment between two towns that nd subsequent years). Proportions paved in the years prior are derived from field notes with the timing of the onset and conclusion of paving of that segment, with a linear interpolation of paving proportions during the intervening time period. Vegetation dynamics: EVI2 Data for the enhanced vegetation index (EVI2) used in this analysis were which applies an algorithm to translate two band data from the Advanced Very High R esolution Radiometer (AVHRR) into MODIS EVI (Z. Jiang et al., 2008) AVHRR data have been collected since 1982. The data used in this analysis (1987 2009) were obtained from the VIP lab in October 2013 in monthly time steps and at a 0.05 resolution. Area weighted time series were extracted for each community polygon. Data correction was performed to address outliers and discrep ancies between AVHRR derived EVI (1982 1999) and MODIS EVI (2000 2010), because AVHRR derived EVI exhibited consistently lower values (an overall average of 0.387 vs. 0.513) see the link in Supplementary Materials to data and code This is attributed to t he lower quality of AVHRR data in areas with high cloud density (pers. comm. Dr. K. Didan). For the remainder of this study, this variable will be referred to as EVI or vegetation dynamics.

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137 Biophysical variables from reanalysis data sets Monthly data sets were sourced in June 2013 from the Climatic Research Unit (CRU) at the University of East Anglia Covariates include the minimum mean and maximum temperature s precipitation and potential evapotranspiration (MINT, MEANT, MAXT, P, PET). The m ean, minimum a nd maximum temperature s (in C) and precipitation (in mm) were obtained at a resolution of 0.5 x 0.5 (Harris et al., 2013) and were assigned to each community polygon in an area weighted manner. Potential evapotranspiration (in mm) is also included in the CRU data set and is calculated fr om a variant of the Penman Monteith formula, using mean, minimum and maximum temperature, vapor pressure and cloud cover (Harris et al., 2013) Soil moisture (SM) comes from the NOAA Climate Prediction Center (CPC) model at a resolution of 0.5 x 0.5, which uses CPC precipitation data and t emperature data from the NCEP/NCAR Reanalysis (Fan, 2004) The data are provided as average soil moisture in terms of water height equivalents (mm) A s with the other data sets the soil moisture data are calculated as an area weighted time series for each community polygon. Climate indices The AMO, PDO and MEI time series were all obtai ned from the NOAA Earth System Research Laboratory. For the AMO we used the unsmoothed version (Enfield et al., 2001) This time series is an i ndex of surface temperature of the North Atlantic Ocean. The PDO consists of the first principal component of monthly anomalies of sea surface temperature of the North Pacific Ocean (Mantua et al., 1997; Zhang et al., 1997) The MEI is a composite index that is believed to better reflect the El Nio/Southern Oscillation (ENSO) phenomenon than simply sea surface temperatures

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138 (Wolter and Timlin, 2012) It incorporates sea level pressure, surface air t emperature, sea surface temperature, cloudiness fraction, zonal and meridional components of surface wind over the tropical Pacific Ocean. All data used in analyses described below were normalized first. Methods Time series clustering We applied a time ser ies clustering based on an adaptive similarity matrix (Chouakria and Nagabhushan, 2007) In order to cluster variables based on their shared dynamics and not just values, this method contains a scaling function wh ich allows both behavior as well as values to be taken into account the similarity matrix calculation. Behavior is defined as the direction and steepness of the time series between two points in time. Parameter which ranges from 0 to 5 determines how m uch behavior contributes to the similarity matrix, see Equations 3 1 through 3 4 in Chapter 3. Behavior similarity is expressed as temporal correlation, and Euclidian distance is used for value similarity. for 1 to 10 clusters, and with varying between 0 and 5. To obtain the most objective selection of the appropriate number of clusters, all results were evaluated with the Dunn Index and the Silhouette Width (Brock et al., 2008) schemes that base va lidation only on the data themse lves The Dunn Index compares within cluster variation (compactness) and the distance with other clusters (separation). It compares the minimum distance between points not in the same cluster and the maximum within cluster distance, and ranges from 0 to in finity. The Silhouette Width attempts the same, but by comparing each point to its own cluster (cohesion) and to other clusters (separation), with the final value being the average over

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139 all points in the cluster. It lies between 1 and 1, and should be abo ve 0 for decently separated clusters. Negative values indicate some clusters overlap. Both measures should be maximized. We chose the number of clusters that maximized both indicators. After clustering, all variables (except climate indices) were transform ed to area weighted averages for each VDC for further analysis. Singular spectrum analysis Phase space, the plotting of time series against its own lagged versions, is the basis for analysis of dynamic systems with deterministic components, which is known other in phase space (e.g. in 3D for 3 variables) will reveal an attractor, a specific pattern or path. Examples are predator prey relationships or the Lorenz attractor. Oft en though, we do not know the causal relationships from which to construct an attractor. these lagged versions, we can obtain a shadow attractor which is topologically si milar to the real attractor. These properties can be used in causality analysis. Real life time series are often subject to a fair amount of noise, particularly in ecology and environmental sciences. The first step is to separate noise and signals in the t ime series, since noise complicates the construction of an attractor (Figure 5 1). SSA deconstructs and reconstructs time series by identifying regular oscillatory components of different frequencies (deconstruction) which are simply added together to reco into orthogonal components through Singular Value Decomposition (SVD) of a Toeplitz matrix (Golyandina, 2010) A Toeplitz matrix contains lagged copies of the original time

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140 series in its columns, which makes it a matrix with constant diagonals from left to ri ght. For a matrix this takes the form: The window length (the number of columns) for creating the matrix was the multiple of the dominant periodic component of the da ta, not exceeding N /2 ( N = number of observations in the time series). Using this window length makes it more likely that SSA will find the most important frequencies (or periodic components) in the time series. The dominant periodic component was determin ed by spectral analysis, which applies a Fourier transform and returns the power spectral density of frequencies present in the time series. The SVD aims to separate the original Toeplitz matrix into elementary matrices. The method returns so called eigen triples: each is a combination of a singular value (the square root of an eigenvalue), a left eigenvector and a right eigenvector. Multiplication of the singular value, left eigenvector and transposed right eigenvector gives an elementary matrix (Golyandina and Zhigljavsky, 2013) The original Toeplitz matrix is the sum of all elementary matrices. Some of the eigentriples (or elementary matrices) can be grouped together to form unique, separable signals which is what we are after for signal reconstruction. To decide which to group together, first the elementary matrices are converted to time series with diag onal averaging: averages of diagonals give the time series values at each time (see for instance the layout of theToeplitz matrix, diagonal averaging will return the original time series). This produces a large number of time series, which when added to gether form the original time series.

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141 However, we are not interested in all these components. Decomposing the original time series in periodic components and noise (and sometimes a trend), the purpose of SSA, is only informative if these additive component s are separable. This can be evaluated with a w correlation matrix, the weighted correlation between the time series components obtained through the SVD and diagonal averaging. The weight reflects the number of times an element appears in the elementary ma trix (explained in detail in Golyandina et al. (2013)). This correlation is a measure of orthogonality (0) or non orthogonality (1) of two time series. We can also perform visual inspection of scatterplots of pairs. Paired periodic time series with the sam e frequencies will exhibit high correlation with each other and not with others, and will form regular shapes when plotted against each other in a scatterplot. The selected time series components (i.e. eigentriple pairs) are the basis of oscillatory compon ents of the time series and after decomposition by each periodic time series was calculated as the weighted norm of the eigenvectors as percentage of the total weig hted norm of the original time series. Adding those of the selected periodic time series signify the total contribution to the steps incorporated in this method ensu re that the signal is separable from the noise. To test for stationarity of the signals, nonlinear cross prediction was employed (Huffaker et al., 2017) This method measures the skill with which segments of the time series predict other segments of the same time series using nonlinear prediction methods. If the prediction skill decreases with remote segments, t he time series is deemed non stationary. The method starts with dividing the series into segments, and

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142 for each the appropriate embedding dimension is calculated (i.e. the maximum lag at which lagged time series of the original still share information with the original the first average mutual information index minimum for the series). These segments are then embedded with this lag to create matrices with lagged copies of themselves. Each is used as learning and testing sets alternatively: as a testing se t the segment is used to predict future points using the nearest neighbors approach. These predictions are then evaluated against a learning set using the Nash Sutcliffe coefficient, a measure of goodness of fit (Huffaker et al., 2016b; Nash and Sutcliffe, 1970; Ritter and Muoz Carpena, 2013b) ; i.e. if we have 5 segments, each will be used to predict the other 4. After confirming stationarity, surrogate data testing was applied to provide statistica l proof of the likelihood that the reconstructed time series is not generated by a linear stochastic system, but by a deterministic system. This done by shifting values in the time series in such a way that the serial structure is destroyed, but the statis tical properties are conse rved. The surrogate data that are produced is then tested for characteristics of nonlinear dynamics, comparing those to the characteristics of the original signal. The null hypothesis is that the signal is generated by a linear st ochastic system meaning that the characteristics of the surrogate data resemble those of the signal. This type of testing is widely accepted as a suitable measure to test the null hypothesis of a time series being a representation of a particular type of system (Dolan and Spano, 2001; Small and Tse, 2003; 2002; Theiler et al., 1992) The surrogate data testing approach we applied for this study has been used in previous studies (Huffaker, 2015; Huffaker et al., 2017; 2016b) and guidance on implementation has been taken from these works. We also refer to these documents for the detailed methodology and

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143 implementation. We applied algorithms that produce amplitude adjusted F ourier transform (AAFT) surrogates (Theiler et al., 1992) and pseudoperiodic (PPS) surrogates (Small and Tse, 2003) The double surrogate testing covers two potential types of data: linearly filtered noise processes (AAFT) and periodic orbits with uncorrelated noise (PPS). The discriminating statistics that were estima ted were nonlinear prediction skill and entropy complexity. The prediction skill is expressed as the Nash Sutcliffe coefficient of efficiency, NSE (Ritter and Muoz Carpena, 2013a) which is calculated for the earlier described nonlinear prediction of segments of the time series of other segments of itself (Sugihara et al., 2012) Entropy complexity expresses uncertainty and randomness of a data set: lower values point to high predictability whereas higher values indicate independently and uniformly distributed values (the null hypothesis). For the t ests, nonparametric rank order statistics were applied, with =0.05 and parameter =5 (the number of surrogates needed for values of ) to give us surrogates for a one tailed hypothesis test. The null hypothesis is accepted if the statistic value of the signal falls within the largest or smallest values produced by the surrogates. The test for prediction skill is an upper tailed test since we only reject the null hypothesi s if the surrogate data predict with better skill than the signal. The test for entropy complexity is a lower tailed test as we are looking for lower entropy values for the signal than the surrogate data. If the null hypothesis is rejected, we conclude there is sufficient evidence for deterministic structure and use the s ignals for further causality analysis.

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144 Convergent cross mapping CCM is a relatively new method (Sugihara et al., 2012) but has gained a lot of popularity over the years with a number of variations in implemented on different types of data set s (Clark et al., 2015; Huffaker et al., 2016a; Ma et al., 2014; Mnster et al., 2016; Van Nes et al., 2015) We used the original approach by (Sugihara et al., 2012) as implemented by (Huffaker et al., 2017) This method is based on phase space reconstructions: if two variables interact in a deterministic fashion with each other, phase space reconstruction of each variable with delayed coordinates (shadow attractors) would map exactly onto the phase space that we could create from both variables (the original attractor). Hence they should also map perfectly to each oth er. CCM takes a shadow attractor for and with a nonlinear prediction algorithm (nearest neighbors) estimates points on another shadow attractor coefficient ( ) between the original and estimated points of the second shad ow attractor is referred to as cross map skill, see Sugihara et al. (2012) and Huffaker et al. (2017) for details. If this is high, has causal influence on There is a convergence requirement: that the cross map skill should converge to a certain value as the time series portion used for cross mapping (libraries) gets longer. The final value for is the average of a fraction of the total libraries tested. We set this fraction to 0.33, of the last (longest) libraries tested. Only were included in causal network construction. CCM has been found to work well on systems with weak to moderate coupling. occur, with high cross mapping skill both ways (Sugihara et al., 2012) Regular CCM generally cannot distinguish between true bidirectional causality, or strong unidirectional

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145 forcing. By forcing asynchrony on the data though, the true directionality can be established (Ye et al., 2015) Extended CCM applies both positive and negative lags to the driving s ignal. If it is truly the driving signal, the highest will be detected at a negative lag as the dynamic of the driver has to occur first. Variables with but their highest at a positive lag were deemed false positives and not drivers. Only res ults where the difference between the and was larger than were considered (Hu ffaker et al., 2017) The lags have additional significance, in the sense that they can indicate the order of effects in a transitive network (Ye et al., 2015) Data Availability Data collected and processed for this study can be found at 10.6084/m9.figshare.c.3933388 as well as the R code that was used for processing and analysis. Results Identification of Four Vegetation Dynamics Clusters along a Road Paving Gradient The time series clustering resulted in the identification of 4 clusters, with behavior contributing 76.2% t o the similarity matrix ( ). These clusters also showed spatial consistency (Figure 5 2a). In the remainder of this study they will be referred to as Vegetation Dynamics Clusters (VDCs). The collection of EVI time series per VDC shows different temporal patterns (Figure 5 2b), though their long term average, median and standard deviations are similar for each VDC. The area weighted average road paving was calculated for each VDC (Figure 5 2d), and the average road paving for each community individually ( Figure 5 2c) was plotted per VDC in a boxplot (Figure 5 2e). Based on the distinct differences in the time

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146 series in Figure 5 2b, and the exponential trend in paving extent (a loess curve through the medians), VDCs were ordered from least associated with r oad paving to highly associated with road paving. VDCs 1 and 4 and be considered the two extreme states, unpaved and paved, within the system. VDC 2 and 3 are then transitional in terms of road paving, with most communities having had road paving less than 50% of the study period. Signal separation reveals different signals for vegetation in each VDC The analysis reconstructed different EVI signals for each VDC, with different periodicities (see Figure 5 3, Table 5 1, Figures B 2 to B 6). All signals have a 12 month oscillation, but the presence of oscillations of 4, 5 or 6 months vary between VDCs. There is also a difference in the periodicity of the low frequency signals. Figure 5 4 demonstrates the differences between the VDCs even clearer, and also sho ws there is general agreement of patterns of low and high EVI values between observed data (first column) and reconstructed data (second column). For VDC 1, lower EVI values occur from June to August, but there is another dry period in some years at the be ginning of the year. This is less prominent in the other VDCs. Higher EVI values are stronger in October December for VDC 1 and 2, less strong for VDC 3 and 4. The low frequency signals are visible as bands of years with lower EVI around 1992 1995 and 2000 2004 for VDC 2 for example, but with more frequent low EVI years for VDC 4. We found that even though the reconstructed signals for biophysical variables seemed similar between VDCs (Figure 5 3), the periodicities used for reconstruction were different (T able 5 1). Cycles of 12 and 6 months persisted for all VDCs for maximum, mean and minimum temperature as well as PET, and precipitation and soil moisture also had a clear annual cycle. Beyond that, there is a large variation in cycles

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147 included in the signa ls. It is of interest to note that for all biophysical variables the lower frequency periodicities mostly occur in VDC 3 and/or 4. Variables with the most variation between VDCs are maximum temperature and precipitation, which is clear in B 7. Precipitatio n in VDC 4 has a more distinct low frequency signal, with drier and wetter periods of about 4 years. Across all VDCs, higher maximum temperatures appear to slowly shift to occur slightly earlier in the year. The soil moisture signal lags about 2 months beh ind precipitation: June September is a drier period, but soil moisture drops below average in August November. The contribution to the decomposition is high for most variables (Table 5 1), with EVI and maximum temperature yielding the lower contributions ( 40 60%). For the climate indices, MEI shows periodicities of approximately 5 years, 2 3 years and 9 months, which is in line with previous studies (Kuss and Gurdak, 2014; Park and Dusek, 2013; Roy, 2010; Velasco et al., 2017) The AMO contains periodicities of 8.3 years, approximately 1 year, and 4.5 months. The PDO contains an annual periodicity, 2.5 years and almost 2 years. Due to the length of the time series, we are potentially missing out on longer temporal cycles, since other studies also found 15 25 year cycles for the PDO and 50 70 year cycles for the AMO (D'Aleo and Easterbrook, 2010; Kuss and Gurdak, 2014; Park and Dusek, 2013) This probably also explains the lower contribution to decomposition for the PDO (40%) and AMO (46%). The non linear predictive skill for the variables was tested using 5 segments (Figure B 8). We concluded that for VDC 4 the EVI is non stationary, with a clear downward skill, making it unsuitable for further CCM analysis. For the other VDCs and the climate variab les, while the skill was low for some variables and somewhat

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148 ambiguous in some cases (e.g. AMO), we decided there is sufficient stationarity to continue with subsequent testing for determinism. Surrogate data testing rejected the null hypothesis of linear stochastic dynamics with either surrogate test, AAFT or PPS, for all signals based on both discriminating statistics (predictive skill and entropy complexity). For two signals, EVI signals for VDC 2, and mean temperature for VDC 3, the rejection is not as strong as for others (Table 5 2). Causality testing of signals for three VDCs indicates an increase in causal relationships for EVI As outlined in the methods, after calculating the cross mapping skill (Table B 2 ), we applied extended CCM to distinguish bidirectionality from strong unidirectional forcing for VDCs 1, 2 and 3 and climate variables. While our calculations generate numeric results for passing or not passing extended CCM (see Methods), this evaluation was also based on visual inspection of plots of the delays, as not all results were as obvious as previous studies suggest they could be (Ye et al., 2015) see Table B 3 The final results, for and filtered with extended CCM are summarized in Table 5 3. Note that the absence of does not imply there is no cross mapping skill at al l; simply that it fell below the cut off. Considering the dense network of causality that appeared for this system, we wanted to focus on the most significant causal connections. Biophysical variables This study shows biophysical variables in the Southwestern Amazon form a tight causal network of their nonlinear deterministic components, with bidirectionality in all ways for VDC 1 3 (Table 5 3): maximum, average, minimum temperature, precipitation, potential evapotranspiration and soil moisture. T his points to strong feedback loops; and

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149 these are not altered with the extent of highway paving. Extended CCM gives an indication of order, since lags from this an alysis differ per VDC (Table B 3 ). In the following construction and discussion of causality networks the bidirectional relationships for the biophysical variables are not depicted, to enhance the readability of the graphs. Climate variables Figure 5 5 shows the CCM results for the nonlinear deterministic components for EVI driving other varia bles. The results for variables driving EVI and climate indices, and climate indices as drivers, are shown in Figure B 9. The AMO and MEI are being driven by an increasing number of variables across the VDC 1 3. The MEI is mostly driven by moisture related variables; precipitation and soil moisture. While neither of these could physically directly affect the MEI, we suspect there is an indirect effect here through cloudiness and/or actual evapotranspiration. The AMO is more driven by temperature related var iables; maximum and minimum temperature and potential evapotranspiration. Again, we suspect that there is some relationship with cloudiness and/or actual evapotranspiration. This would be a mechanistic explanation for the influence of biophysical (local) v ariables on climate indices (Arias et al., 2010; Klein et a l., 1999) The AMO is the only climate index that appears to drive biophysical variables, temperature and soil moisture. It is also the only climate index driving the other two, the PDO and the MEI. Note that these results do not imply there was no caus al effect at all from the MEI onto the PDO or AMO, but its was below the cut off (Table B 2 ). The indication that EVI drives the AMO across all three VDCs, and the MEI in VDC 1 (Figure 5 5 and B 9), can be interpreted as indirect effects as well. The st rength

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150 of this causal relationship increases from VDC 1 3 (shown in the colors of the arrows in Figure 5 5), but the number of causal relationships from EVI to biophysical variables (Figure 5 5), as well as the number and strength of biophysical variables to the AMO (Figure B 9) also increases along the VDCs. It is plausible that the mechanistic causal path is from EVI to biophysical and/or atmospheric variables to (other, not included variables to) sea surface temperature anomalies or climate indices. Vege tation dynamics The vegetation dynamics (EVI) signals are driven by all biophysical variables, which does not change across VDCs except for some variations in strength of the causal relationships (Figure B 9). In VDC 1, maximum temperature, potential eva potranspiration and soil moisture are the strongest drivers of EVI, while for VDC 3 this has evened out more, with only minimum temperature having a slightly stronger influence. Surprisingly, we see an increase in feedback from EVI from VDC 1 to 3 (Figure 5 5): whereas EVI does not seem to drive any of the biophysical variables in VDC 1, this increases to EVI driving maximum, mean and minimum temperature, precipitation and soil moisture in VDC 3. Discussion Vegetation Dynamics Clusters and Signals From the cluster analysis results, we conclude there are indeed clusters of vegetation dynamics that are distinguishable based on their values and, mostly, their temporal behavior. The signals extracted from the area weighted time series provide more support for t his as EVI signals incorporate different frequencies. This is an interesting finding considering that previous research considered the whole area to be in (F. B. Silva et al., 2013 ) That study divided the Amazon in

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151 regions based on intra annual variation in NDVI, and the MAP area fell into a region potentially a small area of our study area in Peru season from May to September. NDVI and EVI are not the same though, and EVI is known for better reflecting vegetation changes in dense forest and tropical regions (Huete et al., 2002) This study highlights that the forests in the Amazon are even more heterogeneous than suggested in previous studies though we offer support for the hypothesis that in our study area this is due to anthropogenic influences, specifically highway paving. Another potential explanation for the VDCs or any chang es that we see across VDCs could be soil or forest types (Baraloto et al., 2015; Quesada et al., 2012 ) However, a classification for this area (in development) indicates that on average respectively 78%, 57%, 87% and 69% of VDCs 1 4 are terra firme forest over soils with low /medium fertility, with bamboo and without bamboo different types of flooded forest. In the absence of any other variables currently along which to order VDCs, the road paving gradient is intuitive. Application of Causality Analyses on Complex Systems: Implications of Findin gs and Methods Scientific findings The strong bidirectional biophysical network that we identified is a finding that is to be expected for this area: vegetation in tropical areas, specifically the Amazon, are known for their feedback loops (Betts et al., 2004; Quesada et al., 2012 ) It is encouraging to see that these connections were maintained across 3 VDCs, which physically not possible: two variables cannot change at the same tim e and also drive

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152 each other at the same time. Our data set consists of monthly average values, which lends more credence to the bidirectionality since this does not represent the instantaneous change imagined by critics. While we also recorded lags from ex tended CCM between variables, detailed analysis of these fell outside the scope of this study. Future work should include an analysis of the chains or order of effects for this network. In terms of vegetation dynamics, the most striking finding is the incr ease in causality from EVI to biophysical variables from VDC 1 to 3. This implies there is an increasingly stronger feedback mechanism along the road paving gradient, causing greater connectivity within the regional system. While several studies have point ed out the importance of climate vegetation feedback in the Amazon at a global scale in general (Betts et al., 2004; Papagiannopoulou et al., 2017; Quesada et al., 2012 ; Tuttle and Salvucci, 2016) our results indicate that at a regional level there might be differences. The moderately disturbed area has stronger local or regional feedback from vegetation to biophysical variables. In the undisturbed state the vegetation has less or no impact on the local biophysical variables. In this case, the biophysical variables operate more independently from local vegetation dynamics, which decreases impacts of (anthr opogenic) vegetation changes to the system as a whole locally. For the more disturbed system this is not the case: similar changes could now affect local climate, and disturbances can cascade through the system. This is in line with resilience literature (Gunderson and Holling, 2002) that points out that higher connectivity makes a system more vulnerable: any changes in vegetation dynamics now also reverberate through the multiple feedback loops onto itself Amplification of disturbance is also a risk for these systems. These systems are generally seen as more sensitive to collapse

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153 (Gunderson and Holling, 2002) Why there is an increase in connectivity canno t be definitively answered with these results and requires further research. We pose that the different vegetation dynamics (and thus different causal network) means the structure and composition of vegetation differs between the unpaved and paved state, w ith the paved state containing vegetation that interacts more with biophysical variables. Most likely the vegetation is more strongly seasonal, hence mechanistic processes such as stomatal opening and closing (affecting evapotranspiration and carbon exchan ge with the atmosphere) and greening/senescence have a more direct effect on local biophysical variables. Stationarity results of the EVI excluded VDC 4 from CCM analysis, which is another important finding of this study. This result implies that this sys tem, specifically vegetation dynamics, is already undergoing some change (at the regional level). This is one of the more defined states, i.e. the paved state, so it would be important to understand the dynamics in more detail. In particular since this is the state that all other VDCs are trending towards in terms of paving status. It is suggested to do more research on the EVI signal, potentially exploring signals and causality for segments of the time series. Further work into change point analysis is als o recommended, ideally at the community level. Even though the relationships between the AMO, PDO and MEI were not the main objective of this study, we found that the relationships we identified for the deterministic components of the time series confir m and clarify previous work (Enfield et al., 2001; Kuss and Gurdak, 2014; Roy, 2010) The AMO appears to be the most influential climate index in our study area. This study adds insight to the relationship

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154 between climate indices and biophysical variables, but there is a need for further research on the actual mechanisms linking these. The methods applied here go beyond correlation analyses which often leave questions of drivers (Wang et al., 2013) but reveal the directionality of causality clearer. We must caution that the length of the time series could have prevented us from picking up longer term oscillations that might be relevant as well, and that the results presented in Figure 5 5 and B 9 do not imply a complete absence of causality between some indices, simply t hat they were below the cut off (see Table 5 3 and Table B 2 ). Also, we cannot assume we have included all variables that could fill in the complete causal path. Variables such as actual evapotranspiration, evaporation, cloudiness and wind could be importa nt in sea surface temperature anomalies, as previous studies have suggested that these play a role (Klein et al., 1999; Mitchell and Wallace, 1992) Another study that examined sea level pressure and sea surface temperature concluded that in the atmosphere ocean interaction, it is the atmosphere driving the ocean (Davis, 1976) This gives credence to the findings in this study, though confirmation of causality of these global phenomena would have to come from a much larger and comprehensive study incorporating several regions. Applicability of methods While we pr opose that (nonlinear deterministic) CCM is more suitable than (linear stochastic) GC analysis for a system as the one we studied here, there are caveats to consider with this method too. The length of the time series influences the signals that can be ide ntified with SSA, especially low frequency signals. The quality of the reconstructed signals is dependent on the interpretation of the researcher as well. Up to now, there are not many guidelines on cut offs for separability, stationarity or causal

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155 strengt h. And as we found in this study, if a signal appears to undergo change over the course of the time period (VDC 4), CCM cannot be applied. Finally, if a system has no low dimensional deterministic structure, but is instead high dimensional, CCM is not a su itable causality detection method. In this study, as will be the case with many studies of environmental systems, there still remains the question how much a reconstructed EVI scored the lowest in this regard, but because of the inherent noisiness of this data, we deemed it sufficient to proceed with CCM. Lastly, while extended CCM is very promising, application to strongly coupled systems with bidirectionality gives ambi guous results in terms of values and shapes of results over all the tested lags. We used a rather arbitrary cutoff of to decide whether or not to evaluate the results from the lagged CCM, but further research is required on appropriate cutoff s, especially in the light of results that do not exhibit the across results from the lagged CCM). Lastly, as has been expressed throughout this study, there is always the possibility that variables that a re of importance have not been included. Some of these are actual evapotranspiration, cloudiness, fire, and potentially anthropogenic variables that vary monthly or intra annually (water use, food or timber prizes). Concluding Remarks This research has pro vided support to our hypothesis that vegetation dynamics differ along a road paving gradient, not just in their appearance (the signal), but also structurally. All biophysical indicators are implicated as drivers across the VDCs associated with road paving with varying strength. Most notably though, is an increase in feedback from vegetation onto biophysical indicators, locally with increased paving

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156 Also, the different nature of the vegetation dynamics signal in the paved state (VDC 4), which excludes i t as a candidate for CCM analysis, is of interest. Non stationarity implies a change in the signal over time. This suggests that increased infrastructure development could lead to a more locally connected system, which would be more sensitive to (anthropog enic) disturbances due to amplification. While this is not necessarily a new suggestion, we have been able to back this up with real life data. Unfortunately, the exact mechanics behind this cannot be pinpointed with this research, but should be the focus of further research. The results of this study provide support for policies that aim at monitoring a suite of variables after highway paving has been implemented. Studies have suggested that imminent thresholds and regime shifts can be detected from time series by monitoring critical slowing down, in terms of recovery of variance and autocorrelation after disturbances (Dakos et al., 2014; 2011; 2012; Scheffer et al., 2009 ) With vegetation dynamics being a difficult variable to monitor and measure at larger scales in tropical areas, it is recommended to intensively measure other local variables such as the ones included in this study: the most straightforward ones being temperature and precipitation. Considering the increased connectivity with increased road paving, these could be indicators of impending (local) system changes. With forest areas worldwide under threat of the current infrastructure development paradigm ( Laurance et al., 2014) monitoring forest areas and limiting impacts should be high on the agenda of any nation or development agency.

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157 Table 5 1. Periodicities that were selected to create reconstructed signals of time series and the contribution of each signal to the decomposition (value of the weighted norm of the signal as percentage of the total weighted norm of the time series). Total contribution of the signals combined is highlighted in bold. EVI2 = Enhanced vegetation Index2, MAXT = maximum temperature, MEANT = average temperature, MINT = minimum temperature, P = precipitation, PET = potential evapotranspiration, SM = soil moisture, AMO = Atlantic Multidecadal Oscillation, PDO = Pacif ic Decadal Oscillation, MEI = Multivariate ENSO Index. VDC 1 VDC 2 VDC 3 VDC 4 Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution EVI2 31.1 12.0 6.1 4.0 47% 19% 20% 4% 4% 12.0 36.0 33.3 4.9 4.4 44% 19% 16% 5% 2% 2% 12.0 46.4 6.1 9.1 49% 26% 15% 5% 3% 12.0 40.6 19.8 4.7 3.7 41% 24% 14% 2% 1% 1% MAXT 12.0 6.0 4.0 55% 33% 20% 2% 12.0 6.0 4.0 13.8 58% 32% 21% 3% 2% 12.0 6.0 30.8 10.9 4.1 60% 33% 17% 4% 3% 3% 12.0 6.0 6.4 4.0 57% 32% 21% 2% 2% MEANT 12.0 6.0 2.2 63% 43% 19% 1% 12.0 6.0 3.3 6.4 66% 50% 14% 1% 1% 12.0 6.0 5.3 4.0 19.3 6.2 70% 46% 15% 3% 3% 2% 1% 12.0 6.0 6.3 131.0 65% 40% 20% 3% 2%

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158 Table 5 1. Continued. VDC 1 VDC 2 VDC 3 VDC 4 Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution MINT 12.0 6.0 15.9 2.7 6.3 2.2 86% 70% 12% 1% 1% 1% 1% 12.0 6.0 2.7 2.8 82% 73% 7% 1% 1% 12.0 6.0 4.0 84% 73% 9% 2% 12.0 6.0 5.3 4.0 12.1 6.3 6.3 2.7 2.8 89% 70% 13% 1% 1% 1% 1% 1% 1% 0.4% P 12.0 13.7 10.3 64% 60% 3% 1% 12.0 6.0 4.0 2.2 6.1 69% 59% 4% 3% 2% 1% 12.0 20.3 4.0 2.2 4.0 5.6 5.6 67% 59% 3% 3% 2% 2% 2% 1% 12.0 47.1 12.8 63% 48% 9% 6% PET 12.0 6.0 4.0 2.4 3.0 12.0 89% 75% 10% 2% 1% 1% 0.3% 12.0 6.0 4.0 6.0 2.4 6.5 90% 71% 11% 5% 1% 1% 1% 12.0 6.0 4.0 3.0 2.4 9.0 89% 74% 9% 4% 1% 1% 0.3% 12.0 6.0 3.9 3.0 2.4 27.8 13.7 90% 72% 11% 2% 2% 2% 0.5% 0.3%

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159 Table 5 1. Continued. VDC 1 VDC 2 VDC 3 VDC 4 Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution Periodicity (months) Decomposition contribution SM 12.0 6.7 81% 80% 1% 12.0 57.0 6.0 90% 78% 6% 6% 12.0 69.8 85% 81% 4% 12.0 10.9 6.7 85% 83% 1% 0.5% AMO* 100.7 12.2 13.2 4.5 46% 38% 6% 1% 1% PDO* 11.8 30.7 22.9 40% 23% 9% 8% AMO* 100.7 12.2 13.2 4.5 46% 38% 6% 1% 1% Climate variables are not VDC specific.

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160 Table 5 2. Surrogate data test results VDC 1 2 3 Enhanced Vegetation Index 2 Predictive skill Signal 0.97 0.87 0.93 AAFT (high low) 0.72 0.96 0.69 0.88 0.66 0.93 PPS (high low) 0.43 0.94 0.42 0.95 0.43 0.95 H 0 (AAFT / PPS) reject / reject accept / accept reject / accept Entropy complexity Signal 0.80 0.81 0.75 AAFT (high) 0.75 0.79 0.73 PPS (high) 0.96 0.96 0.95 H 0 (AAFT / PPS) accept / reject accept / reject accept / reject Maximum temperature Predictive skill Signal 1 0.98 0.99 AAFT (high low) 0.55 0.94 0.59 0.94 0.63 0.93 PPS (high low) 0.37 0.93 0.36 0.95 0.43 0.95 H 0 (AAFT / PPS) reject / reject reject / reject reject / reject Entropy complexity Signal 0.65 0.77 0.73 AAFT (high) 0.74 0.75 0.75 PPS (high) 0.96 0.96 0.96 H 0 (AAFT / PPS) reject / reject accept / reject reject / reject Mean temperature Predictive skill Signal 0.97 0.98 0.60 AAFT (high low) 0.32 0.97 0.41 0.90 0.47 0.88 PPS (high low) 0.43 0.96 0.39 0.96 0.42 0.95 H 0 (AAFT / PPS) accept / reject reject / reject accept / accept Entropy complexity Signal 0.81 0.74 0.78 AAFT (high) 0.76 0.78 0.79 PPS (high) 0.96 0.96 0.96 H 0 (AAFT / PPS) accept / reject reject / reject reject / reject

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161 Table 5 2. Continued. VDC 1 2 3 Minimum temperature Predictive skill Signal 0.89 0.97 0.95 AAFT (high low) 0.42 0.82 0.56 0.86 0.56 0.89 PPS (high low) 0.39 0.96 0.39 0.96 0.36 0.96 H 0 (AAFT / PPS) reject / accept reject / reject reject / accept Entropy complexity Signal 0.80 0.71 0.51 AAFT (high) 0.79 0.78 0.74 PPS (high) 0.96 0.96 0.96 H 0 (AAFT / PPS) accept / reject reject / reject reject / reject Precipitation Predictive skill Signal 0.99 0.85 0.88 AAFT (high low) 0.86 0.96 0.63 0.91 0.57 0.84 PPS (high low) 0.43 0.96 0.38 0.95 0.38 0.96 H 0 (AAFT / PPS) reject / reject accept / accept reject / accept Entropy complexity Signal 0.69 0.76 0.75 AAFT (high) 0.68 0.76 0.77 PPS (high) 0.96 0.96 0.96 H 0 (AAFT / PPS) reject / reject reject / reject reject / reject Potential evapotranspiration Predictive skill Signal 0.99 0.99 1 AAFT (high low) 0.68 0.94 0.62 0.94 0.72 0.95 PPS (high low) 0.43 0.96 0.39 0.96 0.42 0.95 H 0 (AAFT / PPS) reject / reject reject / reject reject / reject Entropy complexity Signal 0.73 0.72 0.80 AAFT (high) 0.77 0.71 0.76 PPS (high) 0.96 0.96 0.96 H 0 (AAFT / PPS) reject / reject accept / reject accept / reject

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162 Table 5 2. Continued. VDC 1 2 3 Soil moisture Predictive skill Signal 1 0.99 0.99 AAFT (high low) 0.83 0.96 0.89 0.96 0.90 0.97 PPS (high low) 0.42 0.97 0.43 0.96 0.40 0.97 H 0 (AAFT / PPS) reject / reject reject / reject reject / reject Entropy complexity Signal 0.68 0.66 0.67 AAFT (high) 0.72 0.69 0.69 PPS (high) 0.96 0.96 0.96 H 0 (AAFT / PPS) reject / reject reject / reject reject / reject Non VDC related AMO PDO MEI Predictive skill Signal 0.88 0.96 0.96 AAFT (high low) 0.32 0.83 0.74 0.90 0.73 0.93 PPS (high low) 0.38 0.96 0.44 0.93 0.50 0.93 H 0 reject / accept reject / reject reject / reject Entropy complexity Signal 0.62 0.71 0.59 AAFT (high) 0.80 0.71 0.71 PPS (high) 0.96 0.96 0.96 H 0 reject / reject reject / reject reject / reject

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163 Table 5 3. S ignificant cross skill mapping after applying extended CCM ( ). The driving variable s are in the columns, acting upon the variables in the rows. The analysis was applied to each VDC separately. Drivers EVI2 MAXT MEANT MINT P PET SM AMO PDO MEI VDC 1 EVI 0.97 0.97 0.94 0.94 0.99 0.99 MAXT 0.98 0.96 0.97 1.00 1.00 0.92 MEANT 0.98 0.97 0.95 0.98 0.98 MINT 0.87 0.97 0.93 0.88 0.88 P 0.99 0.99 0.97 0.99 0.99 PET 0.99 0.97 0.95 0.94 SM 0.98 0.98 0.95 0.94 0.99 0.99 AMO 0.83 0.85 0 0.85 0.89 0.89 PDO MEI 0.68 0.76 0.73 0.83 0.77 VDC 2 EVI 0.88 0.9 0.91 0.9 0.92 0.92 MAXT 0.74 0.97 0.98 0.92 0.98 0.95 MEANT 0.97 0.99 0.93 0.98 0.96 MINT 0.96 0.98 0.92 0.96 0.95 P 0.92 0.95 0.96 0.93 0.94 PET 0.71 0.98 0.97 0.97 0.93 0.96 SM 0.82 0.97 0.97 0.98 0.94 0.97 0.78 AMO 0.82 0.85 0.87 0.89 PDO MEI 0.67 0.69 0.75 0.83 0.77 VDC 3 EVI 0.81 0.88 0.96 0.89 0.9 0.95 MAXT 0.67 0.93 0.97 0.91 0.99 0.96 MEANT 0.68 0.8 0.94 0.87 0.77 0.87 MINT 0.81 0.91 0.92 0.95 0.95 0.96 0.93 P 0.74 0.9 0.91 0.98 0.97 0.96 PET 0 0.89 0.87 0.97 0.89 0.96 0.66 SM 0.79 0.89 0.94 0.99 0.91 1.00 AMO 0.86 0.84 0.83 0.87 0.86 0.89 0.9 0.66 PDO 0.66 0.72 0.68 0.66 0.75 MEI 0.66 0.68 0.73 0.83 0.74

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164 Figure 5 1. Analysis frame work for causality analysis. Ad a p ted from Huffaker et al. (2016b).

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165 Figure 5 2 Characteristics of the study area after clustering analysis. a) The study area with 4 VDCs. b) Minimum, median, maximum monthly Enhanced Vegetation Index (EVI2) time series per VDC. c) Map of the study area, with 99 communities and their average paving extent for the period 1987 2009. d) Area weighted average paving extent per Vegetation Dynamics Cluster (0=road section associated with the community is unpaved,1=road section associated with the community is fully paved). VDCs are based on the adaptive dissimilarity index of EVI2. e) Average paving extent of the communities in each VDC, with an upward non linear tendency from VDC 1 t o 4. The tendency is a loess curve based on all average paving values.

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166 Figure 5 3 Reconstructed time series, the signals, after Singular Spectrum Analysis. EVI = Enhanced Vegetation Index 2, MAXT = maximum temperature, MEANT = mean tempera ture, MINT = minimum temperature, P = precipitation, PET = potential evapotranspiration, SM = soil moisture, AMO = Atlantic Multidecadal Oscillation, PDO = Pacific Decadal Oscillation, MEI = Multivariate ENSO Index.

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167 Figure 5 4. Heat maps for the o bserved EVI2 (column 1), reconstructed EVI2 (column 3), and line plots for the observed and reconstructed EVI2 (column 3) for VDC 1 (A), VDC 2 (B), VDC 3 (C) and VDC 4 (D). The heat maps have months along the x axis (Jan Dec) and years along the y axis ( 1987 to 2009 from top to bottom).

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168 Figure 5 5 Networks of cross mapping skill ( ) of deter ministic signals of EVI ( ) per VDC, after testing for false positives due to synchronicity. Bidirectional causality between minimum mean, maximum temperature, precipitation, potential evapotransporation and soil moisture are not shown. EVI = Enhanced Vegetation Index 2, MAXT = maximum temperature, MEANT = mean temperature, MINT = minimum temperature, P = precipitation, PET = potentia l evapotranspiration, SM = soil moisture, AMO = Atlantic Multidecadal Oscillation, PDO = Pacific Decadal Oscillation, MEI = Multivariate ENSO Index.

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169 CHAPTER 6 CONCLUSIONS Main Findings Scientific Findings For an area in the Amazon that has been subject to road paving, this study answered questions pertaining to resilience of a forest system in the face of infrastructure development and increased anthropogenic influences and disturbances. Based on existing literature on resilience, tipping points and road d evelopment impacts human system in the SW Amazon in the MAP area is affected by road paving, beyond s have already shown that roads are key drivers of deforestation, less is known about forest degradation at larger, regional scales. D egradation is generally an ill defined concept (Putz and Redford, 2010; Sasaki and Putz, 2009) and the definition of Putz and Redford (2010) is [old growth] forests that lose their defining attributes (e.g., anci ent trees, fauna, and coarse woody debris) through logging, market hunting, wildfires, or invasion by exotic species, become degraded forest different from many global climate change agreements that generally refer to degradation in ter ms of loss of canopy cover of carbon stock (Sasaki and Putz, 2009) Degradation is affected not only by these spatial scales of road paving but also different temporal scales: detecting change generally requires long time series, which are not always available. Hence, the availability o f multidisciplinary, long term data for a region in the SW Amazon that has been subject to highway paving provides the unique opportunity to answer those questions. In particular, this study uniquely combines

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170 available local socio economic data, long term remote sensing data, and information on natural variables from re analysis projects. We conducted data driven research to draw conclusions from characteristics from, and relationships between, data set s. Considering that road paving is ongoing in coupled n atural human systems in many parts of the world, results from this research are of interest to a wide audience, for instance researchers on road ecology and disturbances, policy makers dealing with environmental impact assessments and conservation issues, as well as international organizations involved in conservation, climate change and financing of infrastructure development. T his study focused on vegetation dynamics as an expression of the forest system state This is driven by the concept of ecosystem services in a coupled natural human system. E cosystem services for both humans and nature are provided by the functions of an ecosystem and some examples of functions are wa ter regulation, soil stability, primary producti vity, nutrient cycling For a numb er of functions, such as the timing of water and carbon cycles and primary productivity, p henology of vegetation (timing of growth and senescence) plays an important role P (cycles and dynamics over time) and vegetati on structure and composition are closely related: different species will respond differently to certain conditions Thus, a distinct change in vegetation dynamics over time can imply a shift in vegetation composition (especially if climatic conditions have not changed), or a change in timing of responses. The latter also impacts ecosystem services. Ideally long term record s of species abundance and vegetation structure would allow quantification of road paving degrad ation over time as we consider these an attribute of the system Unfortunately,

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171 this information is not typically available and if available, usually only locally. However, spatio temporal vegetation dynamics records based on remote sensing vegetation i ndices provide a powerful proxy for analyses of changes from ongoing road paving. The Enhanced Vegetation Index (EVI) was chosen as a suitable index, since it is known to maintain its sensitivity under high biomass conditions (Huete et al., 2002) and it is associated with Leaf Area Index and primary productivity (Cabello et al., 2012; Potter et al., 2009) which are linked to ecosystem services. We used monthly EVI2 ( (Z Jiang et al., 2008) as it provides long EVI from MODIS since then. AVHRR suffers more from cloud cover and other atmospheric issues, so we anticipated the first period of our data set to have di fferent characteristics than the second period. This made it difficult to do a before/after road paving analysis of each time series itself. Instead, we assembled monthly EVI2 with other existing data for 99 communities along the Inter Oceanic Highway that were subject to paving at different points in time. To exclusively focus on dynamics, we only used normalized time series of all variables. The research was ordered around 3 sub hypotheses to answer the main hypothesis. First, we asked the question if we could find commonalities (shared variance and shared behavior) in the monthly time series for EVI2 vegetation dynamics spatially aggregated over each of the 99 local communities. All communities were located along the Inter Oceanic Highway that was paved d uring the period of study (1987 2009), but paving started and finished at different times across communities. If there was any effect from road paving on vegetation dynamics, clustering might group communities together with a similar road paving history. A fter applying a time series

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172 clustering technique based on values and behavior, we identified 4 Vegetation Cluster Dynamics (VDCs) that we could associate with average road paving extent for the study f average EVI2 over time (and a breakpoint analysis) showed that there were differences between the clusters. Since the number of states (dominant values in a histogram) is associated with dynamics, this provided an early indication that dynamics differed between VDCs as was the purpose of the time series clustering technique. The existence of 4 VDCs confirmed our first sub transitional states from unpaved to paved road information on soil and general forest types did not associate strongly with the clustering. The dynamics of natural variables failed to cluster in the same way, a confirmation that there was no single variable driving for the clus ter results. We used the cluster results to build unique Dynamic Factor Models for each VDC. This was done to vegetation dynamics (in terms of variance) differ across a road paving gradient, with use trends and variables as shared explanatory factors across the VDCs and assign importance per community. The strength of DFA is that it gives outputs for each community individually (spatial effects), an d it includes times series of observed covariates and auto regressive (orthogonal) trends (temporal effects). Trends represent unique shared variance between communities, essentially indicating the existence of one or more explanatory variables not include d in the analysis. This analysis revealed a number of things, beyond simply answering the sub hypothesis. It showed that human factors, such as enforcement of

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173 tenure rules, family density and travel time to market explained more of the variance in vegetati on dynamics under the paved condition. In addition, we also found that the number of trends and the importance in explaining vegetation dynamics reduced from the unpaved to the paved state. Thus, the variables included in the DFMs in the paved state explai n more of the vegetation dynamics. Another important finding of this study was the fact that the change in importance of trends and variables, and human and natural variables, was a complete switch for each pair. When plotting this shift for all communiti es along their average road paving extent, this switch happened at an average paving extent of 75% (for our 23 year period), i.e. more or less between VDC 3 and 4. Lastly, by defining different DFMs for each VDC, this method showed that the VDCs were not j ust different in the expression of the vegetation dynamics, but potentially also in what drives the dynamics. The last sub causal network underlying vegetation dynamics would be disrupted and b ecome deeper by applying (statistical) causality analyses. The associated methods applied in this study are based on identifying deterministic signals that represent a low dimensional nonlinear deterministic system, i .e. an attractor. Singular Spectrum Analysis (SSA) decomposes time series in components from which a signal can be reconstructed removing noise that would otherwise complicate further analysis. The technique to determine causality, Convergent Cross Mappi ng (CCM), is novel and is specifically suited for these low dimensional nonlinear deterministic systems, where linear approaches (such as Granger causality) do not suffice for these systems because of the entanglement of information in time series. In

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174 this analysis, the area weighted averages of biophysical variables and EVI2 per cluster were used, and the method was able to identify signals for each. After rigorous testing for stationarity and determinism, VDC 1 3 were found suitable for CCM. For VDC 4 the EVI2 signal was non stationary. The resulting causality networks partly corroborated the hypothesis and indicated differences in causal networks between VDCs. However, it also showed an increase in causal connections from vegetation dynamics to natural va riables, instead of a decrease. Increased connectivity has been associated with less resilience and a higher risk of collapse as any disturbances can travel and/or amplify through the system (Gunderson and Ho lling, 2002) While causality between all biophysical variables was strong and stayed the same across VDCs, the increase in connectivity came from increased feedback from vegetation. Hence, while vegetation/climate feedbacks and correlations have been f ound in previous studies (Betts et al., 2004; Notaro et al., 2006) this study shows that the direction of these relationships might vary locally or regionally, particularly in the presence of human disturbance. In the undisturbed state, ve getation dynamics are driven by biophysical variables, which themselves are not influenced by vegetation, but this changes for more disturbed systems. The feedback from EVI2 implies that any further changes in vegetation dynamics will impact biophysical va riables too. The tight causal network also i.e. the reduced ability to recover from small perturbations) could be applied to only one, or a few variables, but can serv e as an early warning for the whole system. The fact that the EVI2 signal was non stationary implies that it was undergoing change over the period of study. A suggestion here is that during road paving vegetation dynamics

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175 indeed undergo change (increased c onnectivity from VDC 1 3) and eventually results in a change of state (non stationarity in VDC 4). Dynamic Factor Analysis also shows shifts between the importance of trends versus variables, and human versus natural variables between VDC 3 and 4. Overall this study confirms the first part of the main hypothesis: t he identity of the socio ecological system in the SW Amazon in the MAP area is affected by road pa ving, beyond only deforestation. However, the second part, that different stable states exist c ould not be conclusively answered. The non stationary nature of the EVI2 signal in VDC 4 in particular suggests this area is undergoing change. While it was challenging to work with composite data (EVI2, socio economical and biological), it is of utmost importance that research on the development of the products, and analysis on them, continues unabated. In order to find out how human disturbances affect systems long term, we need to do research on disturbances that have already taken place; we cannot aff ord to only do research future or recent disturbances. This poses challenges in obtaining data that go as far back as needed (e.g. EVI2 data transformed from AVHRR, estimated socio economic data), but with the know ledge we gain from analyzing the s e data, w hile keeping uncertainties in mind, we can contribute to adaptive management and the development of improved methodologies and data set s. With the amount of undisturbed systems declining already in 1995, almost 75% of the habitable surface on earth was d isturbed at least in part by humans (Hannah et al., 1994; Sanderson et al., 2002) the time to understand long term effects is now.

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176 Methodological Findings After applying evaluation criteria to find the appropriate number of clusters, the study found that seemingly similar criteri a (the Dunn Index and Silhouette Width) still gave different results. Besides the two criteria applied, there are a number of other criteria available; some measure internal stability, others do external comparisons. So, while the use of these criteria att empts to remove the subjectivity of clustering, it is worth remembering that choosing the criteria also involves subjectivity. Combining criteria that evaluate a similar measure is advisable in cluster studies. The use of clusters made DFA application suit able, as this method seeks to explain the shared variance among different locations throughout time. However, it did make interpretation of the results more challenging, as analysis now included comparisons between DFMs, not just within DFMs. Another chall enge was the number of variables included in these analyses, which limited the preferred approach of assessing all possible combinations of variables. We consider the backwards elimination method based on variance decomposition (partial R 2 ) a good alternative, but acknowledge there are other approaches to model specification that are just as valid. Overall, we found DFA to be a useful tool in assessing areas undergoing change, with each being at different points of the change process. While the uncovered relationships do not imply causality, the analysis gave an indication that the VDCs are potentially structurally different. CCM has stringent requirements on the signals to which CCM can be applied, in terms of stationarity and determinism. This proved to be limiting in analyzing VDC 4, and highlighted that for areas actively undergoing change CCM might not be suitable. It was encouraging that SSA uncovered signals for the time series, especially for EVI2,

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177 which is considered noisy data. The re is still a noise component that remains unexplained, but we do not know how much of this is observation error and how much process error. As with DFA, the number of variables included made this a time consuming analyses, since many of the pre processing steps involve manual and visual decisions and calculation settings. An advantage is that this allows the researcher to become intimately involved with the data and the methods, gaining a better understanding of their potential and their limitations. It do es, however, also complicate analyses of systems involving many variables. The methods applied in this research are novel and take full advantage of methods that have evolved over the years and current computational power. Compared to what was possible yea rs ago, it is an exciting time to do research on large long term data set s. The major challenge nowadays is evaluating applicability and the results that are generated. The next section will touch on this and give recommendations for future work. Limitati ons And Future Research When working with ecological data, issues with noisiness generally arise. This study was no exception. This makes it difficult in some case to evaluate goodness of fit of methods or model performance. In addition, remotely sensed pr oducts from tropical areas are notorious for noisiness because of cloud cover and potential saturation at high biomass values. While EVI2 purportedly solves the latter, there are still questions around the validity of EVI2 representing vegetation. Since th ere is no clear answer to this question as of yet, and the majority of studies and research articles support the use of EVI2 for this purpose, it was deemed justified to use this variable in this study.

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178 However, for future studies it would be interesting t o compare EVI data and more locally specific data, such as LiDAR, to find commonalities and anomalies. The data that were used representing natural variables all come from reanalysis studies. This means these are not actual measured values in most places. These studies however use sophisticated methods to calculate and estimate values, and several checks are in place to validate results. Considering the scarcity of data for areas such as our study area, these data are invaluable to gain insight into process es in the area. Since the methodologies applied in this research were time series analyses, there are variables that would have been interesting to include, but that were not available as a time series, e.g. general forest type or land cover. Future work c an look at expanding the existing database with additional time series. In the DFA analysis, variables are assigned coefficients that can be interpreted as the strength of the variable in explaining the response variable, though there is some discussion in the scientific community about this. Certain conditions on collinearity need to be met to make this true, and this is hardly ever the case. This is why this study uses methods to counter this (calculation of Variance Inflation Factors, VIF), and also uses the average semi partial R 2 for interpretation of results. It is recommended to generally use two indicators (coefficients and semi partial R 2 ) to draw conclusions. Regarding the inclusion of several trends in each model, part of the information containe d in the trend could refer to variables that we either failed to include or could not include due to time series length. The could be variables such as cloudiness, fire, actual evapotranspiration and human factors with a time series signature (food, timber gold or Brazil nut prices, selective logging intensity). There could also be a common observation error time

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179 series, associated with typical remote sensing limitations in the tropics that are often quite noisy. While Cross Convergent Mapping is the most novel method to identify causality, mathematical equations. Eventually CCM results still rely on some form of correlation, albeit in a much more complex and nonli near application. With that limitation said, CCM is an innovative procedure with a solid foundation based on decades of research into deterministic systems. Results from this research, as well as other studies (Lusch et al., 2016; Sugihara et al., 2012) suggest that this method is preferred for causality analysis over Granger cau sality analysis. Considering the earlier mentioned concerns about EVI2 data, future research into characterizing EVI2 with CCM would provide interesting insights into other phenological systems around the world. For example, comparing results from more tem perate regions and tropical regions might result in more clarity about the potential error and noisiness of EVI in tropical areas. We found that extended CCM offers exciting prospects, but yielded ambiguous results in some cases (e.g. biophysical variables wrongly driving climate indices). This could be due to drivers possibly acting indirectly (but strongly), so future research should focus on including other variables that might play a role, such as cloudiness, wind, etc. Future work should also include a closer look at the bi directionality between some of the tightly coupled biophysical variables: the results from the extended CCM include information that can inform causal pathways. For the CCM procedure overall (including all pre processing), more resea rch should lead to insights into cutoffs or significant values, as the ones

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180 applied in this research are all derived from other methods, or are based on statistics and common sense but not necessarily experience. This research only focuses on vegetation dynamics from a time series point of view. While the results give us important insights into potential degradation, it does not study detailed mechanisms of vegetation dynamics. Future research should focus on mechanistic modeling of the system, to simula te the conditions this study in order to gain more insight into underlying processes. In general, limitations associated with this research stem from data and methodology limitations. First, there will most likely be variables missing in the analyses, whic certain findings (trends in FDA, certain causal relationships in CCM). We should also be cautious about the actual data we have: vegetation indices are still only a proxy of vegetation dynamics, and we make assumptions about its relationship with the real world. Second, methodological constraints limit the certainty with which we can draw conclusions. DFA finds relationships, but not necessarily causality. With CCM uncovering statistical causality, we can make suggestions about real world causality, but these are still inferences. In addition, the stringent requirements on signals to apply CCM to (stationarity, low dimensional deterministic) excludes the application of this app roach to systems that are non stationary and are undergoing change, and high dimensional systems. This is still a challenge, and a major topic for future research. This research uncovered interesting potential relationships and potential change points, but a large part of its contribution also lies in the evaluation of the usefulness and applicability of advanced time series analyses to complex coupled natural and human systems.

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181 Broader Impacts This research has shown that, even in the absence of deforest ation, road construction potentially decreases the resilience of forest systems at larger regional scales. While this research has not pinpointed the exact mechanisms, a relevant point is that this disturbance and their drivers are often hidden due to the scale and complexity of the effects. For example, on remote sensing images, these areas can still look forested, but the structure and the dynamics might not be the same anymore. In particular in CNH systems this is of importance, as ecosystem services are an integral part of the connected system. The study shows that the change in forest dynamics resulting from the road disturbance can potentially affect ecosystem services at much larger scales through feedback mechanisms. For example, changes in temperatu re regulation and carbon sequestration over large areas such as the Amazon could trigger global hemispherical processes. Overall, the findings of this research have implications for management of reas along roads would be recommended, with a focus on enforcement early on. Mostly though, the findings have bearing on monitoring campaigns that can influence policy and management: ongoing monitoring and analysis of data will highlight change or potenti al change and contribute to adaptive management. Adaptive management will be required if indeed (the timing of) ecosystem services changes in the area. It would thus be advisable to implement monitoring programs that focus on vegetation dynamics on a long term basis. This could be done with existing remote sensing products such as MODIS, but ideally with newer and more locally applicable technologies such as LiDAR, combined with new orer,

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182 FLEX). Research projects are underway to identify canopy structure, and even species, from these technologies (Graves et al., 2016; Immitzer et al., 2012; Olivier et al., 2017; Rybansky et al., 2016; Verrelst et al., 2015) As these technologies will become more available as time goes by, regional (state) governments dealing with road paving projects could be in a position to employ them. Effor ts to educate local stakeholders on these opportunities and transfer the results to improve management should be sustained though long term campaigns. We acknowledge this will be difficult for the more general stakeholder population, considering the slow a nd long term changes we are considering here, and the more immediate, short term pressing needs of the local population. There are conservation organizations in the area though (e.g. the Amazon Conservation Association) and research initiatives which woul d be prominent stakeholders, particularly for monitoring and transferring adaptive management solutions. Additionally, since causality analysis implies a strong link between biophysical variables with increased paving, it is also advisable to monitor thes e closely. This is usually easier than monitoring vegetation dynamics and many places already have stations in place that monitor temperature and precipitation. However, ongoing analysis of the data is key: other research has shown that time series charact eristics undergo (Dakos and Bascompte, 2014; Scheffer et al., 2009 ) Considering the causal relationships, a change in one (easily measured) variable could serve as a warning for the overall system Note that it would be useful in this context to have more insight into causal (mechanistic) pathways mentioned earlier to ensure the appropriate variables are monitored.

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183 Lastly, many road infrastructure projects in remote areas receive funding from Inter American Development Bank or the International Finance Corporation). This research supports the urgent re focusing by these organizations on forest degradation in their environmental sustainability performance standards, especially focusing on ongoing monitoring and analysis of vegetation dynamics and other socio ecological variables. While long term effects are more complicated and costly to monitor than immediate effec ts, the pay offs are potentially greater. Preventing forest degradation will conserve ecosystem services for the environment and humans for generations to come, and should be part of corporate and organizational social responsibility.

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184 APPENDIX A SUPPLEMENTARY MATERIALS FOR CHAPTER 4 Table A 1. Overview of communities included in the study. Number Name km 2 Country X_1 3 Arroyos 124.6 Bolivia X_2 Vera Cruz 104.3 X_3 Mukden 125.5 X_4 Extrema 87.8 X_5 Sena 222.5 X_6 Santa Rita 41.0 X_7 Santa Mara 117.5 X_8 San Antonio (Km. 60) 70.7 X_9 Santa Luca 182.1 X_10 Trinchera 70.4 X_11 Litoral 7.5 X_12 San Lus 7.1 X_13 Nuevo Triunfo 0.0 X_14 Barzola (Villa Rosario) 0.9 X_15 Marapani 4.0 X_16 Santa Rosa de Abun 32.2 X_17 Conqusta 27.1 X_18 Porvenir 7.7 X_19 Villa Rojas 5.9 X_20 Pontn 2.4 X_21 Santa Elena 12.7 X_23 Molienda 64.5 X_24 Irak 55.7 X_25 El Maty (San Antonio del) 160.0 X_26 Mandarino 115.8 X_27 Avaroa 39.1 X_28 Batraja 6.0 X_29 El Carmen 29.9 X_30 Karamano 5.0 X_31 Santa Lourdes 48.1 X_32 Primero de Mayo 14.0 X_33 Las Abejas 20.5 X_34 Jeric 5.0 X_35 Nueva Vida 22.3 X_36 Limera 0.0 X_37 Monterrey (Pando) 99.4

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185 Table A 1. Continued Number Name km 2 Country X_38 C.N. Belgica 533.9 X_39 Villa Roco 202.1 X_40 Union Progreso 29.8 X_41 Shiringayoc 72.1 Peru X_42 Santo Domingo 4.8 X_43 Santa Rita Baja 33.4 X_44 Santa Rosa (Las Piedras) 46.4 X_45 San Bernardo 17.2 X_46 Villa Primavera 59.7 X_47 Planchon 113.9 X_48 Centro Poblado de Alegra 148.4 X_49 La Pastora 22.8 X_50 San Isidro De Chilin 75.6 X_51 Sudadero 170.4 X_52 Centro Poblado Menor de Mavila 196.5 X_53 Florida Baja 20.5 X_54 Florida Alta 42.4 X_55 A.C. Agraria Arca Pacahuara 81.4 X_56 Santa Rosa (Laberinto) 6.1 X_57 C.P. Alerta 46.1 X_58 Inapar 26.4 X_59 Portillo 44.3 X_60 Loromayo 167.0 X_61 Virgen de la Candelaria 49.5 X_62 El Prado 14.8 X_63 Abeja 108.0 X_64 Nueva Esperanza 23.5 X_65 Chilina 15.1 X_66 San Antonio Abad 16.1 X_67 Ponalillo 17.5 X_68 La Merced 15.9 X_69 San Francisco de Ass 9.4 X_70 Monterrey (MDD) 83.5 X_71 Cachuela Alta 11.9 X_72 Otilia 5.5 X_73 Centro Cachuela 8.0 X_74 Asentamiento Humano El Trunfo 0.8 X_75 Alto Libertad 52.5

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186 Table A 1. Continued. Number Name km 2 Country X_76 Seringal Filipinas 550.4 X_77 PA Benfica 57.0 X_78 PA Moreno Maia 227.9 X_79 PA Alcobras 107.1 X_80 PAE Remanso 431.2 X_81 PAE Santa Quiteria 693.1 X_82 PAD Quixada 529.9 X_83 PAE Chico Mendes 289.1 Brazil X_84 PAE Porto Rico 118.9 X_85 PA Baixa Verde 50.7 X_86 PA Paraguassu 121.1 X_87 Sagarana 341.5 X_88 Seringal Sao Francisco do Iracema 505.2 X_89 Seringal Icuria 657.4 X_90 Seringal Independencia 121.7 X_91 Seringal Paraguacu 168.0 X_92 Polo Agroflorestal Brasileia 5.3 X_93 Polo Estrada da Borracha 2.3 X_94 Polo da Variante 3.4 X_95 PCA Helio Pimenta 1.4 X_96 PA Colibri 15.6 X_97 PA Vista Alegre 10.3 X_98 PA Limeira 22.8 X_99 KM 52 101.0 X_100 Seringal Sao Francisco 304.4 Abbreviations: PA/PAD = settlement projects, traditional projects of individual land concessions to small farmers PAE = Projectos de Assentamentos Agroextrativis (agro extractive settlement projects, aimed at wild collector communities, mainly rubber tappers and Brazil nut collectors) PCA = projeto casulo (peri urban settlement project for agricultural and ranching activities )

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187 Table A 2 Statistical characteristics of monthly EVI2 time series (1982 2010) per VDC: mean ( ), median ( M ), standard deviation ( ), minimum ( min ) and maximum ( max ). n is the number of time series in a VDC. EVI2 is a combination of two band and three band Enhanced Vegetation Indexes, which are indexes calculated from surface reflectance measured by satellites. It represents vegetation dynamics and characteristics such a s biomass and structure. VDC M min max 1 ( n =18) 0.50 0.53 0.50 0.54 0.06 0.08 0.23 0.38 0.65 0.75 2 ( n =24) 0.42 0.53 0.43 0.53 0.05 0.08 0.14 0.35 0.56 0.76 3 ( n =43) 0.49 0.54 0.50 0.54 0.05 0.08 0.05 0.35 0.65 0.72 4 ( n =14) 0.44 0.54 0.45 0.53 0.06 0.08 0.20 0.38 0.58 0.73

PAGE 188

188 Table A 3 Statistical properties of the monthly area weighted time series of Candidate Explanatory Variables (January 1987 to December 2009, n =276) per VDC : mean ( ), median ( M ), standard deviation ( ), minimum ( min ) and maximum ( max ) Human explanatory variables ( hum ) Natural explanatory variables ( nat ) VD C M min max M min max 1 ENF 0.05 0.02 0.02 0.09 FOR 98 99 95 99 2 0.07 0.04 0.01 0.20 85 85 74 89 3 0.27 0.28 0.02 0.42 89 91 79 95 4 0.43 0.49 0.05 0.61 89 92 75 97 1 FAM 43 43 37 52 MAXT 31.6 31.5 28.3 34.5 2 159 153 127 221 30.0 30.0 25.9 33.5 3 169 168 150 193 30.9 30.8 27.6 33.9 4 184 184 179 191 31.6 31.5 28.8 34.3 1 FAMD 0.004 0.004 0.004 0.006 AVET 26.3 26.6 22.3 28.4 2 0.066 0.044 0.010 0.200 24.6 25.0 20.1 27.1 3 0.006 0.006 0.006 0.007 25.3 25.7 21.0 27.6 4 0.013 0.013 0.012 0.014 26.3 26.6 22.5 28.3 1 PNC 19 666 16 997 7 299 43 323 MINT 21.0 21.7 15.9 24.0 2 38 543 36 750 18 576 65 584 19.1 19.7 14.3 22.4 3 157 891 157 855 96 192 218 239 19.8 20.5 14.5 23.0 4 210 659 211 489 130 361 285 455 21.1 21.7 16.1 24.0 1 PNM 1 363 1 280 666 2 398 P 150 124 1 592 2 7 356 6 969 3 239 13 017 204 189 1 649 3 7 790 7 384 3 842 13 112 163 149 3 571 4 12 436 12 238 7 596 17 757 176 132 1 709 1 PAV 0.00 0.00 0.00 0.00 PET 101 101 75 131 2 0.09 0.00 0.00 0.82 108 107 77 136 3 0.37 0.27 0.00 0.88 99 99 76 126 4 0.65 0.85 0.04 0.98 92 92 71 114 1 TEN 0.63 1.00 0.10 1.00 SM 465 469 220 652 2 0.77 1.00 0.49 1.00 468 473 256 657 3 0.36 0.40 0.28 0.45 456 465 221 680 4 0.15 0.15 0.13 0.19 476 484 229 651 1 TTC 196 214 163 214 SR 306 305 300 315 2 95 95 79 95 141 140 123 154 3 246 234 184 313 107 103 83 130

PAGE 189

189 Table A 3. Continued. Human explanatory variables ( hum ) Natural explanatory variables ( nat ) VDC M min max M min max 4 126 109 106 162 66 64 36 94 1 TTM 40 40 40 40 2 25 25 19 25 3 47 47 43 49 4 62 59 59 69

PAGE 190

190 Table A 4 Lags applied to time series of candidate explanatory variables. The lags ( in months) are based on the highest cross correlation coefficient ( ) between the lagged area weighted average candidate explanatory variable ( X ) and area weighted average EVI2 time series ( Y ) The minus ( ) sign indi cates that the explanatory variable value occurs before the EVI2 value it has the highest correlation with. Text in bold highlights instances where the cros s correlation is significant at VDC 1 VDC 2 VDC 3 VDC 4 Candidate Explanatory Variable ENF Enforcement of tenure rules (0 to 1: with 0=least, 1=most) 9 0.01 16 0.04 21 0.04 13 0.14 FAM Number of families in the community (polygon) 15 0.06 3 0.07 15 0.07 13 0.26 FAMD Family Density (families/km 2 ) 21 0.11 4 0.06 0 0.10 6 0.27 PGC Population growth at nearest state capital 15 0.03 4 0.10 15 0.05 13 0.08 PGM Population growth at nearest market 15 0.05 3 0.10 21 0.02 13 0.06 PAV Paving (0 to 1, with 0=no paving, 1=fully paved) 21 0.04 21 0.04 13 0.20 TEN Percentage of deforestation allowed under tenure rules (0 to 1: e.g. 0.1=maximum of 10% deforestation allowed) 16 0.01 4 0.03 21 0.04 5 0.12 TTC Travel time to capital (minutes) 21 0.03 0 0.07 15 0.10 13 0.20 TTM Travel time to nearest market (minutes) 0 0.06 0 0.05 5 0.20 AVET Mean temperature (C) 12 0.40 12 0.35 13 0.44 13 0.40 FOR Forest area as percentage of polygon area 21 0.07 4 0.06 21 0.05 0 0.06 MAXT Maximum temperature (C) 13 0.33 14 0.40 14 0.43 14 0.41 MINT Minimum temperature (C) 0 0.40 11 0.37 0 0.47 0 0.44 P Precipitation (mm) 4 0.35 17 0.35 0 0.37 1 0.34 PET Potential evapotranspiration (mm) 14 0.41 14 0.45 14 0.47 15 0.43 SM Soil moisture (mm) 3 0.39 10 0.42 4 0.44 4 0.41 SR Species richness (alpha diversity) i 19 0.22 0 0.09 13 0.06 1 0.11

PAGE 191

191 Table A 5 Results of Variation Inflation Factor (VIF) analysis for explanatory variables included in dynamic factor analyses per VDC All candidate explanatory variables (CEVs) with VIF > 10 are excluded. Lagged time se ries of the CEVs (as per Table A 3) are used in the VIF analysis. Explanatory Variable VIF values VDC 1 VDC 2 VDC 3 VDC 4 ENF Enforcement of tenure rules (0 to 1: with 0=least, 1=most) 2.09 1.96 5.34 FAMD Family Density (families/km 2 ) 4.55 2.62 1.19 PAV Paving (0 to 1, with 0=no paving, 1=fully paved) 2.00* 7.58 TEN Percentage of deforestation allowed under tenure rules (0 to 1: e.g. 0.1=maximum of 10% deforestation allowed) 1.81 4.06 4.70 TTM Travel time to nearest market (minutes) 2.00* 6.30 2.60 FOR Forest area as percentage of polygon area 5.46 MAXT Maximum temperature (C) 2.00 3.44 3.26 1.83 AVET Mean temperature (C) 2.21 2.40 2.29 2.16 MINT Minimum temperature (C) 2.24 3.17 3.22 2.98 P Precipitation (mm) 2.37 2.27 2.21 1.66 PET Potential evapotranspiration (mm) 3.70 6.55 4.66 3.40 SM Soil moisture (mm) 3.99 3.14 2.97 3.86 SR Species richness (alpha diversity) i 1.16 1.16 3.59 Paving and travel time to market are constant over time and not included in further Dynamic Factor Analysis

PAGE 192

192 Table A 6 Dynamic Factor Model (Model I, trends only) goodness of fit results of selected (best) models for individual communities. VDC Community C eff RMSE 1 X_5 0.59 0.65 X_6 0.62 0.60 X_7 0.86 0.38 X_8 0.77 0.47 X_9 0.86 0.37 X_17 0.60 0.63 X_21 0.68 0.57 X_24 0.85 0.39 X_25 0.87 0.35 X_26 0.81 0.44 X_27 0.87 0.36 X_28 0.75 0.50 X_29 0.71 0.54 X_32 0.50 0.71 X_33 0.48 0.72 X_34 0.74 0.51 X_35 0.63 0.60 X_37 0.75 0.50 2 X_39 0.87 0.36 X_40 0.53 0.70 X_41 0.87 0.36 X_42 0.90 0.31 X_43 0.56 0.67 X_44 0.74 0.52 X_45 0.61 0.64 X_47 0.92 0.29 X_48 0.91 0.30 X_49 0.61 0.63 X_51 0.86 0.38 X_52 0.89 0.33 X_53 0.49 0.73 X_54 0.98 0.15 X_56 0.54 0.69 X_60 0.53 0.70 X_61 0.74 0.51 X_62 1.00 0.01 X_70 0.89 0.33 X_71 0.59 0.65 X_72 0.64 0.61 X_73 1.00 0.01 X_74 0.68 0.58 X_75 0.91 0.30

PAGE 193

193 Table A 6. Continued. VDC Community C eff RMSE 3 X_1 0.89 0.34 X_2 0.79 0.46 X_3 0.79 0.46 X_4 0.87 0.36 X_10 0.57 0.67 X_11 0.52 0.70 X_12 0.72 0.54 X_13 0.72 0.53 X_14 0.72 0.53 X_15 0.63 0.61 X_18 0.57 0.66 X_19 0.66 0.58 X_20 0.72 0.53 X_23 0.77 0.48 X_30 0.56 0.66 X_31 0.63 0.62 X_36 0.67 0.58 X_38 0.91 0.31 X_46 0.74 0.51 X_50 0.78 0.47 X_55 0.75 0.50 X_57 0.68 0.57 X_58 0.80 0.45 X_59 1.00 0.02 X_63 0.90 0.32 X_64 0.63 0.62 X_65 0.72 0.53 X_66 0.67 0.58 X_67 0.61 0.63 X_68 0.79 0.46 X_69 1.00 0.02 X_76 0.88 0.35 X_81 0.85 0.39 X_82 0.88 0.35 X_83 0.79 0.46 X_84 0.81 0.44 X_86 0.72 0.54 X_87 0.82 0.43 X_89 0.84 0.41 X_91 0.85 0.39 X_92 0.70 0.55 X_99 0.78 0.47 X_100 0.91 0.31

PAGE 194

194 Table A 6. Continued. VDC Community C eff RMSE 4 X_16 0.29 0.85 X_77 0.68 0.57 X_78 0.81 0.44 X_79 0.72 0.54 X_80 0.81 0.44 X_85 0.68 0.57 X_88 0.92 0.29 X_90 0.81 0.45 X_93 0.56 0.66 X_94 0.50 0.72 X_95 0.56 0.66 X_96 0.70 0.55 X_97 0.65 0.60 X_98 0.66 0.58

PAGE 195

195 Table A 7 Average relative importance of trends and explanatory variables in dynamic factor analyses (Model II, trends and explanatory variables) simulating EVI2. Backward selection is applied; the variables with the lowest mean relative importance (LMG ) are eliminated one by one until the Bayesian Information Criterion (BIC) reaches its lowest point. Italic = selected models. VDC 1 VDC 2 VDC 3 VDC 4 EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC 1 0.21 9994 1 0.17 10390 4 0.27 19010 1 0.19 8100 2 0.19 4 0.14 1 0.15 FAMD 0.16 4 0.19 3 0.12 2 0.10 3 0.16 ENF 0.06 2 0.10 6 0.08 TTM 0.10 AVET 0.05 TTM 0.07 PET 0.05 2 0.06 MINT 0.04 PAV 0.06 5 0.05 PET 0.05 3 0.04 7 0.04 SM 0.04 MINT 0.05 PET 0.04 PET 0.04 MINT 0.04 AVET 0.05 FOR 0.04 6 0.04 FAMD 0.04 MAXT 0.05 SR 0.04 SM 0.04 AVET 0.04 P 0.04 SM 0.03 MAXT 0.04 MAXT 0.04 ENF 0.04 FAMD 0.03 5 0.03 3 0.03 SM 0.03 MAXT 0.02 P 0.03 P 0.03 TEN 0.02 P 0.02 MINT 0.02 TEN 0.02 AVET 0.02 SR 0.02 SR 0.02 ENF 0.01 TEN 0.01 1 0.21 9958 1 0.19 10322 3 0.28 18900 1 0.19 8076 2 0.20 7 0.14 1 0.15 FAMD 0.19 4 0.19 3 0.13 2 0.10 2 0.16 ENF 0.05 2 0.10 6 0.08 TTM 0.09 AVET 0.05 PAV 0.06 5 0.05 3 0.06 MINT 0.05 TTM 0.06 PET 0.05 PET 0.05 PET 0.04 4 0.05 MINT 0.04 MINT 0.05 3 0.04 6 0.05 SM 0.04 AVET 0.05 SR 0.04 PET 0.04 MAXT 0.04 MAXT 0.05

PAGE 196

196 Table A 7. Continued. VDC 1 VDC 2 VDC 3 VDC 4 EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC SM 0.04 SR 0.03 AVET 0.04 ENF 0.05 FOR 0.03 MAXT 0.03 FAMD 0.04 P 0.04 MAXT 0.02 SM 0.03 4 0.03 SM 0.03 FAMD 0.02 5 0.03 P 0.03 P 0.02 TEN 0.02 MINT 0.02 SR 0.02 AVET 0.02 1 0.21 9923 1 0.17 10266 3 0.28 18817 FAMD 0.20 8054 2 0.19 7 0.14 1 0.17 2 0.20 4 0.19 3 0.13 2 0.10 1 0.16 FOR 0.06 2 0.09 6 0.08 TTM 0.08 ENF 0.06 PAV 0.06 PET 0.05 PET 0.06 AVET 0.05 TTM 0.05 0.04 MINT 0.06 MINT 0.05 6 0.05 MINT 0.04 3 0.05 PET 0.04 4 0.05 SM 0.04 AVET 0.05 3 0.04 SR 0.05 MAXT 0.04 MAXT 0.05 SR 0.04 PET 0.04 AVET 0.04 ENF 0.05 SM 0.04 SM 0.04 FAMD 0.04 P 0.05 MAXT 0.02 MAXT 0.04 4 0.03 5 0.03 P 0.03 P 0.03 TEN 0.02 MINT 0.03 1 0.22 9896 1 0.20 10244 3 0.27 18695 1 0.21 8056 4 0.19 4 0.16 1 0.17 FAMD 0.21 2 0.18 3 0.14 2 0.10 2 0.16 FOR 0.08 2 0.10 0.08 PET 0.07 AVET 0.06 PAV 0.06 FAMD 0.06 MINT 0.07 MINT 0.05 TTM 0.06 5 0.05 3 0.07 ENF 0.05 7 0.05 PET 0.05 TTM 0.06

PAGE 197

197 Table A 7. Continued. VDC 1 VDC 2 VDC 3 VDC 4 EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC PET 0.05 5 0.05 MINT 0.04 AVET 0.06 SM 0.04 PET 0.04 SM 0.04 MAXT 0.05 SR 0.04 SM 0.04 MAXT 0.04 ENF 0.05 3 0.04 MAXT 0.04 AVET 0.04 6 0.03 4 0.03 P 0.02 P 0.03 SR 0.02 1 0.20 9939 1 0.20 10262 3 0.27 18590 3 0.19 3 0.15 1 0.17 2 0.17 6 0.14 2 0.10 FOR 0.13 2 0.10 6 0.08 AVET 0.06 PAV 0.06 FAMD 0.06 MINT 0.05 TTM 0.06 PET 0.05 SR 0.05 5 0.05 5 0.05 PET 0.05 PET 0.05 SM 0.05 ENF 0.04 SM 0.04 MINT 0.05 SM 0.04 7 0.04 AVET 0.04 MAXT 0.04 MAXT 0.04 4 0.03 4 0.03 SR 0.02 3 0.30 18664 4 0.18 2 0.09 1 0.09 FAMD 0.06 PET 0.05 SM 0.05

PAGE 198

198 Table A 7. Continued. VDC 1 VDC 2 VDC 3 VDC 4 EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC EV LMG (mean) BIC MINT 0.05 AVET 0.04 MAXT 0.04 5 0.04

PAGE 199

199 Table A 8 Dynamic Factor Model (Model II, trends and explanatory variables) goodness of fit results of selected (best) models for individual communities. VDC Community C eff RMSE 1 X_5 0.61 0.63 X_6 0.62 0.60 X_7 0.86 0.37 X_8 0.78 0.47 X_9 0.87 0.36 X_17 0.63 0.61 X_21 0.68 0.57 X_24 0.87 0.36 X_25 0.88 0.35 X_26 0.83 0.41 X_27 0.81 0.44 X_28 0.75 0.50 X_29 0.74 0.51 X_32 0.51 0.70 X_33 0.49 0.71 X_34 0.75 0.50 X_35 0.67 0.58 X_37 0.77 0.48 2 X_39 0.87 0.36 X_40 0.55 0.69 X_41 0.88 0.34 X_42 0.91 0.30 X_43 0.58 0.65 X_44 0.74 0.52 X_45 0.62 0.63 X_47 0.93 0.27 X_48 0.91 0.30 X_49 0.62 0.62 X_51 0.86 0.38 X_52 0.90 0.32 X_53 0.52 0.70 X_54 0.98 0.15 X_56 0.56 0.68 X_60 0.58 0.66 X_61 0.79 0.47 X_62 1.00 0.01 X_70 0.90 0.33 X_71 0.62 0.63 X_72 0.68 0.58 X_73 1.00 0.01 X_74 0.68 0.57

PAGE 200

200 Table A 8. Continued. VDC Community C eff RMSE X_75 0.91 0.30 3 X_1 0.89 0.33 X_2 0.81 0.44 X_3 0.80 0.45 X_4 0.87 0.36 X_10 0.59 0.65 X_11 0.61 0.63 X_12 0.76 0.49 X_13 0.73 0.52 X_14 0.72 0.53 X_15 0.67 0.58 X_18 0.58 0.65 X_19 0.67 0.58 X_20 0.71 0.54 X_23 0.80 0.45 X_30 0.57 0.65 X_31 0.64 0.61 X_36 0.68 0.57 X_38 0.91 0.31 X_46 0.75 0.50 X_50 0.78 0.47 X_55 0.78 0.48 X_57 0.69 0.56 X_58 0.81 0.45 X_59 1.00 0.02 X_63 0.91 0.31 X_64 0.64 0.61 X_65 0.74 0.51 X_66 0.67 0.58 X_67 0.63 0.61 X_68 0.79 0.46 X_69 1.00 0.02 X_76 0.87 0.37 X_81 0.85 0.39 X_82 0.88 0.36 X_83 0.80 0.45 X_84 0.82 0.43 X_86 0.75 0.50 X_87 0.82 0.43 X_89 0.84 0.40 X_91 0.84 0.40 X_92 0.70 0.55 X_99 0.80 0.45

PAGE 201

201 Table A 8. Continued. VDC Community C eff RMSE X_100 0.92 0.29 4 X_16 0.33 0.83 X_77 0.70 0.55 X_78 0.81 0.43 X_79 0.72 0.54 X_80 0.81 0.44 X_85 0.68 0.57 X_88 0.92 0.28 X_90 0.84 0.40 X_93 0.61 0.62 X_94 0.49 0.72 X_95 0.59 0.65 X_96 0.74 0.52 X_97 0.66 0.60 X_98 0.66 0.59

PAGE 202

202 Table A 9 Beta coefficients (weightings ) of the explanatory variables for the selected Dynamic Factor Models II (trends and explanatory variables). VDC 1 ENF FAMD PAV TEN TTM FOR MAXT AVET MINT P PET SM SR X_5 0.35 0.37 0.23 0.01 0.01 0.29 0.10 X_6 0.32 0.59 0.05 0.12 0.01 0.31 0.14 X_7 0.17 0.57 0.12 0.18 0.21 0.09 0.19 X_8 0.32 0.68 0.10 0.17 0.01 0.24 0.18 X_9 0.40 0.67 0.04 0.23 0.27 0.09 0.15 X_17 0.46 0.48 0.19 0.10 0.07 0.12 0.09 X_21 0.60 0.65 0.11 0.14 0.17 0.06 0.17 X_24 1.02 0.61 0.21 0.20 0.11 0.14 0.21 X_25 0.72 0.59 0.22 0.15 0.07 0.01 0.24 X_26 0.84 0.78 0.17 0.07 0.08 0.05 0.24 X_27 1.37 0.87 0.08 0.18 0.05 0.16 0.34 X_28 0.49 0.27 0.26 0.13 0.12 0.20 0.13 X_29 0.87 0.66 0.15 0.05 0.28 0.09 0.16 X_32 0.45 0.58 0.17 0.21 0.05 0.02 0.19 X_33 0.55 0.55 0.26 0.15 0.13 0.19 0.15 X_34 0.66 0.41 0.14 0.22 0.10 0.10 0.16 X_35 0.65 0.60 0.04 0.27 0.16 0.05 0.12 X_37 0.88 0.76 0.23 0.06 0.26 0.27 0.13 VDC 2 X_39 0.96 1.31 0.03 0.10 0.15 0.19 0.11 X_40 2.00 1.12 0.03 0.01 0.33 0.20 0.15 X_41 1.21 1.52 0.03 0.04 0.24 0.11 0.04 X_42 0.76 0.62 0.06 0.07 0.05 0.09 0.22 X_43 1.86 0.80 0.16 0.06 0.03 0.02 0.19 X_44 0.86 1.32 0.04 0.11 0.02 0.17 0.12

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203 Table A 9. Continued. VDC 2 ENF FAMD PAV TEN TTM FOR MAXT AVET MINT P PET SM SR X_45 0.22 0.44 0.21 0.10 0.22 0.17 0.19 X_47 1.67 1.55 0.08 0.00 0.09 0.20 0.11 X_48 1.61 1.76 0.07 0.05 0.07 0.18 0.12 X_49 0.80 0.69 0.08 0.08 0.05 0.17 0.04 X_51 1.43 1.29 0.09 0.02 0.03 0.17 0.02 X_52 1.13 1.43 0.16 0.05 0.01 0.23 0.14 X_53 0.73 0.31 0.16 0.28 0.03 0.09 0.18 X_54 0.34 0.30 0.02 0.01 0.10 0.10 0.30 X_56 0.03 0.03 0.04 0.01 0.28 0.09 0.04 X_60 0.58 0.24 0.04 0.14 0.26 0.14 0.04 X_61 2.76 1.40 0.12 0.03 0.03 0.08 0.12 X_62 0.03 0.27 0.01 0.08 0.27 0.04 0.01 X_70 1.92 1.91 0.03 0.12 0.07 0.07 0.10 X_71 1.38 1.19 0.06 0.05 0.04 0.21 0.05 X_72 0.81 0.69 0.04 0.11 0.16 0.02 0.03 X_73 0.03 0.27 0.01 0.08 0.27 0.04 0.01 X_74 1.76 0.90 0.12 0.00 0.18 0.16 0.15 X_75 3.31 1.71 0.10 0.01 0.12 0.04 0.16 VDC 3 X_1 0.08 0.01 0.14 0.19 0.33 0.13 X_2 0.05 0.05 0.02 0.25 0.20 0.02 X_3 0.02 0.07 0.01 0.22 0.07 0.04 X_4 0.09 0.05 0.11 0.16 0.38 0.10 X_10 0.41 0.08 0.07 0.07 0.50 0.11 X_11 0.31 0.01 0.01 0.07 0.00 0.12 X_12 0.24 0.19 0.12 0.03 0.00 0.04

PAGE 204

204 Table A 9. Continued. VDC 3 ENF FAMD PAV TEN TTM FOR MAXT AVET MINT P PET SM SR X_13 0.25 0.17 0.10 0.03 0.04 0.31 X_14 0.42 0.17 0.07 0.02 0.09 0.24 X_15 0.47 0.02 0.08 0.14 0.18 0.18 X_18 0.38 0.01 0.01 0.03 0.05 0.28 X_19 0.34 0.21 0.06 0.06 0.21 0.40 X_20 0.28 0.16 0.09 0.06 0.07 0.26 X_23 0.10 0.14 0.11 0.18 0.44 0.03 X_30 0.33 0.03 0.10 0.08 0.47 0.10 X_31 0.44 0.10 0.06 0.01 0.11 0.05 X_36 0.26 0.05 0.02 0.09 0.10 0.18 X_38 0.28 0.12 0.05 0.09 0.04 0.15 X_46 0.32 0.22 0.07 0.13 0.19 0.16 X_50 0.18 0.03 0.00 0.15 0.13 0.11 X_55 0.17 0.17 0.04 0.04 0.11 0.20 X_57 0.10 0.13 0.04 0.16 0.07 0.12 X_58 0.20 0.26 0.18 0.04 0.42 0.32 X_59 0.03 0.00 0.06 0.07 0.09 0.01 X_63 0.21 0.12 0.07 0.19 0.05 0.08 X_64 0.17 0.19 0.13 0.16 0.09 0.26 X_65 0.12 0.22 0.05 0.01 0.03 0.24 X_66 0.24 0.17 0.01 0.05 0.21 0.18 X_67 0.24 0.24 0.03 0.08 0.05 0.11 X_68 0.16 0.03 0.13 0.18 0.13 0.08 X_69 0.03 0.00 0.06 0.07 0.09 0.01 X_76 0.57 0.07 0.02 0.17 0.27 0.00 X_81 0.01 0.10 0.14 0.14 0.03 0.14

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205 Table A 9. Continued. VDC 3 ENF FAMD PAV TEN TTM FOR MAXT AVET MINT P PET SM SR X_82 0.35 0.19 0.13 0.03 0.15 0.27 X_83 0.45 0.12 0.03 0.17 0.37 0.01 X_84 0.49 0.14 0.02 0.05 0.03 0.19 X_86 0.24 0.25 0.04 0.18 0.21 0.09 X_87 0.62 0.03 0.03 0.11 0.16 0.04 X_89 0.13 0.13 0.07 0.16 0.17 0.00 X_91 0.09 0.14 0.14 0.11 0.03 0.08 X_92 0.46 0.17 0.12 0.06 0.18 0.35 X_99 0.44 0.06 0.12 0.05 0.25 0.05 X_100 0.34 0.24 0.06 0.12 0.14 0.13 VDC 4 X_16 0.44 0.66 0.36 0.11 0.01 0.28 0.16 0.05 X_77 0.73 1.06 0.95 0.25 0.08 0.01 0.06 0.14 X_78 0.53 1.33 0.46 0.13 0.01 0.13 0.24 0.15 X_79 0.51 1.11 0.61 0.19 0.02 0.17 0.14 0.13 X_80 0.45 1.07 0.33 0.17 0.00 0.26 0.13 0.12 X_85 0.54 0.81 0.91 0.19 0.13 0.05 0.02 0.21 X_88 0.33 0.97 0.14 0.17 0.09 0.14 0.10 0.09 X_90 0.26 0.84 0.09 0.18 0.01 0.18 0.17 0.10 X_93 0.62 0.86 0.65 0.15 0.09 0.08 0.11 0.29 X_94 0.52 0.81 0.75 0.09 0.14 0.08 0.02 0.13 X_95 0.48 1.00 0.67 0.20 0.02 0.18 0.04 0.05 X_96 0.63 0.91 1.07 0.15 0.08 0.08 0.09 0.26 X_97 0.52 1.35 0.32 0.13 0.04 0.11 0.05 0.19 X_98 0.59 1.01 0.79 0.15 0.08 0.05 0.15 0.18

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206 Table A 10 Factor loadings (weightings ) of the trends for the selected Dynamic Factor Models II (trends and explanatory variables), for each community. 1 2 3 4 5 6 7 VDC 1 X_5 0.54 0.32 0.06 0.25 X_6 0.09 0.53 0.12 0.11 X_7 0.23 0.58 0.03 0.25 X_8 0.20 0.62 0.08 0.14 X_9 0.29 0.52 0.04 0.35 X_17 0.60 0.30 0.10 0.17 X_21 0.19 0.24 0.07 0.63 X_24 0.78 0.22 0.29 0.45 X_25 0.68 0.35 0.18 0.42 X_26 0.56 0.35 0.14 0.60 X_27 0.30 0.21 0.54 0.31 X_28 0.77 0.18 0.08 0.29 X_29 0.35 0.15 0.18 0.69 X_32 0.34 0.40 0.10 0.13 X_33 0.31 0.21 0.08 0.46 X_34 0.71 0.22 0.12 0.48 X_35 0.18 0.17 0.09 0.63 X_37 0.51 0.28 0.10 0.60 VDC 2 X_39 0.71 0.12 0.27 0.14 0.01 0.32 0.09 X_40 0.33 0.57 0.28 0.03 0.05 0.04 0.01 X_41 0.69 0.08 0.07 0.23 0.01 0.42 0.05 X_42 0.17 0.24 1.00 0.13 0.03 0.04 0.00 X_43 0.20 0.60 0.37 0.09 0.02 0.03 0.04

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207 Table A 10. Continued. 1 2 3 4 5 6 7 X_44 0.75 0.07 0.18 0.17 0.02 0.12 0.12 X_45 0.47 0.16 0.50 0.17 0.06 0.06 0.04 X_47 0.81 0.33 0.15 0.11 0.01 0.20 0.09 X_48 0.86 0.23 0.08 0.12 0.02 0.09 0.00 X_49 0.40 0.12 0.31 0.64 0.10 0.09 0.02 X_51 0.69 0.27 0.21 0.27 0.04 0.14 0.15 X_52 0.78 0.12 0.13 0.18 0.00 0.19 0.04 X_53 0.09 0.31 0.36 0.26 0.04 0.20 0.12 X_54 0.21 0.33 1.04 0.09 0.04 0.01 0.01 X_56 0.26 0.19 0.60 0.39 0.07 0.08 0.10 X_60 0.17 0.33 0.39 0.31 0.03 0.11 0.37 X_61 0.23 0.75 0.31 0.20 0.05 0.06 0.08 X_62 0.18 0.02 0.18 1.28 0.09 0.04 0.12 X_70 0.87 0.32 0.18 0.09 0.06 0.12 0.06 X_71 0.59 0.22 0.20 0.38 0.01 0.12 0.13 X_72 0.45 0.16 0.31 0.67 0.19 0.01 0.06 X_73 0.18 0.02 0.18 1.28 0.09 0.04 0.12 X_74 0.16 0.28 0.05 0.60 0.05 0.02 0.32 X_75 0.20 0.84 0.07 0.05 0.06 0.04 0.02 VDC 3 X_1 0.75 0.19 0.28 0.01 0.01 0.17 X_2 0.71 0.30 0.31 0.12 0.07 0.26 X_3 0.48 0.45 0.40 0.13 0.08 0.34 X_4 0.76 0.20 0.26 0.02 0.00 0.18 X_10 0.37 0.08 0.56 0.06 0.05 0.13 X_11 0.53 0.26 0.48 0.22 0.08 0.31

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208 Table A 10. Continued. 1 2 3 4 5 6 7 X_12 0.06 0.08 0.45 0.02 0.28 0.16 X_13 0.20 0.19 0.49 0.11 0.09 0.15 X_14 0.17 0.18 0.62 0.10 0.01 0.27 X_15 0.26 0.09 0.63 0.05 0.10 0.45 X_18 0.27 0.04 0.52 0.13 0.05 0.16 X_19 0.10 0.12 0.54 0.18 0.00 0.36 X_20 0.23 0.10 0.53 0.20 0.00 0.22 X_23 0.61 0.18 0.31 0.23 0.04 0.40 X_30 0.34 0.18 0.45 0.13 0.06 0.18 X_31 0.30 0.03 0.59 0.09 0.09 0.01 X_36 0.23 0.24 0.52 0.03 0.05 0.30 X_38 0.40 0.63 0.26 0.04 0.03 0.43 X_46 0.49 0.48 0.23 0.06 0.02 0.55 X_50 0.59 0.25 0.26 0.08 0.12 0.43 X_55 0.41 0.36 0.23 0.04 0.01 0.94 X_57 0.60 0.31 0.27 0.03 0.04 0.49 X_58 0.24 0.36 0.29 0.12 0.25 0.52 X_59 0.35 0.22 0.27 0.24 0.07 1.89 X_63 0.75 0.20 0.25 0.12 0.07 0.55 X_64 0.20 0.41 0.34 0.17 0.08 0.56 X_65 0.44 0.31 0.27 0.06 0.04 0.78 X_66 0.41 0.22 0.19 0.08 0.14 0.87 X_67 0.58 0.17 0.22 0.19 0.07 0.42 X_68 0.73 0.20 0.23 0.06 0.12 0.38 X_69 0.35 0.22 0.27 0.24 0.07 1.89 X_76 0.25 0.26 0.70 0.24 0.08 0.14

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209 Table A 10. Continued. 1 2 3 4 5 6 7 X_81 0.27 0.45 0.47 0.05 0.04 0.31 X_82 0.12 0.28 0.65 0.12 0.00 0.37 X_83 0.34 0.23 0.61 0.19 0.02 0.02 X_84 0.24 0.13 0.66 0.08 0.08 0.10 X_86 0.25 0.61 0.32 0.08 0.05 0.60 X_87 0.10 0.29 0.71 0.29 0.06 0.28 X_89 0.27 0.53 0.34 0.07 0.01 0.27 X_91 0.31 0.57 0.38 0.02 0.03 0.13 X_92 0.05 0.13 0.61 0.10 0.02 0.25 X_99 0.07 0.31 0.66 0.04 0.05 0.13 X_100 0.38 0.70 0.26 0.01 0.03 0.31 VDC 4 X_16 0.27 0.26 0.00 X_77 0.21 0.63 0.00 X_78 0.40 0.58 0.07 X_79 0.41 0.54 0.00 X_80 0.58 0.34 0.01 X_85 0.26 0.57 0.06 X_88 0.72 0.18 0.01 X_90 0.77 0.15 0.01 X_93 0.10 0.54 0.04 X_94 0.28 0.46 0.05 X_95 0.30 0.56 0.01 X_96 0.19 0.67 0.08 X_97 0.18 0.58 0.13 X_98 0.17 0.59 0.01

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210 T able A 11 Frequencies, cycle lengths and spectral power density values for the Pacific Decadal Oscillation (PDO). PDO time series retrieved from http://research.jisao.washington.edu/pdo/ Frequency Cycle length (months) Spectral density 0.010416667 96.000000 16.7503 0.006944444 144.000000 16.08569 0.017361111 57.600000 15.88946 0.013888889 72.000000 12.06892 0.083333333 12.000000 10.85286 0.086805556 11.520000 9.179929 0.045138889 22.153846 8.745924 0.034722222 28.800000 5.536357 0.031250000 32.000000 5.178698 0.038194444 26.181818 4.893092

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211 Figure A 1. Simulated (solid black line) and observed (blue line) monthly Enhanced Vegetation Index (EVI2) time series. The simulations are results of applications of the selected Dynamic Factor Models II. For each cluster a time series simulation is shown for a community for which the Nash Sutcliffe coefficient ( C eff ) closely resembles the median C eff for the whole cluster.

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212 APPENDIX B SUPPLEMEN TARY MATERIALS FOR CHAPTER 5 Data and code for calculations (including explanations) can be found on 10.6084/m9.figshare.c.3933388 Table B 1 Cycle lengths (months) used to set the window length in Singular Spectrum Analysis (based on spectral density results). Cycle lengths (m) VDC EVI MAXT MINT P PET SM SR AMO PDO MEI 1 12 12 12 12 12 12 32 12 12 12 2 12 12 12 12 12 12 12 3 12 12 12 12 12 12 12 4 12 12 12 12 12 12 12

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213 Table B 2 Weighted adjacency matrices EVI MAXT MEANT MINT P PET SM AMO PDO MEI VDC 1 EVI 0.99 0.98 0.96 0.97 1.00 0.99 0.75 0.31 0.25 MAXT 0.99 0.98 0.96 0.97 1.00 0.99 0.92 0.46 0.13 MEANT 0.99 0.98 0.97 0.95 0.99 0.99 0.11 0.25 0.21 MINT 0.95 0.87 0.97 0.93 0.88 0.96 0.06 0.15 0.01 P 0.99 0.99 0.99 0.97 0.99 0.99 0.36 0.24 0.00 PET 0.99 0.99 0.97 0.95 0.94 0.99 0.65 0.32 0.02 SM 0.99 0.98 0.98 0.95 0.94 1.00 0.06 0.17 0.21 AMO 0.82 0.85 0.84 0.85 0.90 0.89 0.91 0.61 0.51 PDO 0.63 0.64 0.67 0.74 0.78 0.71 0.81 0.71 0.37 MEI 0.54 0.50 0.57 0.65 0.76 0.61 0.73 0.83 0.82 VDC 2 EVI 0.90 0.92 0.94 0.92 0.92 0.92 0.55 0.37 0.02 MAXT 0.76 0.99 0.98 0.94 0.98 0.96 0.21 0.16 0.20 MEANT 0.76 0.98 0.98 0.94 0.99 0.98 0.68 0.33 0.06 MINT 0.50 0.94 0.98 0.92 0.96 0.95 0.45 0.44 0.21 P 0.55 0.91 0.95 0.96 0.93 0.94 0.34 0.29 0.03 PET 0.81 0.98 0.98 0.97 0.93 0.96 0.60 0.26 0.14 SM 0.88 0.96 0.98 0.98 0.94 0.97 0.78 0.34 0.09 AMO 0.85 0.88 0.88 0.87 0.86 0.89 0.88 0.61 0.51 PDO 0.63 0.58 0.72 0.78 0.75 0.67 0.80 0.71 0.37 MEI 0.73 0.53 0.63 0.67 0.69 0.61 0.75 0.83 0.82 VDC 3 EVI 0.81 0.88 0.96 0.91 0.90 0.94 0.51 0.38 0.11 MAXT 0.67 0.93 0.97 0.94 0.99 0.95 0.60 0.46 0.14 MEANT 0.68 0.80 0.94 0.85 0.77 0.86 0.28 0.32 0.18 MINT 0.81 0.91 0.92 0.96 0.95 0.96 0.93 0.40 0.17 P 0.70 0.88 0.89 0.98 0.98 0.96 0.32 0.35 0.14 PET 0.65 0.89 0.87 0.97 0.92 0.95 0.66 0.49 0.05 SM 0.79 0.89 0.93 0.99 0.94 1.00 0.03 0.18 0.06 AMO 0.86 0.84 0.83 0.87 0.88 0.89 0.90 0.61 0.51 PDO 0.65 0.62 0.71 0.78 0.77 0.70 0.81 0.71 0.37 MEI 0.70 0.58 0.61 0.66 0.71 0.60 0.73 0.83 0.82 VDC 4 EVI 0.82 0.85 0.88 0.74 0.85 0.91 0.22 0.28 0.32 MAXT 0.62 0.98 0.97 0.92 0.99 0.99 0.56 0.28 0.13 MEANT 0.63 0.99 0.97 0.89 0.98 0.98 0.87 0.39 0.18 MINT 0.68 0.98 0.98 0.82 0.99 0.99 0.46 0.39 0.03 P 0.54 0.92 0.93 0.92 0.92 0.95 0.82 0.36 0.16 PET 0.81 0.97 0.96 0.97 0.78 0.99 0.42 0.25 0.12 SM 0.50 0.96 0.94 0.96 0.74 0.99 0.11 0.02 0.08 AMO 0.71 0.86 0.86 0.86 0.87 0.87 0.91 0.61 0.51 PDO 0.56 0.61 0.71 0.75 0.75 0.68 0.81 0.71 0.37 MEI 0.72 0.50 0.57 0.64 0.81 0.60 0.72 0.83 0.82

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214 Table B 3 Relevant lags identified with extended CCM. Lags are only relevant under the following circumstances, in this order: i) and ii) the lag is negative, indicating a true driver. A value of NA indicates that the highest occurred at lag 0 or a pos itive lag, but the significance requirement of a 5% difference between the highest and the lowest over a range of 6 to +6 lags was not met. EVI MAXT MEANT MINT P PET SM AMO PDO MEI VDC 1 EVI 5 NA 2 NA 3 5 6 MAXT 6 NA 3 4 2 2 3 MEANT 5 4 6 NA NA 5 MINT 5 0 6 2 4 P 5 4 6 0 4 4 PET 2 2 6 6 3 3 0 SM NA 2 NA 2 NA NA AMO 1 1 2 PDO 6 6 4 5 6 MEI 5 5 3 NA 2 VDC 2 EVI NA 6 6 5 NA NA MAXT 6 6 6 5 1 NA MEANT 1 0 0 0 NA NA MINT 1 3 0 4 4 P 5 NA 0 NA 5 PET 1 0 NA 6 5 4 SM NA NA NA 6 0 NA AMO 4 0 1 PDO 6 6 6 4 6 MEI 5 4 3 NA 2 VDC 3 EVI NA 1 1 6 NA NA MAXT 4 5 4 4 NA NA

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215 Table B 3 Continued. EVI MAXT MEANT MINT P PET SM AMO PDO MEI MEANT 5 4 6 NA 4 MINT 0 NA NA 3 NA 4 P 3 NA 5 1 NA 5 PET 3 NA 6 6 2 2 SM 6 1 4 6 2 3 AMO NA 6 5 1 2 PDO 6 6 6 4 5 6 MEI 6 5 NA NA 2 VDC 4 EVI NA 5 0 NA NA MAXT 6 6 1 5 NA MEANT 0 NA 1 NA 4 6 MINT NA 6 0 NA NA NA P 0 0 2 0 NA PET 1 2 2 2 NA 4 SM NA 5 NA 4 0 AMO 1 1 PDO 6 6 6 4 5 6

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216 Figure B 1. Observed, area weighted time series for each VDC

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217 Figure B 2 Results of Singular Value Decomposition (VDC) of time series of VDC 1. From left to right: eigenvectors, scatterplots of pairs of eigenvectors, and weighted correlation plots of pairs of eigenvectors

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218 Figure B 2 Continued.

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219 Figure B 2 Continued.

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220 Figure B 2 Continued.

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221 Figure B 3 Results of Singular Value Decomposition (VDC) of time series of VDC 2 From left to right: eigenvectors, scatterplots of pairs of eigenvectors, and weighted correlation plots of pairs of eigenvectors

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222 Figure B 3 Continued.

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223 Figure B 3 Continued.

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224 Figure B 3 Continued.

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225 Figure B 4 Results of Singular Value Decomposition (VDC) of time series of VDC 3. From left to right: eigenvectors, scatterplots of pairs of eigenvectors, and weighted correlation plots of pairs of eigenvectors

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226 Figure B 4 Continued.

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227 Figure B 4 Continued.

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228 Figure B 4 Continued.

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229 Figure B 5 Results of Singular Value Decomposition (VDC) of time series of VDC 4. From left to right: eigenvectors, scatterplots of pairs of eigenvectors, and weighted correlation plots of pairs of eigenvectors

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230 Figure B 5 Co ntinued.

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231 Figure B 5 Continued.

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232 Figure B 5 Continued.

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233 Figure B 6 Results of Singular Value Decomposition (VDC) of time series of climate indices a) eigenvectors, b) scatterplots of pairs of eigenvectors, and c) weighted correlation plots of pairs of eigenvectors

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234 Figure B 7 Lineplots and heatmaps of original and reconstructed time series of all variables for all 4 VDCs: maximum, mean and minimum temperature, precipitation, potential evapotranspiration and soil moisture (A = VDC 1, B = VDC 2, C = VDC 3, D = VDC 4). In order: maximum temperature, mean temperature, minimum temperature, precipitation, potential evapotranspiration, soil moisture and climate indices. Climate variables (AMO, PDO, MEI) are not VDC related. First column i s observed data, second column reconstructed. Months on th e x axis for the first two columns of plots.

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235 Figure B 7 Continued.

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236 Figure B 7 Continued.

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237 Figure B 7 Continued.

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238 Figure B 7 Continued.

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239 Figure B 7 Continued.

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240 Figure B 7 Continued.

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241 Figure B 8. Nonlinear cross prediction skill to determine stationarity of signals, per VDC. Five segments are tested (black lines), and an average is calculated across tests (red line).

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242 Figure B 9. Networks of cross mapping skill ( ) of deter ministic signals ( ) per VDC, after testing for false positives due to synchronicity. Bidirectional causality between minimum, mean, maximum temperature, precipitation, potential evapotransporation and soil moisture a re not shown. Species richness did not have a deterministic signal, so cross mapping skill could not be determined. EVI = Enhanced Vegetation Index 2, MAXT = maximum temperature, MEANT = mean temperature, MINT = minimum temperature, P = precipitation, PET = potential evapotranspiration, SM = soil moi sture AMO = Atlantic Multidecadal Oscillation, PDO = Pacific Decadal Oscillation, MEI = Multivariate ENSO Index.

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243 APPENDIX C ADDITIONAL NOTES ON GRANGER CAUSALITY ANALYSIS Granger P rediction CG analysis is more traditional causality analyses that we can apply to variables (systems) that do not pass the tests for stationarity or (low dimensional) determinism. The basic tenet for GC is that if the prediction of a variable is improved by the inclusion of another var formalized this with a series of linearized models ( G ranger, 1969 ) In order to remove seasonality, which could bias the results to indicate causality due to strong corresponding seasonality in two time series, we applied Multivariate Singular Spectrum Analysis (MSSA). This method is similar to SSA, but i t estimates signals that a number of time series have in common and allows for signal reconstruction for each time series separately. After removal of these shared seasonalities for each VDC, GC analysis was applied to the remainders of each time series. F or GC analysis, time series needed to be stationary so any remaining trends over time needed to be removed. All time series were evaluated for their order of integration with the KPSS test and differentiated where necessary. On the resulting time series, V ector Autoregression (VAR) was applied; it captures linear interdependencies between multiple variables while also taking into account the stochastic nature with the autoregressive components. The first VAR model for Y consists of components with p lagged vectors of the available variables (including Y ) and an error component: (C 1) in which Y is the variable that is being tested for being driven by X Z is the collection of all other variables, a b and c are coefficients (for c a collection of

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244 coefficients for each variable in Z ), is the error component and p is the appropriate lag. The latter was determined by first developing models for lags 1 12. The residuals were checked for autocorrelation with the Ljung Box test, and models with autocorrelated residuals were discarded. Well specified models should have residuals that are free of autocorrelation. Next, the Aikaike Information Criterion (AIC) wa s calculated for the remaining models, and out of these, the model with the lowest AIC was selected as the best model. Next, using the same p a second VAR model is developed without variable X the variable we want to test for Granger causing Y : (C 2) If the first model (with X ) significantly improves the prediction of Y (i.e. the variance contained in is less than in ), X is said to Granger cause Y This is measured with an F statistic: (C 3) with RSS the residual sum of squares for respectively VAR model 2 and VAR model 1. If the presence of Z mediates any influence from X b i will equal to zero, and the F statistic will be zero since the error term has not changed. Conversely, less variance contained in generates a positive F statistic. The null hypothesis is that there is no causality between variables, with Because of the presence of Z th is approach only considers X and Y Other variables could (indirectly) affect this relationship, and by taking into account this influence, otherwise misleading links ar e removed. Note that the results of Granger analysis (or the VARs built) are not necessarily predictive tools, since they do not evaluate goodness of fit specifically nor evaluate which covariates to

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245 include or exclude. They give an indication of (potentia l) drivers of variables, which can be used in the development of predictive models. Results for Granger P rediction GC analysis was applied to VDC 4 (see Chapter 3): since the EVI signal in VDC 4 violated the stationarity requirement (Chapter 5), this was the alternative causality test. This way we could also test the CCM and GC results for agreement. The same variables that were used in the CCM analysis were used in this test. Species richness was also included in this analysis it was excluded from the C CM analysis since no MSSA. Table C 1 and Figure C 1 summarizes the GC results. Tables C 2 and C 3 contain more details on the VAR models and full GC analysis. Take note tha t while p values give a relative indication as to how much improvement a variable brings to predicting another, GC analysis does not assign any strength to causal relationships. This analysis shows a markedly different picture than CCM, with less dense cau sality networks. Comparison with the previous analyses casts doubts on the completeness of the causal networks and the results themselves. The GC analysis captures some of causality that was also identified with CCM that we would continue to see, such as t he influence of EVI on minimum, maximum and mean temperature. Many causal relationships that we expected to see are not identified with GC analysis, especially the relationships between biophysical variables themselves (Table 5 3 and 5 4). There are effect s from variables onto the PDO, and from the MEI to a variable in GC analysis, while CCM highlights the AMO as a central climate index. These variables do not differ between VDCs, so results should be similar. Previous studies have found that GC analysis mi sidentifies or misses causal relationships in comparison to CCM for known

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246 systems (Lusch et al., 2016; Sugihara et al., 2012) and we conclude this is also the case here. The only indication from this analysis is that the causality from EVI onto maximum, mean and minimum temperature potentially increases. However, we deem the res ults unsuitable as a representation of the complete causal network for the system. Discussion In terms of methodology, as a result from these tests we would caution against using GC analyses as a method to determine causality until there is a better understanding of the conditions that affect performance of the analyses. Recent research has shown that this method can give different results when input s are only slightly changed, and that accuracy varies with the density of the networks being estimated (Lusch et al., 2016) For this study, where input data are either from reanalysis sources or re mote sensing, relying on GC would carry risk. We suspect that the EVI data are subject to considerable noise due to the difficulty of measuring reflectance in the tropics during times of high cloud cover and fires. The effect that this has on GC analysis i s unknown. While GC is spreading in popularity in environmental sciences (Damos, 2016; Detto et al., 2012; B. Jiang et al., 2015; Kaufmann et al., 2003; 2004b; Notaro et al., 2006; Papagiannopoulou et al., 2017; Tuttle and Salvucci, 2016) and many variations have been developed on the original concept, it is not advised to use it as a tool to do causal network mapping.

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247 Table C 1. Results of Granger causality analysis for VDC 4. A variable Granger causes another variable if The Nash Sutcliffe Coefficient of Efficiency (NSE) indic ates the goodness of fit of the full model (all variables included). Variable Granger causes Order of AR model Ljung Box p value NSE of full model F statistic p value EVI MAXT 1 0.25 0.29 0.02 0.03 MEI 0.02 0.01 EVI MEANT 1 0.36 0.31 0.12 0.00 MAXT 0.02 0.04 MEI 0.03 0.00 EVI MINT 10 0.16 0.76 0.20 0.00 MEI AMO 2 0.05 0.11 0.03 0.03 MAXT PDO 6 0.59 0.27 0.07 0.02

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248 Table C 2 VAR models with p value for the Ljung Box test > 0.05 Variable AR order AIC NSE Ljung Box test: p value Cluster 1 EVI 2 0.51 0.37 0.48 EVI 3 0.50 0.39 0.25 EVI 4 0.50 0.41 0.21 EVI 5 0.50 0.44 0.73 EVI 6 0.49 0.45 0.54 EVI 7 0.49 0.48 0.60 EVI 8 0.48 0.53 0.61 EVI 9 0.48 0.57 0.10 EVI 10 0.47 0.60 0.44 EVI 11 0.47 0.67 0.43 EVI 12 0.49 0.70 0.08 MAXT 1 0.42 0.42 0.43 MAXT 2 0.45 0.45 0.89 MAXT 3 0.48 0.48 0.69 MAXT 4 0.52 0.54 0.53 MAXT 5 0.53 0.58 0.28 MAXT 6 0.54 0.60 0.52 MAXT 7 0.53 0.62 0.39 MAXT 8 0.54 0.64 0.62 MAXT 9 0.58 0.67 0.42 MAXT 10 0.62 0.69 0.23 MAXT 11 0.66 0.71 0.12 MAXT 12 0.68 0.73 0.29 MEANT 1 0.78 0.26 0.55 MEANT 2 0.78 0.29 0.68 MEANT 3 0.77 0.34 0.80 MEANT 4 0.77 0.39 0.65 MEANT 5 0.76 0.46 0.66 MEANT 6 0.75 0.49 0.91 MEANT 7 0.75 0.53 0.83 MEANT 8 0.74 0.57 0.65 MEANT 9 0.74 0.60 0.59 MEANT 10 0.74 0.63 0.42 MEANT 11 0.76 0.67 0.12 MEANT 12 0.80 0.69 0.16 MINT 1 1.33 0.44 0.11 MINT 2 1.33 0.50 0.67 MINT 3 1.35 0.52 0.61 MINT 4 1.37 0.56 0.44 MINT 5 1.41 0.60 0.72 MINT 6 1.42 0.62 0.73 MINT 7 1.46 0.67 0.78 MINT 8 1.47 0.70 0.63 MINT 9 1.46 0.72 0.59 MINT 10 1.46 0.75 0.49 MINT 11 1.51 0.77 0.15 MINT 12 1.57 0.79 0.12 P 1 0.77 0.25 0.41 P 2 0.77 0.28 0.32 P 3 0.77 0.32 0.85 P 4 0.78 0.33 0.14

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249 Table C 2 Continued. Variable AR order AIC NSE Ljung Box test: p value P 7 0.91 0.45 0.17 P 8 0.92 0.48 0.24 P 9 0.92 0.52 0.35 P 10 0.92 0.56 0.31 P 11 0.94 0.58 0.08 P 12 0.97 0.64 0.07 PET 2 1.51 0.65 0.57 PET 3 1.71 0.69 0.13 PET 4 1.71 0.72 0.38 PET 5 1.77 0.75 0.71 PET 8 1.81 0.80 0.11 PET 10 1.90 0.84 0.09 PET 12 2.17 0.88 0.06 SM 5 3.18 0.75 0.41 SM 6 3.30 0.76 0.62 SM 7 3.31 0.78 0.40 SM 8 3.34 0.79 0.30 SM 9 3.33 0.81 0.39 SM 10 3.33 0.82 0.59 SM 11 3.34 0.82 0.21 SM 12 3.33 0.84 0.29 SR 3 1.10 0.36 0.08 SR 4 1.09 0.40 0.38 SR 5 1.12 0.47 0.06 SR 8 1.13 0.56 0.06 SR 9 1.16 0.59 0.08 SR 11 1.19 0.67 0.06 AMO 1 2.02 0.73 0.37 AMO 2 2.01 0.75 0.41 AMO 3 2.00 0.77 0.61 AMO 4 2.00 0.79 0.24 AMO 5 1.99 0.80 0.33 AMO 6 1.98 0.80 0.30 AMO 7 1.99 0.81 0.26 AMO 8 2.00 0.83 0.32 AMO 9 2.00 0.84 0.22 AMO 10 1.99 0.85 0.05 PDO 6 1.59 0.30 0.36 PDO 7 1.59 0.34 0.26 PDO 8 1.58 0.38 0.37 PDO 9 1.58 0.42 0.30 PDO 10 1.57 0.45 0.50 PDO 11 1.56 0.47 0.45 PDO 12 1.57 0.52 0.09 MEI 1 2.56 0.18 0.38 MEI 3 2.55 0.27 0.06 MEI 4 2.57 0.32 0.39 MEI 5 2.56 0.37 0.61 MEI 6 2.56 0.40 0.65 MEI 7 2.56 0.43 0.49 MEI 8 2.56 0.46 0.31 MEI 9 2.57 0.49 0.15 MEI 10 2.56 0.56 0.08

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250 Table C 2 Continued. Variable AR order AIC NSE Ljung Box test: p value MEI 11 2.56 0.59 0.09 MEI 12 2.56 0.61 0.15 Cluster 2 EVI 10 0.34 0.66 0.08 EVI 11 0.36 0.69 0.12 EVI 12 0.35 0.71 0.13 MAXT 1 0.39 0.45 0.35 MAXT 3 0.49 0.59 0.37 MAXT 4 0.51 0.59 0.37 MAXT 5 0.51 0.60 0.37 MAXT 6 0.53 0.63 0.36 MAXT 7 0.53 0.66 0.39 MAXT 8 0.54 0.69 0.86 MAXT 9 0.54 0.71 0.81 MAXT 10 0.60 0.74 0.73 MAXT 11 0.69 0.77 0.76 MAXT 12 0.68 0.80 0.38 MEANT 1 0.88 0.30 0.57 MEANT 2 0.87 0.33 0.15 MEANT 3 0.87 0.44 0.22 MEANT 4 0.86 0.46 0.47 MEANT 5 0.86 0.47 0.38 MEANT 6 0.86 0.50 0.37 MEANT 7 0.86 0.55 0.19 MEANT 8 0.85 0.59 0.59 MEANT 9 0.84 0.61 0.70 MEANT 10 0.85 0.66 0.71 MEANT 11 0.90 0.69 0.94 MEANT 12 0.94 0.74 0.61 MINT 1 1.31 0.44 0.05 MINT 2 1.30 0.49 0.33 MINT 3 1.33 0.56 0.22 MINT 4 1.34 0.57 0.49 MINT 5 1.38 0.59 0.28 MINT 6 1.39 0.61 0.37 MINT 7 1.39 0.65 0.19 MINT 8 1.38 0.70 0.41 MINT 9 1.40 0.71 0.55 MINT 10 1.40 0.75 0.56 MINT 11 1.47 0.77 0.92 MINT 12 1.52 0.81 0.61 P 1 0.77 0.29 0.19 P 2 0.78 0.35 0.17 P 3 0.80 0.41 0.30 P 4 0.80 0.43 0.10 P 6 0.90 0.51 0.17 P 7 0.93 0.54 0.75 P 8 0.93 0.56 0.83 P 9 0.92 0.58 0.45 P 10 0.92 0.64 0.68 P 11 0.92 0.66 0.65 P 12 0.91 0.68 0.60

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251 Table C 2 Continued. Variable AR order AIC NSE Ljung Box test: p value PET 3 1.57 0.64 0.06 PET 5 1.67 0.69 0.07 PET 7 1.72 0.73 0.10 PET 8 1.72 0.75 0.14 PET 9 1.73 0.77 0.08 PET 10 1.78 0.80 0.11 PET 11 1.84 0.82 0.24 PET 12 2.00 0.85 0.11 SM 4 2.74 0.67 0.64 SM 5 2.76 0.69 0.64 SM 6 2.78 0.71 0.64 SM 7 2.84 0.72 0.43 SM 9 2.90 0.78 0.11 SM 10 2.89 0.79 0.13 SM 11 2.89 0.81 0.18 SR 3 0.55 0.99 0.07 SR 4 0.54 0.99 0.05 SR 5 0.53 0.99 0.17 SR 12 0.59 0.99 0.06 AMO 1 2.02 0.73 0.34 AMO 2 2.01 0.75 0.93 AMO 3 2.00 0.76 0.55 AMO 6 1.98 0.79 0.38 AMO 7 1.99 0.79 0.44 AMO 8 2.00 0.80 0.89 AMO 9 2.00 0.81 0.53 AMO 10 1.99 0.83 0.67 AMO 11 1.98 0.85 0.51 AMO 12 1.98 0.86 0.31 PDO 6 1.59 0.30 0.34 PDO 7 1.59 0.33 0.80 PDO 8 1.58 0.35 0.76 PDO 9 1.58 0.39 0.97 PDO 10 1.57 0.44 0.15 PDO 11 1.56 0.48 0.58 PDO 12 1.57 0.51 0.27 MEI 1 2.56 0.16 0.54 MEI 3 2.55 0.27 0.10 MEI 4 2.57 0.34 0.59 MEI 5 2.56 0.39 0.87 MEI 6 2.56 0.43 0.79 MEI 7 2.56 0.44 0.68 MEI 8 2.56 0.50 0.26 MEI 9 2.57 0.52 0.06 MEI 10 2.56 0.55 0.27 MEI 11 2.56 0.59 0.19 MEI 12 2.56 0.62 0.06 Cluster 3 EVI 2 0.71 0.39 0.82 EVI 3 0.71 0.40 0.68 EVI 4 0.70 0.42 0.34 EVI 5 0.70 0.47 0.34

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252 Table C 2 Continued. Variable AR order AIC NSE Ljung Box test: p value EVI 6 0.69 0.50 0.16 EVI 10 0.67 0.62 0.07 EVI 11 0.67 0.65 0.05 MAXT 1 0.72 0.23 0.89 MAXT 2 0.71 0.29 0.72 MAXT 3 0.71 0.35 0.34 MAXT 4 0.71 0.37 0.59 MAXT 5 0.70 0.40 0.61 MAXT 6 0.70 0.43 0.69 MAXT 7 0.69 0.46 0.56 MAXT 8 0.69 0.53 0.38 MAXT 9 0.68 0.56 0.28 MAXT 10 0.68 0.59 0.10 MAXT 11 0.70 0.61 0.19 MAXT 12 0.72 0.65 0.11 MEANT 1 0.61 0.42 0.25 MEANT 2 0.65 0.48 0.93 MEANT 3 0.66 0.51 0.59 MEANT 4 0.67 0.53 0.87 MEANT 5 0.68 0.56 0.89 MEANT 6 0.68 0.59 0.77 MEANT 7 0.69 0.62 0.61 MEANT 8 0.72 0.65 0.28 MEANT 9 0.77 0.67 0.32 MEANT 10 0.85 0.69 0.13 MEANT 11 0.88 0.71 0.28 MEANT 12 0.89 0.74 0.11 MINT 1 1.37 0.46 0.09 MINT 2 1.36 0.54 0.60 MINT 3 1.38 0.57 0.86 MINT 4 1.42 0.59 0.51 MINT 5 1.44 0.62 0.87 MINT 6 1.45 0.65 0.89 MINT 7 1.46 0.69 0.69 MINT 8 1.45 0.71 0.12 MINT 9 1.45 0.72 0.19 MINT 10 1.48 0.75 0.08 MINT 11 1.55 0.76 0.15 P 1 0.83 0.23 0.40 P 2 0.82 0.30 0.13 P 3 0.83 0.34 0.44 P 4 0.83 0.37 0.21 P 5 0.87 0.45 0.17 P 6 0.90 0.47 0.29 P 7 0.92 0.49 0.24 P 8 0.93 0.51 0.60 P 9 0.93 0.56 0.39 P 10 0.92 0.60 0.53 P 11 0.93 0.62 0.82 P 12 0.95 0.65 0.70 PET 3 1.64 0.65 0.06 PET 4 1.64 0.69 0.32 PET 5 1.73 0.71 0.15

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253 Table C 2 Continued. Variable AR order AIC NSE Ljung Box test: p value PET 8 1.76 0.79 0.27 PET 9 1.76 0.82 0.40 PET 10 1.86 0.84 0.54 PET 11 1.93 0.85 0.65 PET 12 2.19 0.88 0.10 SM 5 3.14 0.93 0.33 SM 6 3.13 0.94 0.21 SM 7 3.16 0.94 0.06 SM 9 3.18 0.95 0.14 SM 10 3.18 0.95 0.16 SM 11 3.18 0.96 0.41 SM 12 3.17 0.96 0.36 SR 2 1.01 0.59 0.07 SR 3 1.01 0.60 0.20 SR 4 1.03 0.62 0.22 SR 5 1.03 0.64 0.45 SR 10 1.08 0.76 0.13 AMO 1 2.02 0.73 0.35 AMO 2 2.01 0.75 0.82 AMO 3 2.00 0.76 0.59 AMO 4 2.00 0.77 0.22 AMO 5 1.99 0.78 0.18 AMO 6 1.98 0.78 0.14 AMO 7 1.99 0.79 0.36 AMO 8 2.00 0.80 0.95 AMO 9 2.00 0.81 0.63 AMO 10 1.99 0.82 0.21 AMO 12 1.98 0.86 0.06 PDO 6 1.58 0.30 0.38 PDO 7 1.58 0.34 0.91 PDO 8 1.57 0.37 0.86 PDO 9 1.56 0.43 0.66 PDO 10 1.56 0.45 0.27 PDO 11 1.55 0.49 0.23 MEI 1 2.56 0.17 0.28 MEI 4 2.57 0.33 0.23 MEI 5 2.56 0.37 0.41 MEI 6 2.56 0.41 0.54 MEI 7 2.56 0.43 0.69 MEI 8 2.56 0.48 0.36 MEI 9 2.57 0.52 0.14 MEI 10 2.56 0.53 0.24 MEI 11 2.56 0.58 0.34 MEI 12 2.56 0.62 0.24 Cluster 4 EVI 2 0.52 0.31 0.71 EVI 5 0.54 0.46 0.22 EVI 6 0.54 0.47 0.32 EVI 7 0.53 0.50 0.23 EVI 8 0.53 0.55 0.13 EVI 9 0.52 0.58 0.10 EVI 10 0.54 0.63 0.08

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254 Table C 2 Continued. Variable AR order AIC NSE Ljung Box test: p value MAXT 1 0.46 0.45 0.96 MAXT 2 0.52 0.47 0.67 MAXT 3 0.54 0.49 0.94 MAXT 4 0.56 0.52 0.19 MAXT 5 0.57 0.56 0.13 MAXT 6 0.58 0.57 0.09 MAXT 7 0.57 0.62 0.08 MAXT 8 0.60 0.65 0.55 MAXT 9 0.63 0.67 0.49 MAXT 10 0.68 0.70 0.21 MEANT 1 0.79 0.22 0.80 MEANT 2 0.78 0.25 0.65 MEANT 3 0.78 0.30 0.94 MEANT 4 0.77 0.32 0.09 MEANT 5 0.76 0.40 0.12 MEANT 6 0.76 0.44 0.08 MEANT 7 0.75 0.52 0.05 MEANT 8 0.75 0.56 0.58 MEANT 9 0.74 0.58 0.37 MEANT 10 0.74 0.61 0.12 MINT 1 1.39 0.46 0.44 MINT 2 1.38 0.49 0.80 MINT 3 1.40 0.51 0.40 MINT 8 1.49 0.71 0.36 MINT 9 1.50 0.72 0.33 MINT 10 1.53 0.74 0.08 P 9 0.74 0.63 0.05 P 10 0.78 0.65 0.16 PET 2 1.43 0.60 0.14 PET 3 1.60 0.64 0.17 PET 4 1.60 0.67 0.86 PET 5 1.67 0.69 0.69 PET 6 1.67 0.72 0.13 PET 8 1.70 0.76 0.22 PET 9 1.69 0.80 0.52 PET 10 1.80 0.82 0.65 PET 11 1.84 0.83 0.28 PET 12 2.14 0.86 0.12 SM 4 3.22 0.76 0.26 SM 5 3.23 0.78 0.55 SM 6 3.37 0.79 0.82 SM 7 3.38 0.80 0.37 SM 8 3.43 0.82 0.56 SM 9 3.42 0.82 0.67 SM 10 3.42 0.83 0.43 SM 11 3.44 0.85 0.38 SM 12 3.44 0.87 0.34 SR 2 1.92 0.67 0.27 SR 3 1.93 0.69 0.47 SR 4 1.92 0.70 0.10 SR 10 1.94 0.81 0.11 SR 12 1.98 0.84 0.16 AMO 1 2.02 0.73 0.25

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255 Table C 2 Continued. Variable AR order AIC NSE Ljung Box test: p value AMO 2 2.01 0.74 0.77 AMO 3 2.00 0.75 0.52 AMO 4 2.00 0.76 0.21 AMO 5 1.99 0.78 0.16 AMO 6 1.98 0.78 0.31 AMO 7 1.99 0.78 0.59 AMO 8 2.00 0.79 0.87 AMO 9 2.00 0.80 0.95 AMO 10 1.99 0.81 0.66 AMO 11 1.98 0.82 0.40 AMO 12 1.98 0.84 0.29 PDO 6 1.59 0.37 0.61 PDO 7 1.59 0.40 0.25 PDO 8 1.58 0.43 0.51 PDO 9 1.58 0.46 0.23 PDO 10 1.57 0.50 0.22 PDO 11 1.56 0.52 0.28 MEI 1 2.56 0.19 0.38 MEI 4 2.57 0.33 0.33 MEI 5 2.56 0.37 0.56 MEI 6 2.56 0.40 0.54 MEI 7 2.56 0.44 0.71 MEI 8 2.56 0.49 0.22 MEI 9 2.57 0.51 0.23 MEI 10 2.56 0.53 0.14 MEI 11 2.56 0.57 0.13 MEI 12 2.56 0.61 0.27

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256 Table C 3 Granger causality test results for all variables (at selected AR order) Variable Granger causes AR order F statistic p value Cluster 1 MAXT EVI 2 0.01 0.42 MEANT EVI 2 0.02 0.10 MINT EVI 2 0.03 0.03 P EVI 2 0.02 0.07 PET EVI 2 0.01 0.30 SM EVI 2 0.01 0.39 SR EVI 2 0.02 0.05 AMO EVI 2 0.02 0.07 PDO EVI 2 0.00 0.83 MEI EVI 2 0.02 0.14 EVI MAXT 12 0.04 0.93 MEANT MAXT 12 0.18 0.02 MINT MAXT 12 0.21 0.01 P MAXT 12 0.05 0.84 PET MAXT 12 0.07 0.67 SM MAXT 12 0.08 0.57 SR MAXT 12 0.09 0.39 AMO MAXT 12 0.06 0.82 PDO MAXT 12 0.08 0.50 MEI MAXT 12 0.07 0.72 EVI MEANT 12 0.05 0.83 MAXT MEANT 12 0.17 0.03 MINT MEANT 12 0.25 0.00 P MEANT 12 0.08 0.57 PET MEANT 12 0.11 0.27 SM MEANT 12 0.07 0.63 SR MEANT 12 0.09 0.42 AMO MEANT 12 0.07 0.72 PDO MEANT 12 0.09 0.41 MEI MEANT 12 0.07 0.67 EVI MINT 12 0.07 0.65 MAXT MINT 12 0.14 0.08 MEANT MINT 12 0.17 0.03 P MINT 12 0.10 0.37 PET MINT 12 0.17 0.02 SM MINT 12 0.06 0.77 SR MINT 12 0.09 0.47 AMO MINT 12 0.09 0.48 PDO MINT 12 0.12 0.20 MEI MINT 12 0.07 0.61 EVI P 12 0.06 0.75 MAXT P 12 0.12 0.18 MEANT P 12 0.08 0.51 MINT P 12 0.07 0.61 PET P 12 0.07 0.64 SM P 12 0.06 0.74 SR P 12 0.07 0.71 AMO P 12 0.13 0.14 PDO P 12 0.07 0.64 MEI P 12 0.06 0.73 EVI PET 12 0.04 0.93 MAXT PET 12 0.16 0.04

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257 Table C 3. Continued. Variable Granger causes AR order F statistic p value MEANT PET 12 0.17 0.03 MINT PET 12 0.17 0.03 P PET 12 0.04 0.95 SM PET 12 0.13 0.13 SR PET 12 0.11 0.23 AMO PET 12 0.05 0.89 PDO PET 12 0.08 0.54 MEI PET 12 0.06 0.82 EVI SM 8 0.04 0.45 MAXT SM 8 0.06 0.22 MEANT SM 8 0.07 0.13 MINT SM 8 0.08 0.05 P SM 8 0.04 0.57 PET SM 8 0.08 0.09 SR SM 8 0.06 0.25 AMO SM 8 0.05 0.29 PDO SM 8 0.03 0.71 MEI SM 8 0.04 0.52 EVI SR 11 0.11 0.13 MAXT SR 11 0.06 0.70 MEANT SR 11 0.06 0.69 MINT SR 11 0.03 0.93 P SR 11 0.13 0.06 PET SR 11 0.02 0.98 SM SR 11 0.12 0.08 AMO SR 11 0.10 0.18 PDO SR 11 0.06 0.62 MEI SR 11 0.05 0.80 EVI AMO 1 0.00 0.80 MAXT AMO 1 0.00 0.48 MEANT AMO 1 0.00 0.62 MINT AMO 1 0.00 0.57 P AMO 1 0.00 0.87 PET AMO 1 0.00 0.60 SM AMO 1 0.00 0.94 SR AMO 1 0.01 0.23 PDO AMO 1 0.00 0.89 MEI AMO 1 0.00 0.59 EVI PDO 6 0.01 0.97 MAXT PDO 6 0.02 0.62 MEANT PDO 6 0.01 0.93 MINT PDO 6 0.01 0.91 P PDO 6 0.01 0.98 PET PDO 6 0.04 0.31 SM PDO 6 0.02 0.66 SR PDO 6 0.04 0.21 AMO PDO 6 0.05 0.12 MEI PDO 6 0.02 0.80 EVI MEI 9 0.09 0.10 MAXT MEI 9 0.03 0.85 MEANT MEI 9 0.03 0.86 MINT MEI 9 0.04 0.58 P MEI 9 0.08 0.15 PET MEI 9 0.03 0.85

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258 Table C 3. Continued. Variable Granger causes AR order F statistic p value SM MEI 9 0.06 0.32 SR MEI 9 0.03 0.84 AMO MEI 9 0.03 0.80 PDO MEI 9 0.06 0.31 Cluster 2 MAXT EVI 11 0.06 0.60 MEANT EVI 11 0.11 0.16 MINT EVI 11 0.11 0.15 P EVI 11 0.13 0.06 PET EVI 11 0.10 0.23 SM EVI 11 0.10 0.21 SR EVI 11 0.06 0.65 AMO EVI 11 0.07 0.54 PDO EVI 11 0.04 0.86 MEI EVI 11 0.08 0.41 EVI MAXT 11 0.14 0.04 MEANT MAXT 11 0.21 0.00 MINT MAXT 11 0.19 0.00 P MAXT 11 0.03 0.95 PET MAXT 11 0.13 0.05 SM MAXT 11 0.07 0.46 SR MAXT 11 0.10 0.18 AMO MAXT 11 0.06 0.65 PDO MAXT 11 0.11 0.12 MEI MAXT 11 0.06 0.63 EVI MEANT 12 0.15 0.07 MAXT MEANT 12 0.23 0.00 MINT MEANT 12 0.25 0.00 P MEANT 12 0.03 0.98 PET MEANT 12 0.16 0.05 SM MEANT 12 0.14 0.09 SR MEANT 12 0.14 0.08 AMO MEANT 12 0.10 0.29 PDO MEANT 12 0.12 0.16 MEI MEANT 12 0.08 0.59 EVI MINT 12 0.13 0.14 MAXT MINT 12 0.21 0.00 MEANT MINT 12 0.23 0.00 P MINT 12 0.04 0.93 PET MINT 12 0.16 0.04 SM MINT 12 0.11 0.22 SR MINT 12 0.12 0.17 AMO MINT 12 0.12 0.18 PDO MINT 12 0.13 0.15 MEI MINT 12 0.07 0.62 EVI P 7 0.04 0.33 MAXT P 7 0.06 0.14 MEANT P 7 0.06 0.12 MINT P 7 0.06 0.09 PET P 7 0.03 0.55 SM P 7 0.05 0.26 SR P 7 0.12 0.00 AMO P 7 0.09 0.02

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259 Table C 3. Continued. Variable Granger causes AR order F statistic p value PDO P 7 0.05 0.21 MEI P 7 0.01 0.99 EVI PET 12 0.17 0.02 MAXT PET 12 0.14 0.09 MEANT PET 12 0.18 0.02 MINT PET 12 0.17 0.03 P PET 12 0.03 0.97 SM PET 12 0.11 0.25 SR PET 12 0.14 0.09 AMO PET 12 0.10 0.31 PDO PET 12 0.11 0.29 MEI PET 12 0.07 0.70 EVI SM 9 0.08 0.13 MAXT SM 9 0.03 0.83 MEANT SM 9 0.04 0.63 MINT SM 9 0.03 0.76 P SM 9 0.06 0.28 PET SM 9 0.08 0.16 SR SM 9 0.05 0.46 AMO SM 9 0.09 0.10 PDO SM 9 0.09 0.07 MEI SM 9 0.09 0.10 EVI SR 12 0.07 0.61 MAXT SR 12 0.09 0.44 MEANT SR 12 0.11 0.25 MINT SR 12 0.08 0.60 P SR 12 0.04 0.93 PET SR 12 0.11 0.26 SM SR 12 0.07 0.64 AMO SR 12 0.07 0.61 PDO SR 12 0.16 0.05 MEI SR 12 0.03 0.97 EVI AMO 1 0.00 0.81 MAXT AMO 1 0.00 0.91 MEANT AMO 1 0.00 0.34 MINT AMO 1 0.00 0.32 P AMO 1 0.00 0.73 PET AMO 1 0.00 0.29 SM AMO 1 0.00 0.87 SR AMO 1 0.00 0.53 PDO AMO 1 0.00 0.81 MEI AMO 1 0.00 0.55 EVI PDO 6 0.03 0.52 MAXT PDO 6 0.03 0.35 MEANT PDO 6 0.03 0.44 MINT PDO 6 0.02 0.53 P PDO 6 0.05 0.15 PET PDO 6 0.02 0.57 SM PDO 6 0.02 0.57 SR PDO 6 0.02 0.69 AMO PDO 6 0.08 0.01 MEI PDO 6 0.04 0.21 EVI MEI 9 0.03 0.88 MAXT MEI 9 0.05 0.49

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260 Table C 3. Continued. Variable Granger causes AR order F statistic p value MEANT MEI 9 0.02 0.98 MINT MEI 9 0.01 0.99 P MEI 9 0.08 0.16 PET MEI 9 0.05 0.50 SM MEI 9 0.04 0.62 SR MEI 9 0.06 0.28 AMO MEI 9 0.03 0.83 PDO MEI 9 0.06 0.33 Cluster 3 MAXT EVI 2 0.01 0.22 MEANT EVI 2 0.01 0.51 MINT EVI 2 0.03 0.02 P EVI 2 0.02 0.10 PET EVI 2 0.02 0.15 SM EVI 2 0.00 0.65 SR EVI 2 0.01 0.48 AMO EVI 2 0.01 0.34 PDO EVI 2 0.01 0.36 MEI EVI 2 0.01 0.16 EVI MAXT 1 0.00 0.26 MEANT MAXT 1 0.00 0.72 MINT MAXT 1 0.02 0.01 P MAXT 1 0.00 0.75 PET MAXT 1 0.04 0.00 SM MAXT 1 0.00 0.58 SR MAXT 1 0.00 0.99 AMO MAXT 1 0.00 0.41 PDO MAXT 1 0.00 0.95 MEI MAXT 1 0.00 0.50 EVI MEANT 12 0.10 0.36 MAXT MEANT 12 0.09 0.39 MINT MEANT 12 0.08 0.60 P MEANT 12 0.08 0.54 PET MEANT 12 0.09 0.48 SM MEANT 12 0.10 0.33 SR MEANT 12 0.10 0.34 AMO MEANT 12 0.11 0.26 PDO MEANT 12 0.08 0.52 MEI MEANT 12 0.08 0.49 EVI MINT 11 0.08 0.34 MAXT MINT 11 0.09 0.27 MEANT MINT 11 0.10 0.18 P MINT 11 0.07 0.54 PET MINT 11 0.07 0.52 SM MINT 11 0.09 0.27 SR MINT 11 0.05 0.75 AMO MINT 11 0.08 0.35 PDO MINT 11 0.04 0.85 MEI MINT 11 0.06 0.66 EVI P 12 0.10 0.31 MAXT P 12 0.08 0.57 MEANT P 12 0.05 0.88 MINT P 12 0.04 0.93

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261 Table C 3. Continued. Variable Granger causes AR order F statistic p value PET P 12 0.07 0.67 SM P 12 0.07 0.63 SR P 12 0.09 0.48 AMO P 12 0.07 0.72 PDO P 12 0.05 0.86 MEI P 12 0.05 0.90 EVI PET 12 0.10 0.33 MAXT PET 12 0.12 0.19 MEANT PET 12 0.08 0.54 MINT PET 12 0.05 0.89 P PET 12 0.07 0.71 SM PET 12 0.12 0.19 SR PET 12 0.09 0.45 AMO PET 12 0.08 0.60 PDO PET 12 0.10 0.35 MEI PET 12 0.06 0.82 EVI SM 10 0.06 0.56 MAXT SM 10 0.06 0.45 MEANT SM 10 0.02 0.95 MINT SM 10 0.07 0.33 P SM 10 0.05 0.64 PET SM 10 0.12 0.04 SR SM 10 0.06 0.47 AMO SM 10 0.08 0.24 PDO SM 10 0.07 0.40 MEI SM 10 0.04 0.73 EVI SR 10 0.07 0.38 MAXT SR 10 0.03 0.93 MEANT SR 10 0.05 0.67 MINT SR 10 0.05 0.63 P SR 10 0.02 0.95 PET SR 10 0.06 0.46 SM SR 10 0.05 0.63 AMO SR 10 0.06 0.46 PDO SR 10 0.08 0.27 MEI SR 10 0.11 0.07 EVI AMO 1 0.01 0.20 MAXT AMO 1 0.00 0.61 MEANT AMO 1 0.00 0.44 MINT AMO 1 0.00 0.69 P AMO 1 0.00 0.89 PET AMO 1 0.00 0.58 SM AMO 1 0.00 0.80 SR AMO 1 0.00 0.29 PDO AMO 1 0.00 0.99 MEI AMO 1 0.00 0.47 EVI PDO 6 0.04 0.23 MAXT PDO 6 0.01 0.94 MEANT PDO 6 0.01 0.90 MINT PDO 6 0.02 0.69 P PDO 6 0.01 0.81 PET PDO 6 0.03 0.32 SM PDO 6 0.02 0.68 SR PDO 6 0.03 0.41

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262 Table C 3 Continued. Variable Granger causes AR order F statistic p value AMO PDO 6 0.06 0.05 MEI PDO 6 0.03 0.49 EVI MEI 9 0.08 0.16 MAXT MEI 9 0.05 0.45 MEANT MEI 9 0.05 0.44 MINT MEI 9 0.04 0.59 P MEI 9 0.11 0.03 PET MEI 9 0.03 0.88 SM MEI 9 0.07 0.25 SR MEI 9 0.04 0.63 AMO MEI 9 0.04 0.62 PDO MEI 9 0.091 0.081 Cluster 4 MAXT EVI 6 0.03 0.40 MEANT EVI 6 0.03 0.32 MINT EVI 6 0.03 0.49 P EVI 6 0.05 0.09 PET EVI 6 0.06 0.06 SM EVI 6 0.02 0.61 SR EVI 6 0.02 0.68 AMO EVI 6 0.03 0.51 PDO EVI 6 0.01 0.81 MEI EVI 6 0.01 0.84 EVI MAXT 10 0.03 0.90 MEANT MAXT 10 0.14 0.02 MINT MAXT 10 0.14 0.01 P MAXT 10 0.05 0.66 PET MAXT 10 0.03 0.86 SM MAXT 10 0.09 0.17 SR MAXT 10 0.10 0.10 AMO MAXT 10 0.07 0.31 PDO MAXT 10 0.07 0.31 MEI MAXT 10 0.06 0.46 EVI MEANT 1 0.01 0.06 MAXT MEANT 1 0.00 0.63 MINT MEANT 1 0.01 0.24 P MEANT 1 0.00 0.76 PET MEANT 1 0.07 0.00 SM MEANT 1 0.02 0.01 SR MEANT 1 0.01 0.08 AMO MEANT 1 0.01 0.14 PDO MEANT 1 0.00 0.96 MEI MEANT 1 0.00 0.99 EVI MINT 10 0.04 0.83 MAXT MINT 10 0.06 0.51 MEANT MINT 10 0.12 0.05 P MINT 10 0.05 0.66 PET MINT 10 0.04 0.72 SM MINT 10 0.10 0.12 SR MINT 10 0.08 0.27 AMO MINT 10 0.11 0.07 PDO MINT 10 0.06 0.56 MEI MINT 10 0.06 0.52

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263 Table C 3 Continued. Variable Granger causes AR order F statistic p value EVI P 10 0.03 0.88 MAXT P 10 0.04 0.77 MEANT P 10 0.02 0.96 MINT P 10 0.01 1.00 PET P 10 0.05 0.58 SM P 10 0.05 0.63 SR P 10 0.05 0.57 AMO P 10 0.04 0.85 PDO P 10 0.11 0.06 MEI P 10 0.04 0.85 EVI PET 12 0.05 0.86 MAXT PET 12 0.07 0.72 MEANT PET 12 0.09 0.41 MINT PET 12 0.10 0.31 P PET 12 0.03 0.98 SM PET 12 0.08 0.54 SR PET 12 0.08 0.51 AMO PET 12 0.10 0.37 PDO PET 12 0.07 0.64 MEI PET 12 0.05 0.90 EVI SM 12 0.16 0.05 MAXT SM 12 0.15 0.07 MEANT SM 12 0.14 0.09 MINT SM 12 0.12 0.18 P SM 12 0.07 0.70 PET SM 12 0.17 0.03 SR SM 12 0.10 0.38 AMO SM 12 0.16 0.05 PDO SM 12 0.13 0.13 MEI SM 12 0.12 0.18 EVI SR 12 0.13 0.13 MAXT SR 12 0.08 0.57 MEANT SR 12 0.09 0.45 MINT SR 12 0.10 0.37 P SR 12 0.02 1.00 PET SR 12 0.06 0.81 SM SR 12 0.09 0.46 AMO SR 12 0.12 0.18 PDO SR 12 0.07 0.70 MEI SR 12 0.06 0.76 EVI AMO 1 0.01 0.19 MAXT AMO 1 0.00 0.70 MEANT AMO 1 0.00 0.78 MINT AMO 1 0.00 0.75 P AMO 1 0.00 0.56 PET AMO 1 0.00 0.90 SM AMO 1 0.00 0.35 SR AMO 1 0.00 0.88 PDO AMO 1 0.00 0.90 MEI AMO 1 0.00 0.53 EVI PDO 6 0.10 0.00 MAXT PDO 6 0.07 0.03 MEANT PDO 6 0.05 0.12 MINT PDO 6 0.03 0.47

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264 Table C 3. Continued. Variable Granger causes AR order F statistic p value P PDO 6 0.04 0.19 PET PDO 6 0.05 0.09 SM PDO 6 0.02 0.54 SR PDO 6 0.02 0.59 AMO PDO 6 0.06 0.06 MEI PDO 6 0.03 0.34 EVI MEI 9 0.09 0.11 MAXT MEI 9 0.06 0.40 MEANT MEI 9 0.05 0.47 MINT MEI 9 0.05 0.49 P MEI 9 0.02 0.91 PET MEI 9 0.06 0.33 SM MEI 9 0.05 0.43 SR MEI 9 0.05 0.51 AMO MEI 9 0.03 0.83 PDO MEI 9 0.09 0.07

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265 Figure C 1. Conditional Granger causality ( p <0.05) results for VDC 1 and VDC 4. a) Granger causality from other variables onto EVI and climate indices for VDC 1, b) Granger causality from other variables onto EVI and climate indices for VDC 4, c) Granger causality from EVI and climate indices onto other v ariables for VDC 1, d) Granger causality from EVI and climate indoces onto other variables for VDC 4. Colors of the arrows indicate the range of the p values. EVI = Enhanced Vegetation Index 2, MAXT = maximum temperature, MEANT = mean temperature, MINT = m inimum temperature, P = precipitation, PET = potential evapotranspiration, SM = soil moisture, SR = species richness, AMO = Atlantic Multidecadal Oscillation, PDO = Pacific Decadal Oscillation, MEI = Multivariate ENSO Index.

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287 BIOGRAPHICAL SKETCH Geraldine Klarenberg is from The N etherlands. She holds a BSc/ MSc from Wageningen Univ ersity (the Netherlands) in irrigation and water m anagement She has lived in The Netherlands, Australia, Fiji, South Africa and the USA. She lives with her husband, two children, two stepchildren, 2 c ats and a dog in Gainesville, Florida USA