From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

MISSING IMAGE

Material Information

Title:
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
Physical Description:
Mixed Material
Creator:
Brad R Ruhfel
Matthew A Gitzendanner
Pamela S Soltis
Douglas E Soltis
J Gordon Burleigh
Publisher:
Biomed Central
Publication Date:

Notes

Abstract:
Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. Results: We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. Conclusions: Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads+Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.

Record Information

Source Institution:
University of Florida
Holding Location:
University of Florida
Rights Management:
All rights reserved by the source institution.
System ID:
AA00020058:00001

Full Text

PAGE 1

Erodium carvif olium Gossypium barbadense Pinus thunbergii Rhododendron simsii Thurnia sphaerocephala Pinus armandii Morus indica Bambusa emeiensis Lilium superbum Arabis hirsuta Ostreococcus tauri Megaleranthis saniculifolia Antirrhinum majus Meliosma aff. cuneifolia Epifagus virginiana Corynocarpus laevigata Monsonia speciosa Manihot esculenta Lobularia maritima Me d i cag o tru ncatula Pinus monophy lla Cycas taitungensis Prunus persi c a Oryza sativa var. japonica Pinus aristata Pycnoc o ccu s pr o v a s olii Castanea mollissi m a Nicotiana sylvestris Ecdeiocolea monostachya Cedrus deodara Volvox carteri Lept osira terrest ris Cuscuta gron ovi i Ferrocalamus rimosivaginus Agrostis stolonifera Piper cenocladum Pinus taeda Agapanthus praecox Lemna minor Phyllostachys propinqua Juncus effusus Dasypogon bromeliifolius Helicosporidium s p. Sparganium eurycarpum Chlorella vulgaris Pyramimonas parkeae Nic o t iana to m ent o s i f o rmi s Pinus mont i c ola An t hoc e r o s fo rmo s a e Oryza aust raliensis Phormium tenax Ehret ia acuminat a Ceratophyllum demersum Oedogonium cardiacum Liquidambar styraciflua Chlorokybus at mophyt icus Barbarea verna Lathyrus sativus Hydrocotyle s p. Gossypium herbaceum Pinus torreyana subsp. insularis Picea morrisonicola Aucuba japonica Phoradendron serotinum Huperzia lucidula Ephedr a equis e t ina Potamophila parviflora Pinus ponderosa Neoregelia carolinae Lar i x dec idua Zygnema circumcarinatum Panax gins eng Cucumis sat ivus Wolffia australiana Portulaca oleracea Oenot hera argillicola Lomandra longifolia Trif olium subt erraneum Nuphar advena Daucus carota Aneura mirabilis Phalaenopsis aphrodite Solanum bulbocastanum Pteridium aquilinum Selaginella uncinata Tradescantia ohiensis Neoastelia spectabilis Oocystis solitaria Pyrus pyrifolia Lolium perenne Cuscuta exaltata Ptilidium pulcherrimum Davidia involucrata Selaginella moellendorffii Chara vulgaris Gossypium darw ini i Cephalot axus wilsoniana Abolboda macrostachya Wolffiella lingulata Ravenea hildebrandtii Triticum aestivum S e s a m u m indic u m Gnet um parvif olium Pereskia sacharosa Phoenix dactylif e r a Oenot her a elat a Pisum sativum Saccharum hybridus Podocarpus totara Elaeis oleifera Gossypium tomentosum At ropa belladonna Thamnochortus insignis Oncidium sp. Jacobaea vul gari s Nymphaea alba Apostasia wallichii Scenedesmus obliquus Hev ea br a s iliens i s St aphylea colchica Marchantia polymorpha Festuca arundinacea Centrolepis monogyna Oryza meridionalis Broc chinia micrant h a Oryza ni v a r a Acorus americanus Oenothe ra pa rvi f l ora Musa acuminata Opuntia decumbens Kingia australis I llicium oligandrum Cycas micronesica Erodium te x anum Psilotum nudum Ol ea europaea subsp. europaea Ch l amydo m o nas reinhardti i Olimarabidopsis pumila Nandina domestica Neottia nidus-avis Pinus canariensis Silene latifolia Typha latifolia Cucumis melo Welwitschia mirabilis Plat anus occident alis Oryza rufipogon A Belosynapsis ciliat a Pinus contorta Agat his aust ralis E uonymu s am e r i c anus Anredera baselloides Pinus gerardiana Phaseolus vulgaris Joinvillea ascendens Tro c hodendr on ar alioides Anom o c hloa ma r ant oidea Theobroma cacao Ageratina adenophora Hesperaloe parvif lora Pinus resinosa Capsella bursa-pastoris Eu c aly p t u s globulus Maihuenia poeppigii Dunaliella salina Aethionema cordifolium Oryza sativa var. indica Nelum bo lut e a Yucca schidigera Silene conic a Cuscuta reflexa Ginkgo biloba Dillenia indica Asparagus officinalis Trachelium caeruleum Lepidium virginicum Buxus microphylla Albuca kirkii Olea woodiana Eleusine coracana Ilex cornuta Pinus peuc e Physcomitrella patens Pent a ctina rupic ola Populus alba Chaetosphaeridium globosum Chlorophytum rhizopendulum Cuscuta obtusiflora Crucihimalaya wallichii Cheilanthes lindheimeri Amborella trichopoda Portulacaria afra Nicotiana undulata Keteleeria davidiana Oxalis latifolia Solanum tuberosum Leersia tisserantii Jatropha curcas Fragaria vesca Arbutus unedo Gunnera manicata Brachyp o dium di sta c h yon Cathaya argyrophylla St igeoclonium helvet icum Glycine max Ipomoea purpurea Renealmia alpinia G uizot ia abyssinica Dendrocalamus latiflorus Colocasia esculenta Acorus calamus Angiopteris evecta Syntrichia ruralis F loy diella te rre stri s Nephroselmis olivacea Hosta ventricosa Drimys granadensis Microlaena stipoides Nolina at opocarpa Gossypium hirsutum Weingartia kargliana Gossypium thurberi Abies firma Parthenium argentatum Halocarpus kirkii Gossypium arboreum Cic e r ari eti num Nic o t iana tabac u m Plumbago auriculata Pinus banksiana Pinus rzedowskii Puya laxa Pedinomonas minor Pinus krempf i i Picea sitchensis Fagopyrum esculentum Oenot hera biennis Alsophila spinulosa Bambusa oldhamii Passiflora biflora Aethionema grandiflorum Lotus japonicus Pinus pinaster Anthriscus cerefoli u m Spirodela polyrhiza Rhizanthella gardneri Olea eur opaea subsp. m a r occana Blossfeldia liliputana Silene noct i f lora Staurastrum punctulatum Pinus me r kus i i Ximenia americana G eorgeant ha hexandra Equisetum arvense Arabidopsis thaliana Geranium palmatum Pseudotsuga sinensis Solanum lycopersicum C occomyxa s p. Draba nemorosa Mag nolia kw a n gsi e n s i s Bryop s i s hypnoides Pinus sibirica Phyllostachys edulis Quercus nigra Citrus sinensis Iris virginica Panicum virgat u m Chlorella variabilis Pinus strobus Larix occidentalis Strept o c haet a angusti f olia Chamaedorea seifrizii Lonicera japonica Nelumbo nucifera Pinus flexilis Spinacia oleracea Calycanthus floridus Micromonas pusilla Pinus attenuata Adiantum capillus-veneris Navia saxicola Dioscorea elephantipes Gossypium mustelinum Pinus torreyana subsp. torreyana Berberidopsis corallina Taiwania cryptomerioides Pinus ay a c a h uit e Jasminum nudiflorum O l tmannsiello p s i s vi r idis Ricinus communis Didierea madagascariensis Chloranthus spicatus Phyllostachys nigra Fosterella caulescens Pelargonium x sp. Schizomeris leibleinii Millettia pinnata Petroselinum crispum Mollugo verticillata Gossypium raimondii Parachlorella kessleri Populus trichocarpa Crithmum maritimum Pinus cembra Pandanus utilis Pinus leiophylla var. chihuahuana Pseudendoclonium akinetum Bulnesia arborea Pinus parvi f lor a v a r. pent aphy lla Rhynchoryza subulata Pinus lambertiana Franklinia alatamaha Silene vulgaris Nastu rtium offi c inale Ranunculus macranthus Coffea arabica Cornus florida Eleutherococcus senticosus Oryza rufipogon B Curculigo capitulata Isoetes flaccida Micromonas s p. Acidosasa purpurea Lactuca sativa Syngonanthus chrysanthus Pereskiopsis diguet i i Vitis vinifera Puelia olyrif ormis Monomast ix s p. Hordeum vulgare Heuchera sanguinea Eucalyptus grandis Liriodendron tulipifera Vigna radiata Sorghum bicolor Pi tcai r nia felic ian a Pinus squamata Coix lacryma-jobi Pinus albicaulis Potarophytum riparium Car i c a pa p a y a Oenothera glazioviana Mayaca fluviatilis F lagellaria indica Cyperus alternifolius M e s ost igma viride Indoc alam u s longiaur i t u s Pinus koraiensis Heliant hus annuus Pinus nelsonii Boea hygrometrica Oxypolis gr eenm anii Zea mays Cryptomeria japonica F i c u s sp. Olea europaea subsp. cuspidata Scaev ola aem ula Ner ium oleander Anethum graveolens 9 7 100 5 9 9 8 9 0 5 2 100 100 100 7 4 100 5 1 100 9 9 100 9 8 100 9 6 7 3 8 9 6 4 100 8 9 9 9 9 9 9 6 5 4 9 9 100 100 100 100 100 100 100 8 8 100 100 9 3 100 9 4 100 100 100 100 9 6 100 100 100 100 100 100 100 100 100 8 2 9 3 100 100 5 9 9 8 100 100 100 100 9 0 6 9 100 100 100 100 100 100 100 100 100 100 100 100 100 9 7 100 100 100 100 100 100 100 8 8 100 100 100 100 100 100 100 100 100 100 100 5 2 100 100 100 9 3 8 1 7 2 100 100 100 100 100 7 0 100 100 5 4 100 7 8 100 100 100 100 100 7 8 100 100 100 100 100 9 4 100 100 100 100 8 2 9 6 8 3 100 100 5 3 100 100 9 2 100 5 9 100 100 100 8 0 9 3 100 100 100 100 100 100 6 1 7 8 100 100 9 9 100 100 100 100 100 100 8 4 6 5 100 5 2 100 100 100 8 2 7 5 100 100 100 100 8 5 100 100 9 9 8 9 100 5 5 100 100 100 5 2 100 7 0 100 100 100 100 100 8 5 100 9 2 100 100 9 2 100 9 7 100 100 100 100 100 100 100 100 8 2 8 1 8 1 100 100 9 9 100 9 9 100 7 8 7 8 100 100 100 9 2 8 8 100 5 5 100 100 100 100 100 9 1 100 100 8 0 100 100 100 100 100 6 0 8 4 100 100 100 100 100 100 6 9 100 100 100 9 8 100 100 100 100 6 6 100 100 100 9 2 100 100 100 100 6 2 9 9 100 100 100 100 100 8 4 100 100 100 5 2 100 8 9 9 9 100 8 8 5 6 100 100 9 6 100 100 7 7 100 100 100 100 7 0 100 100 100 100 100 100 7 5 100 100 100 9 9 100 100 100 8 5 6 0 100 100 5 2 100 100 100 100 100 100 100 100 100 7 0 100 7 8 8 4 6 7 100 9 9



PAGE 1

F i c u s sp. Heuchera sanguinea Silene vulgaris Phoenix dactylifera Monsonia speciosa Agrostis stolonifera Wolffiella lingulata Cedrus deodara Anredera baselloides Drimys granadensis Hosta ventricosa Rhododendron simsii T hamnochort us insignis Phyllostachys edulis Jacobaea vulgaris E l eusi ne coracana Magnolia kwangsiensis Pisum sativum Oryza rufipogon A Pinus albicaulis P inus ger a r diana Chamaedorea seifrizii Phaseolus vulgaris Oryza australiensis Ximenia americana Dasypogon bromeliifolius Schizomeris leibleinii B elosynaps i s ciliat a Spirodela polyrhiza Meliosma aff. c uneif olia Scenedesmus obliquus Crucihimalaya wallichii Passif lora bif lora Crithmum maritimum Hydrocotyle sp. Huperzia luc idula P inus to rre y ana subsp. ins ular i s Nicotiana sylvestris F o ste r ella c aulescens Solanum lycopersicum Port ulacaria af r a Pseudotsuga sinensis Pycnococcus provasolii A n t i rrhinum majus Q uercus nigra Microlaena stipoides Centrolepis monogyna F loydiella t errest ris Cic e r a r iet inum Selaginella moellendorffii Pinus ayacahuite Lem na m inor Oryza rufipogon B Pinus nelsonii Cycas t ait ungensis Tra c helium caer uleum Volvox cart eri Puya laxa Panicum virgatum Neottia nidus E u c aly p t u s g r andis Liquidambar styraciflua Kingia australis Cucumis sativus Tro c hodendr on ar alioides Bambusa emeiensis Dillenia indica P o t a m ophila parvi f lor a W eingart ia k argliana Silene latifolia Iris virginica Anomochloa marantoidea Gossypium hirsutum Ravenea hildebrandt i i P inus thunber gii Manihot esculenta Pereskia sacharosa Pinus pinaster O n c idium sp. Taiwania cryptomerioides Cryptomeria japonica Corynocarpus laevigata Scaevola aemula Citrus sinensis O lea eur opaea ssp. m a r occana Pinus merkusii O limarabidopsis pumila Hevea brasiliensis Y u cca schidiger a Barbarea verna Renealmia alpinia Coix lacryma-jobi Lolium per enne Ptilid i um pul cherri mum Anethum graveolens Chloranthus spicatus Podocarpus totara Megaleranthis saniculifolia Neoastelia spectabil Chlamydomonas reinhardt i i G o ssypium raim ondii Oxypolis greenmanii Trifolium subterraneum Adi antum capillu s Parachlorella kessleri Aethionema grandiflorum Ranunculus macranthu s Anthriscus cerefolium Vigna radiata Sesamum indicum Cephalotaxus wilsoniana Thurnia sphaerocephala Populus trichocarpa Pinus lambertiana Ferrocalamus rimosivaginus C h l orokybus atmophyticus Coffea arabica Nuphar adv ena Agathis australis Draba nemorosa Aucuba japonica Wolffia australiana Leptosira terrestris Platanus occidentalis Syngonanthus chrysanthus Silene noctiflora Acidosasa purpurea Gnetum parvifolium Tradescant ia ohiensis Nicot iana t oment osif ormis Angiopteris evecta H e licospori d i um sp. Phyllostachys propinqua Ageratina adenophora Chara vulgaris S t aphylea colchica Berberidopsis corallina F ranklinia alat amaha Hordeum vulgare Asparagus officinalis Millettia pinnata Pinus attenuata Pinus monticola Daucus carota Nelumbo lut e a Staurastrum punctulatum G ossypium t hurberi Gossypium darwinii Musa acuminata Halocarpus kirkii Festuca arundinacea Gossypium tomentosum Cheilanthes lindheimeri Mayaca fluviatilis Silene conica Pinus leiophylla var. chihuahuana G i nkgo biloba Jatropha curcas Nandina domest ica J a sminum nudif lor u m Plumbago auriculata Populus alba Pereskiopsis diguetii Pinus t orreyana subsp. t orreyana Aethionema cordifolium Phoradendron serotinum Oocystis solitaria Oenothera elata Pyru s p yri folia Ket eleeria davidiana Pitcairnia feliciana Cuscut a ref lexa G uizot ia abyssinic a Typha latifolia Lonicera japonica Micromonas sp. Atropa belladonna Ric i nus communi s S o r ghum bic olor Gossypium barbadense Micromonas pusilla Curculigo c apit ulat a P inus sibir i c a Pinus banksiana Isoetes flaccida Picea sitchensis N ymphaea alba Pinus cont ort a Fagopyrum esculentum Pinus strobus Solanum tuberosum Pinus f lexilis J unc u s e ffu s u s Chaet osphaeridium globosum Panax ginseng Portulaca oleracea Navia saxicola Calycanthus floridus Oltmannsiellopsis viridis Pinus parvif lora var. pent aphylla Larix decidua Gossypium arboreum Chlorophytum rhizopendulum Lactuca sativa Buxus microphylla Cathaya argyrophylla E phedr a equis e t ina Amborella trichopoda Psilot um nudum Medicago truncatula Z ea m a y s Olea europaea ssp. cuspidata Chlorella vulgaris Helianthus annuus Pinus aristata Solanum bulbocastanum Nelumbo nucifera Abolboda macrostachya Neoregelia carolinae Lobularia maritima Phyllost achys nigra Aco r u s a m e r i c anus O enot her a ar gillic ola Cuscuta gronovii Mesostigma viride B oea hy g r o m e tri c a Alsophila spinulosa Cuscuta exaltata Pseudendoclonium akinetum Cucumis melo Ostreococcus tauri G ossypium must elinum Prunus persica P edinom onas minor Glycine max Dioscorea elephantipes Pinus peuce Nephroselmis olivacea Blossfeldia liliputana Monomastix sp. Lotus japonicus Oryza meridionalis Euonymus americanus Dav idia inv olucra t a Nolina atopocarpa Olea woodiana G e r anium palm a t u m Cyperus alternifolius Apostasia wallichii O enot her a parvi f lor a O punt ia dec u m bens Agapant hus praecox Epifagus virginiana Picea morrisonicola Pinus krempfii Leersia tisserantii Oedogonium cardiacum Oxalis latifolia Nerium oleander Didierea madagascariensis F ragaria vesca Bulnesia arborea Brocchi n i a mi crantha Rhizanthella gardneri Dunaliella salina Bra c h y podium dista c h y o n Rhynchoryza subulata Physcomitrella patens Illicium oligandrum Piper cenocladum Oryza sativa var. japonica Pandanus utilis Oryza sativa var. indica Flagellaria indica Phalaenopsis aphrodite Elaeis oleifera Cuscuta obtusiflora Ipomoea purpurea Dendr o c alam u s lat i f lor u s Marchantia polymorpha Pentactina rupicola Indocalamus longiauritus Georgeantha hexandra Ilex cornuta Gunnera manicata Abies firma Eleutherococcus senticosus Capsella bursa Joinvillea ascendens Liriodendron tulipifera Chlorella variabilis Oenothera glazioviana Pteridium aquilinum Pyramimonas parkeae Welwitschia mirabilis Spinacia oleracea Zygnema circumcarinatum Petroselinum crispum Eucalyptus globulus Lilium superbum P inus canar iens i s Mollugo verti c illata Vitis vinifera Maihuenia poeppigii Cerat ophyllum demersum Tri t i c u m aesti v u m Pinus squamata Coccomyxa sp. Pot arophyt um riparium Aneura mirabilis G o ssypium her bac eum Theobroma cacao Castanea mollissima E h r e t ia ac u m inat a Pinus monophylla Lat h yru s sa t i v u s Carica papaya Nic o t iana t abac u m Phormium tenax Albuca kirkii Erodium carvifolium Pinus cembra Ecdeiocolea monostachya Acorus calamus Pinus resinosa Oenothera biennis Pinus t aeda Cycas micronesica O l ea europaea ssp. europaea O ryza nivara Morus indica Arbut u s unedo Arabidops i s thaliana Nasturtium officinale Pinus armandii Saccharum hybridus Sparganium eurycarpum Nicotiana undulata Cornus florida Bryopsis hypnoides Lar i x o ccident alis Part henium argent a t u m Pinus ponderosa Lomandra longifolia S elaginella unc inat a Colocasia esculenta Pelargonium x sp. Pinus koraiensis Equiset um arvense Anthoceros formosae Lepidium vi r ginic u m Strept o c haet a angusti f olia Bambusa ol dhami i Erodium texanum Pinus rzedowskii Arabis hirsuta Puelia olyriformis Syntrichia ruralis Hesperaloe parvif lora100 100 100 100 9 8 100 9 9 100 8 2 8 0 100 8 1 100 100 9 5 100 100 9 7 100 100 6 0 8 8 100 100 100 100 9 3 100 100 100 6 1 8 5 100 9 8 100 8 0 100 100 9 8 100 9 8 100 100 100 100 7 6 100 100 100 9 7 100 100 100 100 100 100 100 9 8 8 7 100 100 100 100 100 9 6 100 100 6 1 100 100 9 9 100 7 1 8 8 100 8 2 8 6 9 3 100 100 100 6 1 7 5 100 100 6 5 100 100 100 100 5 9 100 9 5 100 100 100 100 100 9 8 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 6 7 100 100 8 6 100 9 3 100 9 7 100 6 5 9 0 7 5 7 9 9 7 9 0 6 2 100 100 100 8 0 100 100 100 100 100 9 9 100 8 3 100 100 100 100 100 9 8 100 100 100 100 100 100 9 0 4 0 9 6 8 0 10 0 100 100 9 9 100 100 100 7 3 100 100 100 100 100 100 100 100 100 100 5 3 9 6 5 7 100 100 100 8 2 100 100 100 100 100 100 100 100 100 6 6 5 4 8 5 9 9 100 100 100 100 100 100 6 2 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 7 9 9 9 100 9 2 9 7 100 5 3 100 100 100 100 5 2 100 7 8 9 6 7 3 100 100 100 8 4 100 5 7 8 9 100 100 9 9 100 100 4 0 100 7 3 100 6 9 100 100 100 100 100 100 100 100 5 1 100 8 8 100 100 9 7 100 100 100 100 100 100 100 100 100 100 100 100 9 9 100 100 100 100 9 0 100 8 2 7 4 100 100 100 100 100 100 100 100 100 7 0 100 100 100 100 5 6 100 100 5 9 100 7 1 100 100 100 6 8 8 7 6 1 100 100 100 6 7 5 9 100 100 9 8 100 100 100 8 8 100 100 100 100 100 5 8 100 5 7 5 2 100 100 5 0 100 100 100 100S t igeoclonium helvet icum 0.3 F i c u s sp. Heuchera sanguinea Silene vulgaris Phoenix dactylifera Monsonia speciosa Agrostis stolonifera Wolffiella lingulata Cedrus deodara Anredera baselloides Drimys granadensis Hosta ventricosa Rhododendron simsii T hamnochort us insignis Phyllostachys edulis Jacobaea vulgaris E l eusi ne coracana Magnolia kwangsiensis Pisum sativum Oryza rufipogon A Pinus albicaulis P inus ger a r diana Chamaedorea seifrizii Phaseolus vulgaris Oryza australiensis Ximenia americana Dasypogon bromeliifolius Schizomeris leibleinii B elosynaps i s ciliat a Spirodela polyrhiza Meliosma aff. cuneif olia Scenedesmus obliquus Crucihimalaya wallichii Passif lora bif lora Crithmum maritimum Hydrocotyle sp. Huperzia luc idula P inus to rre y ana subsp. ins ular i s Nicotiana sylvestris F o ste r ella c aulescens Solanum lycopersicum Port ulacaria af r a Pseudotsuga sinensis Pycnococcus provasolii A n t i rrhinum majus Q uercus nigra Microlaena stipoides Centrolepis monogyna F loydiella t errest ris Cic e r a r iet inum Selaginella moellendorffii Pinus ayacahuite Lem na m inor Oryza rufipogon B Pinus nelsonii Cycas t ait ungensis Tra c helium caer uleum Volvox cart eri Puya laxa Panicum virgatum Neottia nidus E u c aly p t u s g r andis Liquidambar styraciflua Kingia australis Cucumis sativus Tro c hodendr on ar alioides Bambusa emeiensis Dillenia indica P o t a m ophila parvi f lor a W eingart ia k argliana Silene latifolia Iris virginica Anomochloa marantoidea Gossypium hirsutum Ravenea hildebrandt i i P inus thunber gii Manihot esculenta Pereskia sacharosa Pinus pinaster O n c idium sp. Taiwania cryptomerioides Cryptomeria japonica Corynocarpus laevigata Scaevola aemula Citrus sinensis O lea eur opaea ssp. m a r occana Pinus merkusii O limarabidopsis pumila Hevea brasiliensis Y u cca schidiger a Barbarea verna Renealmia alpinia Coix lacryma-jobi Lolium per enne Ptilid i um pul cherri mum Anethum graveolens Chloranthus spicatus Podocarpus totara Megaleranthis saniculifolia Neoastelia spectabilis Chlamydomonas reinhardt i i G o ssypium raim ondii Oxypolis greenmanii Trifolium subterraneum Adi antum capillu s Parachlorella kessleri Aethionema grandiflorum Ranunculus macranthus Anthriscus cerefolium Vigna radiata Sesamum indicum Cephalotaxus wilsoniana Thurnia sphaerocephala Populus trichocarpa Pinus lambertiana Ferrocalamus rimosivaginus C h l orokybus atmophyti cus Coffea arabica Nuphar adv ena Agathis australis Draba nemorosa S t igeoclonium helvet icum Aucuba japonica Wolffia australiana Leptosira terrestris Platanus occidentalis Syngonanthus chrysanthus Silene noctiflora Acidosasa purpurea Gnetum parvifolium Tradescant ia ohiensis Nicot iana t oment osif ormis Angiopteris evecta H e licospori d i um sp. Phyllostachys propinqua Ageratina adenophora Chara vulgaris S t aphylea colchica Berberidopsis corallina F ranklinia alat amaha Hordeum vulgare Asparagus officinalis Millettia pinnata Pinus attenuata Pinus monticola Daucus carota Nelumbo lut e a Staurastrum punctulatum G ossypium t hurberi Gossypium darwinii Musa acuminata Halocarpus kirkii Festuca arundinacea Gossypium tomentosum Cheilanthes lindheimeri Mayaca fluviatilis Silene conica Pinus leiophylla var. chihuahuana G i nkgo biloba Jatropha curcas Nandina domest ica J a sminum nudif lor u m Plumbago auriculata Populus alba Pereskiopsis diguetii Pinus t orreyana subsp. t orreyana Aethionema cordifolium Phoradendron serotinum Oocystis solitaria Oenothera elata Pyrus pyri folia Ket eleeria davidiana Pitcairnia feliciana Cuscut a ref lexa G uizot ia abyssinica Typha latifolia Lonicera japonica Micromonas sp. Atropa belladonna Ric i nus communi s S o r ghum bic olor Gossypium barbadense Micromonas pusilla Curculigo c apit ulat a P inus sibir i c a Pinus banksiana Isoetes flaccida Picea sitchensis N ymphaea alba Pinus cont ort a Fagopyrum esculentum Pinus strobus Solanum tuberosum Pinus f lexilis J unc u s e ffu s u s Chaet osphaeridium globosum Panax ginseng Portulaca oleracea Navia saxicola Calycanthus floridus Oltmannsiellopsis viridis Pinus parvif lora var. pent aphylla Larix decidua Gossypium arboreum Chlorophytum rhizopendulum Lactuca sativa Buxus microphylla Cathaya argyrophylla E phedr a equis e t ina Amborella trichopoda Psilot um nudum Medicago truncatula Z ea m a y s Olea europaea ssp. cuspidata Chlorella vulgaris Helianthus annuus Pinus aristata Solanum bulbocastanum Nelumbo nucifera Abolboda macrostachya Neoregelia carolinae Lobularia maritima Phyllost achys nigra Aco r u s a m e r i c anus O enot her a ar gillic ola Cuscuta gronovii Mesostigma viride B oea hy g r o m e tri c a Alsophila spinulosa Cuscuta exaltata Pseudendoclonium akinetum Cucumis melo Ostreococcus tauri G ossypium must elinum Prunus persica P edinom onas minor Glycine max Dioscorea elephantipes Pinus peuce Nephroselmis olivacea Blossfeldia liliputana Monomastix sp. Lotus japonicus Oryza meridionalis Euonymus americanus Dav idia inv olucra t a Nolina atopocarpa Olea woodiana G e r anium palm a t u m Cyperus alternifolius Apostasia wallichii O enot her a parvi f lor a O punt ia dec u m bens Agapant hus praecox Epifagus virginiana Picea morrisonicola Pinus krempfii Leersia tisserantii Oedogonium cardiacum Oxalis latifolia Nerium oleander Didierea madagascariensis F ragaria vesca Bulnesia arborea Brocchi n i a mi crantha Rhizanthella gardneri Dunaliella salina Bra c h y podium dista c h y o n Rhynchoryza subulata Physcomitrella patens Illicium oligandrum Piper cenocladum Oryza sativaJaponica Pandanus utilis Oryza sativaIndica Flagellaria indica Phalaenopsis aphrodite Elaeis oleifera Cuscuta obtusiflora Ipomoea purpurea Dendr o c alam u s lat i f lor u s Marchantia polymorpha Pentactina rupicola Indocalamus longiauritus Georgeantha hexandra Ilex cornuta Gunnera manicata Abies firma Eleutherococcus senticosus Capsella bursa Joinvillea ascendens Liriodendron tulipifera Chlorella variabilis Oenothera glazioviana Pteridium aquilinum Pyramimonas parkeae Welwitschia mirabilis Spinacia oleracea Zygnema circumcarinatum Petroselinum crispum Eucalyptus globulus Lilium superbum P inus canar iens i s Mollugo verti c illata Vitis vinifera Maihuenia poeppigii Cerat ophyllum demersum Tri t i c u m aesti v u m Pinus squamata Coccomyxa sp. Pot arophyt um riparium Aneura mirabilis G o ssypium her bac eum Theobroma cacao Castanea mollissima E h r e t ia ac u m inat a Pinus monophylla Lat h yru s sa t i v u s Carica papaya Nic o t iana t abac u m Phormium tenax Albuca kirkii Erodium carvifolium Pinus cembra Ecdeiocolea monostachya Acorus calamus Pinus resinosa Oenothera biennis Pinus t aeda Cycas micronesica O l ea europaea ssp. europaea O ryza nivara Morus indica Arbut u s unedo Arabidops i s thaliana Nasturtium officinale Pinus armandii Saccharum hybridus Sparganium eurycarpum Nicotiana undulata Cornus florida Bryopsis hypnoides Lar i x o ccident alis Part henium argent a t u m Pinus ponderosa Lomandra longifolia S elaginella unc inat a Colocasia esculenta Pelargonium x sp. Pinus koraiensis Equiset um arvense Anthoceros formosae Lepidium vi r ginic u m Strept o c haet a angusti f olia Bambusa ol dhami i Erodium texanum Pinus rzedowskii Arabis hirsuta Puelia olyriformis Syntrichia ruralis Hesperaloe parvif lora



PAGE 1

Wolffia australiana Cuscu t a gr onovi i Huperzia lucidula Lepidium virginicum Boea hygrometrica Joinvillea ascendens Podocarpus totara Pinus rzedowskii Pinus attenuata Anredera baselloides Drimys granadensis O enot her a elat a Hordeum vulgare Halocarpus kirkii Alsophila spinulosa Erodium te x anum Triticum aestivum Syngonanthus chrysanthus Lomandra longifolia Spirodela polyrhiza Dillenia indica Typha latifolia Phaseolus vulgaris Nymphaea alba Strept o c haet a angusti f olia Vitis vinifera Pinus ay a c ahuit e Pereskiopsis diguet i i Puelia olyrif ormis Corynocarpus laevigata Saccharum hybridus Fagopyrum esculentum Pinus nelsonii Schizomeris leibleinii Portulaca oleracea Oryza ni vara Chloranthus spicatus Amborella trichopoda Oxalis latifolia Nicotiana sylvestris Chlorokybus at mophyt icus Pinus koraiensis P lat anus occident alis Silene latifolia Silene noct i f lora Berberidopsis corallina Parachlorella kessleri Centrolepis monogyna Aucuba japonica Nelumbo nucifera Pinus peuc e Jacobaea vulgari s Pinus parvi f lor a v a r. pent aphy lla O enot hera argillicola Abolboda macrostachya Anethum graveolens Dendrocalamus latiflorus Pseudotsuga sinensis Pinus cembra Anthriscus cerefolium Thurnia sphaerocephala Fosterella caulescens P ent a ctina rupic ola Solanum bulbocastanum Selaginella moellendorffii Phyllostachys edulis Brach ypodi um di stachyo n Millettia pinnata Solanum lycopersicum Fragaria vesca P anax gins eng Tradescantia ohiensis Potarophytum riparium Gossypium hirsutum Iris virginica Pi tcairni a felic i a n a Populus trichocarpa O l tmanns i e llops i s vi r i d i s Ageratina adenophora Renealmia alpinia Pteridium aquilinum Coix lacryma-jobi Calycanthus floridus Nic o t iana to m ent o s i f o rmi s Equisetum arvense Bryops i s hy pnoid e s Didierea madagascariensis G eorgeant ha hexandra Oryza sativa var. japonica Hydrocotyle s p. Phyllostachys nigra Helicosporidium s p. Oxypolis gr eenm anii Lathyrus sativus Lolium perenne Pisum sativum Gossypium tomentosum Pinus armandii Oncidium sp. Pseudendoclonium akinetum Micromonas s p. Cucumis melo Neoregelia carolinae Marchantia polymorpha Eleusine coracana Dioscorea elephantipes Passiflora biflora Arbutus unedo Asparagus officinali s Acorus calamus Heliant hus annuus Lar i x dec idua Ostreococcus tauri Phalaenopsis aphrodite Picea sitchensis Nephroselmis olivacea Pinus sibirica Gossypium herbaceum Vigna radiata Jatropha curcas Pinus torreyana subsp. insularis Wolffiella lingulata Lactuca sativa Potamophila parviflora Plumbago auriculata Pinus lambertiana O enot hera biennis Cuscuta exaltata Aethionema grandiflorum Chlorella vulgaris Nelum bo lut e a Mayaca fluviatilis F loy diella te rre stri s Cicer ar iet i n u m E u c aly p t u s globulus I pomoea purpurea Lotus japonicus Nuphar advena S t aphylea colchica Phoradendron serotinum Agapanthus praecox Pinus leiophylla var. chihuahuana Neoastelia spectabilis Erodium carvif olium Pinus torreyana subsp. torreyana Lept osira terrest ris Arabidopsis thaliana Ner ium oleander Pinus flexilis Pinus albicaulis Citrus sinensis Lilium superbum Zygnema circumcarinatum Rhododendron simsii Pinus ponderosa Welwitschia mirabilis Eucalyptus grandis Liriodendron tulipifera Car i c a papay a Oryza sativa var. indica Glycine max Acidosasa purpurea Elaeis oleifera Geranium palmatum Microlaena stipoides Psilotum nudum Cyperus alternifolius Keteleeria davidiana Cornus florida G uizot ia abyssinica Anom o c hloa ma r ant oidea Hesperaloe parvif lora Larix occidentalis Oryza rufipogon A Ehret ia acuminata Populus alba Gossypium mustelinum Micromonas pusilla Cephalot axus wilsoniana Thamnochortus insignis Castanea mollissi m a Zea mays Nolina at opocarpa Pinus gerardiana Chlorophytum rhizopendulum Ecdeiocolea monostachya Meliosma aff. cuneifolia Barbarea verna Monsonia speciosa Mesostigm a vi r ide Pyrus pyrifolia Angiopteris evecta Franklinia alatamaha Curculigo capit ulata Agat his aust ralis Leersia tisserantii Oedogonium cardiacum Pinus banksiana Crucihimalaya wallichii Crithmum maritimum Parthenium argentatum Trachelium caeruleum Gunnera manicata Buxus microphylla E uonymu s am e r i c anus Gnet um parvif olium Pinus resinosa Staurastrum punctulatum Gossypium barbadense Isoetes flaccida Pyramimonas parkeae Quercus nigra Olimarabidopsis pumila Cucumis sat ivus Draba nemorosa A t ropa belladonna Sorghum bicolor Puya laxa Pinus contorta Taiwania cryptomerioides Selaginella uncinata Heuchera sanguinea Silene vulgaris Prunus persi c a Davidia involucrata Lobularia maritima Rhizanthella gardneri Lonicera japonica Megaleranthis saniculifolia Cycas taitungensis Hosta ventricosa Pinus squamata Chlorella variabilis Pycnoc o cc u s pr o v a s olii Cuscuta reflexa Sparganium eurycarpum Dasypogon bromeliifolius Oryza aust raliensis Pedinomonas minor Gossypium arboreum T heobroma cacao Eleutherococcus senticosus Scenedesmus obliquus Cycas micronesica Cuscuta obtusiflora Indoc alam u s longiaur i t u s Scaev ola aem ula Pinus mont i c ola F i c u s sp Lemna minor P o rtulac a r ia afra Panicum virgat u m Cedrus deodara Ricinus communis Spinacia oleracea Ptilidium pulcherrimum Jasminum nudiflorum Pinus merk u s i i Bambusa emeiensis Pinus strobus Acorus americanus Pinus pinaste r Abies firma Volvox carteri Mollugo verticillata Morus indica O l ea europaea subsp. europaea Juncus effusus Oenothera glaziovi ana O lea eur opaea subsp. m a r occana Arabis hirsuta Manihot esculenta Weingartia kargliana Nicotiana undulata Ilex cornuta Chaetosphaeridium globosum Solanum tuberosum A n t hoc e r o s fo rmo s a e Pel argo n ium x sp. Medi cago trunca tul a Ephedr a equis e t ina Coffea arabica Adiantum capillus-veneris Pereskia sacharosa Festuca arundinacea Albuca kirkii Gossypium darwinii Bulnesia arborea Picea morrisonicola Cryptomeria japonica Petroselinum crispum Colocasia esculenta Dunaliella salina Navia saxicola Gossypium raimondii Chamaedorea seifrizii Silene conica Olea europaea subsp. cuspidata Kingia australis Yucca schidigera Nic o t iana tabac u m Maihuenia poeppigii Phormium tenax I llicium oligandrum Monomast ix s p. Antirrhinum majus Epifagus virginiana Nastu rtium offi c inale Chlamydomonas rei nhardti i Aethionema cordifolium Ginkgo biloba Nandina domestica O enot her a parvi f lor a Oryza rufipogon B Cheilanthes lindheimeri Phyllostachys propinqua Pinus aristata Belosynapsis ciliat a Physcomitrella patens Blossfeldia liliputana C occomyxa s p. Pandanus utilis Pinus thunbergii S t igeoclonium helvet icum Pinus canariensis Gossypium thurberi Piper cenocladum Bambusa oldhamii Opuntia decumbens Chara vulgaris Ferrocalamus rimosivaginus Apostasia wallichii Hev ea br a s iliens i s Magn o lia kwangsi ensi s Ximenia americana Brocchinia mic rant h a S e s a m u m indic u m Syntrichia ruralis Oocystis solitaria Neottia nidus-avis Daucus carota Cathaya argyrophylla Olea woodiana Ceratophyllum demersum Capsella bursa-pastoris Liquidambar styraciflua Agrostis stolonifera Musa acuminata T rif olium subt erraneum Pinus taeda Pinus monophy lla Ranunculus macranthus Rhynchoryza subulata F lagellaria indica Aneura mirabilis Tro c hodendr on ar alioides Pinus krempf i i Ravenea hildebrandtii Oryza meridionalis Phoenix dactylif e r a 100 100 6 1 100 8 8 100 100 100 100 5 7 9 0 100 100 5 9 9 0 100 100 100 9 5 100 100 100 100 100 9 9 100 8 2 100 100 100 8 3 100 100 100 100 100 100 8 5 100 8 8 100 100 100 100 7 1 100 100 100 100 100 100 7 9 100 5 4 100 100 100 8 0 100 7 0 5 1 100 100 100 100 100 100 8 0 100 100 100 100 8 1 100 9 7 100 100 100 9 8 6 7 100 100 100 8 7 100 100 100 6 7 9 9 100 6 6 100 100 9 7 100 8 0 100 100 100 100 100 8 7 5 6 100 100 100 7 4 100 100 100 100 100 7 5 100 100 100 9 9 100 100 100 8 2 100 100 100 100 100 100 9 6 100 7 9 9 2 100 100 100 100 9 6 100 100 100 100 100 8 2 100 6 9 100 100 100 100 7 6 5 3 100 9 9 100 100 100 100 100 100 100 100 100 100 100 100 9 8 100 100 100 5 8 5 2 100 9 8 100 8 9 100 9 7 100 9 3 100 100 100 100 9 8 100 100 8 2 100 9 3 100 100 7 1 100 100 100 9 8 100 9 7 9 0 100 100 9 8 100 7 3 100 100 100 100 100 100 100 5 3 100 8 8 5 8 9 6 100 100 100 7 5 100 100 6 2 100 6 5 9 8 9 9 100 100 100 100 100 100 100 6 1 100 6 1 100 100 100 7 5 100 100 8 6 7 3 100 100 100 100 100 5 7 100 100 6 8 100 100 100 9 8 100 100 6 1 100 100 100 6 2 100 100 9 5 6 5 100 100 9 7 100 100 5 7 100 100 100 100 100 100 100 5 9 100 100 100 9 3 100 100 100 100 100 100 7 3 100 100 8 6 100 9 7 100 100 6 0 8 5 100 100 100 7 4 100 8 8 100 100 5 9 100 100 100 100 8 0 100 100 9 9 100 5 2 9 9 100 100 100 100 100 100 100 100 9 9 100 100 100 9 6 100 9 0 100 100 8 4 100 7 8 100



PAGE 1

Atropa belladonna Nuphar adv ena Rhizanthella gardneri Millettia pinnata Cornus florida P inus canar iens i s Rhododendron simsii Ptilid i um pul cherri mum P o t a m ophila parvi f lor a J unc u s e ffu s u s Draba nemorosa Dendr o c alam u s lat i f lor u s Oryza australiensis Lonicera japonica Ilex cornuta Solanum tuberosum Ecdeiocolea monostachya Nelumbo nucifera Cuscuta gronovii Silene latifolia Strept o c haet a angusti f olia O limarabidopsis pumila Phyllost achys nigra Pitcairnia feliciana F loydiella t errest ris Morus indica Halocarpus kirkii S o r ghum bic olor P inus thunber gii Coccomyxa s p. Pot arophyt um riparium Monomastix s p. Aethionema cordifolium Nicotiana undulata Tri t i c u m aesti v u m Asparagus officinalis Leersia tisserantii Indocalamus longiauritus Fagopyrum esculentum Oocystis solitaria Calycanthus floridus Angiopteris evecta Sesamum indicum Pereskia sacharosa Crucihimalaya wallichii Theobroma cacao Olea europaea ssp. cuspidata G uizot ia abys sinic a Lolium per enne Lilium superbum Anthriscus cerefolium Rhynchoryza subulata Pinus leiophylla var. chihuahuana Scaevola aemula F i c u s sp. Cuscuta exaltata Ageratina adenophora Ferrocalamus rimosivaginus Gnetum parvifolium Pinus koraiensis Nandina domest ica P edinom onas minor Solanum lycopersicum Phyllostachys propinqua Adi antum capillu s Chlorokybus atmophyticus Helianthus annuus Aneura mirabilis Oxalis latifolia Dillenia indica Pinus lambertiana Ket eleeria davidiana G o ssypium her bac eum Buxus microphylla Pinus nelsonii G ossypium must elinum Thurnia sphaerocephala Dunaliella salina O n c idium sp. Acorus calamus Solanum bulbocastanum Ranunculus macranthus Oxypolis greenmanii Gossypium barbadense Oenothera biennis Pereskiopsis diguetii Schizomeris leibleinii Cuscut a ref lexa Cucumis sativus Pinus krempfii Acidosasa purpurea E u c aly p t u s g r andis Spinacia oleracea T hamnochort us insignis Bra c h y podium dista c h y o n Phyllostachys edulis B oea hy g r o m e tri c a Cathaya argyrophylla Piper cenocladum Arbut u s unedo Georgeantha hexandra E h r e t ia ac u m inat a Coffea arabica Cheilanthes lindheimeri Wolffiella lingulata Portulaca oleracea Pseudendoclonium akinetum Nasturtium officinale Erodium carvifolium Castanea mollissima Picea morrisonicola Oltmannsiellopsis viridis Heuchera sanguinea Bambusa emeiensis Spirodela polyrhiza A n t i rrhinum majus Megaleranthis saniculifolia Pinus parvif lora var. pent aphylla G ossypium t hurberi Marchantia polymorpha Meliosma a ff. c uneif olia Equiset um arvense Pelargonium x sp. Joinvillea ascendens Pyrus pyri folia Ximenia americana Medicago truncatula Vitis vinifera Phalaenopsis aphrodite Hesperaloe parvif lora Neottia nidus P inus to rre y ana ssp. ins ular i s Zygnema circumcarinatum Oryza sativa var. indica Port ulacaria af r a Nicotiana sylvestris Hordeum vulgare Nelumbo lut e a Pinus banksiana Nicot iana t oment osif ormis Pinus pinaster Vigna radiata Nic o t iana t abac u m G i nkgo biloba O enot her a ar gillic ola Carica papaya Tro c hodendr on ar alioides Puya laxa Iris virginica Pinus resinosa Cic e r a r iet inum Cerat ophyllum demersum Pinus peuce Chaet osphaeridium globosum Agrostis stolonifera Staurastrum punctulatum Lotus japonicus Chloranthus spicatus Chara vulgaris Bambusa ol dhami i Curculigo c apit ulat a Pinus ponderosa S elaginella unc inat a Scenedesmus obliquus Volvox cart eri Bulnesia arborea Phormium tenax Capsella bursa-pastoris Psilot um nudum Jatropha curcas G e r anium palm a t u m Apostasia wallichii Maihuenia poeppigii Kingia australis Manihot esculenta Wolffia australiana Pisum sativum Blossfeldia liliputana Dioscorea elephantipes Eucalyptus globulus Cucumis melo Cuscuta obtusiflora Lactuca sativa Silene noctiflora Dasypogon bromeliifolius Anethum graveolens Pinus t orreyana ssp. t orreyana Pinus cont ort a Liquidambar styraciflua P inus ger a r diana F ragaria vesca Pinus monticola Y u cca schidiger a O enot her a parvi f lor a Nerium oleander Silene conica Pteridium aquilinum Sparganium eurycarpum Pinus armandii Agathis australis Microlaena stipoides Nephroselmis olivacea Festuca arundinacea Hosta ventricosa Prunus persica Pyramimonas parkeae Pinus albicaulis Neoregelia carolinae Agapant hus praecox Tra c helium caer uleum Coix lacryma-jobi Anredera baselloides Pinus squamata F ranklinia alat amaha W eingart ia k argliana Didierea madagascariensis Leptosira terrestris Pentactina rupicola D avi d ia involucra t a Syngonanthus chrysanthus Lar i x o ccident alis S t igeoclonium helvet icum Olea woodiana S t aphylea colchica Pinus t aeda F o ste r ella c aulescens Ravenea hildebrandt i i Chlorella variabilis Ipomoea purpurea Huperzia luc idula Ric i nus communi s Alsophila spinulosa Parachlorella kessleri Pandanus utilis Gossypium hirsutum Epifagus virginiana N ymphaea alba Micromonas s p. Arabidops i s thaliana Podocarpus totara Phoenix dactylifera Pinus aristata Aco r u s a m e r i c anus Pinus strobus Citrus sinensis Chlamydomonas reinhardt i i Renealmia alpinia Populus alba O l ea europaea ssp. europaea Anomochloa marantoidea Petroselinum crispum Cephalotaxus wilsoniana Pinus cembra Saccharum hybridus Liriodendron tulipifera Eleutherococcus senticosus Mollugo verti c illata Illicium oligandrum Oryza rufipogon B E l eusi ne coracana Abies firma Pycnococcus provasolii Z ea m a y s Puelia olyriformis Cedrus deodara Cycas t ait ungensis Passif lora bif lora Lepidium vi r ginic u m J a sminum nudif lor u m Hydrocotyle s p. Musa acuminata Aethionema grandiflorum Jacobaea vulgaris Pinus ayacahuite Flagellaria indica Picea sitchensis Pseudotsuga sinensis Taiwania cryptomerioides Oedogonium cardiacum Pinus f lexilis Q uercus nigra Lobularia maritima Hevea brasiliensis Trifolium subterraneum Berberidopsis corallina Syntrichia ruralis G o ssypium raim ondii Anthoceros formosae Arabis hirsuta Phoradendron serotinum O ryza nivara Pinus attenuata P inus sibir i c a Gossypium arboreum Erodium texanum Magnolia kwangsiensis O punt ia dec u m bens Silene vulgaris Glycine max Elaeis oleifera Aucuba japonica Ostreococcus tauri Lat h yru s sa t i v u s Monsonia speciosa Part henium argent a t u m Nolina atopocarpa Brocchini a mi crantha Lem na m inor Amborella trichopoda Drimys granadensis Pinus rzedowskii O lea eur opaea ssp. m a r occana Gunnera manicata Panicum virgatum Pinus monophylla Oryza rufipogon A Platanus occidentalis Oenothera elata Plumbago auriculata Neoastelia spectabilis Centrolepis monogyna Micromonas pusilla Welwitschia mirabilis Oryza meridionalis Typha latifolia Bryopsis hypnoides Euonymus americanus Abolboda macrostachya Navia saxicola Chlorella vulgaris Corynocarpus laevigata Gossypium darwinii Oryza sativa var. japonica Barbarea verna Pinus merkusii Chamaedorea seifrizii Lomandra longifolia H e licospori d i um s p. Crithmum maritimum Mesostigma viride Cycas micronesica Populus trichocarpa Gossypium tomentosum Panax ginseng Chlorophytum rhizopendulum Tradescantia ohiensis Isoetes flaccida Cyperus alternifolius Albuca kirkii Larix decidua Selaginella moellendorffii Colocasia esculenta Daucus carota Oenothera glazioviana Mayaca fluviatilis Physcomitrella patens Phaseolus vulgaris Cryptomeria japonica B elosynaps i s ciliat a E phedr a equis e t ina8 1 100 100 100 100 100 100 100 9 6 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 8 4 100 100 100 7 5 100 100 100 100 6 3 100 100 100 100 8 8 100 100 100 100 100 100 100 100 100 100 100 100 100 100 7 5 9 9 8 6 100 9 8 100 6 1 100 100 100 100 100 8 8 100 9 7 100 100 100 8 3 100 7 6 100 100 100 100 100 100 100 100 100 100 8 1 100 100 100 100 100 7 7 100 100 100 100 100 100 100 100 100 8 5 100 100 100 100 100 100 100 100 100 100 100 100 100 100 8 8 100 100 100 8 1 100 100 100 100 100 100 100 100 100 100 9 6 100 6 3 100 100 6 3 100 100 100 100 6 9 100 100 100 100 7 0 9 4 100 100 6 9 100 100 100 100 100 9 8 10 0 100 100 100 100 9 9 100 100 100 100 100 100 7 2 100 100 6 9 100 100 8 0 100 100 100 100 100 9 2 9 3 100 5 1 100 100 100 100 100 100 100 100 100 100 100 100 5 2 100 100 100 100 100 100 100 9 5 9 9 100 100 100 100 100 100 100 8 7 100 100 9 1 100 100 100 100 5 0 100 100 9 4 9 9 100 5 3 100 100 5 8 100 100 100 100 100 100 9 7 100 8 9 100 6 4 100 100 100 9 7 100 9 3 100 7 4 7 5 9 0 100 6 4 100 6 9 5 5 8 7 100 100 100 100 100 100 9 8 100 100 100 5 0 100 100 100 100 100 8 6 100 100 8 8 100 9 8 7 8 100 100 100 100 100 100 100 9 9 100 5 0 100 100 100 100 100 9 3 100 100 100 100 100 100 100 100 100 7 7 100 100 100 100 100 100 100 100 100 9 5 100 8 1 100 7 3 100 9 7 100 7 5 100 100 100 5 5 100 100 100 100 100 100 100 100 100 100 100 100 100 100 6 8 100 5 9 0.3 Atropa belladonna Nuphar adv ena Rhizanthella gardneri Millettia pinnata Cornus florida P inus canar iens i s Rhododendron simsii Ptilid i um pul cherri mum P o t a m ophila parvi f lor a J unc u s e ffu s u s Draba nemorosa Dendr o c alam u s lat i f lor u s Oryza australiensis Lonicera japonica Ilex cornuta Solanum tuberosum Ecdeiocolea monostachya Nelumbo nucifera Cuscuta gronovii Silene latifolia Strept o c haet a angusti f olia O limarabidopsis pumila Phyllost achys nigra Pitcairnia feliciana F loydiella t errest ris Morus indica Halocarpus kirkii S o r ghum bic olor P inus thunber gii Coccomyxa s p. Pot arophyt um riparium Monomastix s p. Aethionema cordifolium Nicotiana undulata Tri t i c u m aesti v u m Asparagus officinalis Leersia tisserantii Indocalamus longiauritus Fagopyrum esculentum Oocystis solitaria Calycanthus floridus Angiopteris evecta Sesamum indicum Pereskia sacharosa Crucihimalaya wallichii Theobroma cacao G uizot ia abyssinica Lolium per enne Lilium superbum Anthriscus cerefolium Rhynchoryza subulata Pinus leiophylla var. chihuahuana Scaevola aemula F i c u s sp. Cuscuta exaltata Ageratina adenophora Ferrocalamus rimosivaginus Gnetum parvifolium Pinus koraiensis Nandina domest ica P edinom onas minor Solanum lycopersicum Phyllostachys propinqua Adi antum capillu s C h l orokybus atmophyti cus Helianthus annuus Aneura mirabilis Oxalis latifolia Dillenia indica Pinus lambertiana Ket eleeria davidiana G o ssypium her bac eum Buxus microphylla Pinus nelsonii G ossypium must elinum Thurnia sphaerocephala Dunaliella salina O n c idium sp. Acorus calamus Solanum bulbocastanum Ranunculus macranthus Oxypolis greenmanii Gossypium barbadense Oenothera biennis Pereskiopsis diguetii Schizomeris leibleinii Cuscut a ref lexa Cucumis sativus Pinus krempfii Acidosasa purpurea E u c aly p t u s g r andis Spinacia oleracea T hamnochort us insignis Bra c h y podium dista c h y o n Phyllostachys edulis B oea hy g r o m e tri c a Cathaya argyrophylla Piper cenocladum Arbut u s unedo Georgeantha hexandra E h r e t ia ac u m inat a Coffea arabica Cheilanthes lindheimeri Wolffiella lingulata Portulaca oleracea Pseudendoclonium akinetum Nasturtium officinale Erodium carvifolium Castanea mollissima Picea morrisonicola Oltmannsiellopsis viridis Heuchera sanguinea Bambusa emeiensis Spirodela polyrhiza A n t i rrhinum majus Megaleranthis saniculifolia Pinus parvif lora var. pent aphylla G ossypium t hurberi Marchantia polymorpha Meliosma a ff. c uneif olia Equiset um arvense Joinvillea ascendens Pyrus p yri f olia Ximenia americana Medicago truncatula Vitis vinifera Phalaenopsis aphrodite Hesperaloe parvif lora Neottia nidus P inus to rre y ana ssp. ins ular i s Zygnema circumcarinatum Oryza sativa var. indica Port ulacaria af r a Nicotiana sylvestris Hordeum vulgare Nelumbo lut e a Pinus banksiana Nicot iana t oment osif ormis Pinus pinaster Vigna radiata Nic o t iana t abac u m G i nkgo biloba O enot her a ar gillic ola Carica papaya Tro c hodendr on ar alioides Puya laxa Iris virginica Pinus resinosa Cic e r a r iet inum Cerat ophyllum demersum Pinus peuce Chaet osphaeridium globosum Agrostis stolonifera Staurastrum punctulatum Lotus japonicus Chloranthus spicatus Chara vulgaris Bambusa ol dhami i Curculigo c apit ulat a Pinus ponderosa S elaginella unc inat a Scenedesmus obliquus Volvox cart eri Bulnesia arborea Phormium tenax Psilot um nudum Jatropha curcas G e r anium palm a t u m Apostasia wallichii Maihuenia poeppigii Kingia australis Manihot esculenta Wolffia australiana Pisum sativum Blossfeldia liliputana Dioscorea elephantipes Eucalyptus globulus Cucumis melo Cuscuta obtusiflora Lactuca sativa Silene noctiflora Dasypogon bromeliifolius Anethum graveolens Pinus t orreyana ssp. t orreyana Pinus cont ort a Liquidambar styraciflua P inus ger a r diana F ragaria vesca Pinus monticola Y u cca schidiger a O enot her a parvi f lor a Nerium oleander Silene conica Pteridium aquilinum Sparganium eurycarpum Pinus armandii Agathis australis Microlaena stipoides Nephroselmis olivacea Festuca arundinacea Hosta ventricosa Prunus persica Pyramimonas parkeae Pinus albicaulis Neoregelia carolinae Agapant hus praecox Tra c helium caer uleum Coix lacryma-jobi Anredera baselloides Pinus squamata F ranklinia alat amaha W eingart ia k arglian a Didierea madagascariensis Leptosira terrestris Pentactina rupicola Dav idia inv olucra t a Syngonanthus chrysanthus Lar i x o ccident alis S t igeoclonium helvet icum Olea woodiana S t aphylea colchica Pinus t aeda F o ste r ella c aulescens Ravenea hildebrandt i i Chlorella variabilis Ipomoea purpurea Huperzia luc idula Ric i nus communi s Alsophila spinulosa Parachlorella kessleri Pandanus utilis Gossypium hirsutum Epifagus virginiana N ymphaea alba Micromonas s p. Podocarpus totara Phoenix dactylifera Pinus aristata Aco r u s a m e r i c anus Pinus strobus Citrus sinensis Chlamydomonas reinhardt i i Renealmia alpinia Populus alba Anomochloa marantoidea Petroselinum crispum Cephalotaxus wilsoniana Pinus cembra Saccharum hybridus Liriodendron tulipifera Eleutherococcus senticosus Mollugo verti c illata Illicium oligandrum Oryza rufipogon B E l eusi ne coracana Abies firma Pycnococcus provasolii Z ea m a y s Puelia olyriformis Cedrus deodara Cycas t ait ungensis Passif lora bif lora Lepidium vi r ginic u m J a sminum nudif lor u m Hydrocotyle s p. Musa acuminata Aethionema grandiflorum Jacobaea vulgaris Pinus ayacahuite Flagellaria indica Picea sitchensis Pseudotsuga sinensis Taiwania cryptomerioides Oedogonium cardiacum Pinus f lexilis Q uercus nigra Lobularia maritima Hevea brasiliensis Trifolium subterraneum Berberidopsis corallina Syntrichia ruralis G o ssypium raim ondii Anthoceros formosae Arabis hirsuta Phoradendron serotinum O ryza nivara Pinus attenuata P inus sibir i c a Gossypium arboreum Erodium texanum Magnolia kwangsiensis O punt ia dec u m bens Silene vulgaris Glycine max Elaeis oleifera Aucuba japonica Ostreococcus tauri Lat h yru s sa t i v u s Monsonia speciosa Part henium argent a t u m Nolina atopocarpa Brocchi n i a mi crantha Lem na m inor Amborella trichopoda Drimys granadensis Pinus rzedowskii Gunnera manicata Panicum virgatum Pinus monophylla Oryza rufipogon A Platanus occidentalis Oenothera elata Plumbago auriculata Neoastelia spectabilis Centrolepis monogyna Micromonas pusilla Welwitschia mirabilis Oryza meridionalis Typha latifolia Bryopsis hypnoides Euonymus americanus Abolboda macrostachya Navia saxicola Chlorella vulgaris Corynocarpus laevigata Gossypium darwinii Oryza sativa var. japonica Barbarea verna Pinus merkusii Chamaedorea seifrizii Lomandra longifolia H e licospori d i um s p. Crithmum maritimum Mesostigma viride Cycas micronesica Populus trichocarpa Gossypium tomentosum Panax ginseng Chlorophytum rhizopendulum Tradescant ia ohiensis Isoetes flaccida Cyperus alternifolius Albuca kirkii Larix decidua Selaginella moellendorffii Colocasia esculenta Daucus carota Oenothera glazioviana Mayaca fluviatilis Physcomitrella patens Phaseolus vulgaris Cryptomeria japonica B elosynaps i s ciliat a E phedr a equis e t ina Capsella bursa-pastoris Arabidops i s thaliana Pelargonium x sp. Olea europaea ssp. cuspidata O l ea europaea ssp. europaea O lea eur opaea ssp. m a r occana



PAGE 1

100 100 86 100 100 94 100 100 100 100 63 100 100 94 100 97 96 99 100 93 100 100 63 100 100 99 100 100 100 100 100 54 100 66 100 100 100 100 100 100 100 100 100 99 100 100 51 100 97 100 93 100 99 100 62 99 100 100 100 100 79 96 62 100 100 100 100 69 99 100 93 85 53 100 100 100 100 78 99 87 86 100 97 100 69 100 72 100 100 66 80 96 100 100 100 100 81 100 70 100 87 100 100 100 90 100 100 93 100 100 100 100 100 93 100 100 100 100 54 100 100 66 86 95 99 100 100 100 93 59 100 100 100 100 93 100 100 100 97 100 100 100 100 69 100 92 100 100 100 100 100 100 100 69 100 100 100 100 91 100 59 100 62 100 100 100 100 83 100 100 85 100 60 94 96 100 100 100 100 100 100 65 99 100 100 100 88 100 100 79 100 88 56 100 100 100 91 100 70 97 100 100 98 100 100 100 100 100 100 57 100 100 69 100 100 100 53 100 100 71 100 98 100 100 100 100 100 100 53 100 55 100 68 100 62 100 99 100 92 100 100 100 100 100 100 74 100 62 96 66 100 100 100 100 100 100 78 100 100 100 100 100 100 100 100 91 100 100 95 100 76 99 100 100 86 100 91 100 89 100 95 57 93 100 94 67 100 100 100 93 56 100 100 80 100 100 100 100 100 100 100 100 100 100 100 70 100 81 100 100 100 100 100 100 100 100 43 100 100 100 100 100 100 100 100 56 100 99 100 100 77 68 50 100 100 61 100 100 89 78 99 100 100 100 100Silene noctiflora Marchantia polymorpha Puya laxa Centrolepis monogyna Equiset um arvense Monomastix sp. Liriodendron tulipifera Mayaca fluviatilis Kingia australis Nicot iana toment osif ormis Arbut u s unedo Pinus squamata Didierea madagascariensis Mesostigma viride Lonicera japonica Coffea arabica O limarabidopsis pumila Drimys granadensis Gunnera manicata Pinus cont ort a Petroselinum crispum F loydiella terrest ris Erodium texanum Cuscut a ref lexa Navia saxicola Curculigo capit ulat a Nandina domest ica Pinus monophylla Trifolium subterraneum Cuscuta obtusiflora P inus to rre y ana subsp. ins ular i s Tradescantia ohiensis Solanum lycopersicum G uizot ia abys sinic a Phormium tenax Eucalyptus globulus Ptilid i um pul cherri mum Chlorophytum rhizopendulum Mollugo verti c illata Dioscorea elephantipes Theobroma cacao Isoetes flaccida O n c idium sp. Oenothera glazioviana Neoastelia spectabilis Pinus krempfii Pycnococcus provasolii Nicotiana undulata Silene vulgaris Agapant hus praecox Larix decidua Picea morrisonicola P inus thunber gii Oryza sativa var. japonica Angiopteris evecta Cucumis sativus Chloranthus spicatus Crucihimalaya wallichii Thurnia sphaerocephala Georgeantha hexandra Pisum sativum Lem na minor Arabis hirsuta Physcomitrella patens F o ste r ella caulescens Epifagus virginiana Calycanthus floridus Panax ginseng Aco r u s am e r i c anus Podocarpus totara Chamaedorea seifrizii Lar i x occident alis B oea hy g r o m e tri c a Adi antum capillu s Morus indica Ecdeiocolea monostachya Neoregelia carolinae G o ssypium her bac eum Oryza rufipogon B Erodium carvifolium Cephalotaxus wilsoniana Bambusa emeiensis Nasturtium officinale Albuca kirkii Cuscuta gronovii Asparagus officinalis Agathis australis Parachlorella kessleri Part henium argent a t u m O punt ia dec u m bens Volvox cart eri Vitis vinifera T hamnochort us insignis Agrostis stolonifera Y u cca schidiger a Cathaya argyrophylla Bulnesia arborea B elosynaps i s ciliat a Musa acuminata Lomandra longifolia Pinus torreyana subsp. torreyana Huperzia luc idula E l eusi ne coracana Micromonas sp. Spirodela polyrhiza Amborella trichopoda Pitcairnia feliciana Chaet osphaeridium globosum Plumbago auriculata Manihot esculenta Dendr o c alam u s lat i f lor u s Schizomeris leibleinii N ymphaea alba Anthoceros formosae Pinus rzedowskii W eingart ia kargliana Chlorella vulgaris Wolffia australiana P inus sibir i c a Buxus microphylla Fagopyrum esculentu m Bambusa ol dhami i Pinus resinosa Oenothera biennis Phaseolus vulgaris Eleutherococcus senticosus Colocasia esculenta Pinus ponderosa Liquidambar styraciflua Brocchini a mi crantha Cornus florida Cyperus alternifolius Pinus ayacahuite Pereskiopsis diguetii Illicium oligandrum Ipomoea purpurea Phyllost achys nigra Oenothera elata Oedogonium cardiacum O enot her a ar gillic ola Welwitschia mirabilis Syngonanthus chrysanthus Corynocarpus laevigata Selaginella moellendorffii Megaleranthis saniculifolia Pinus strobus Ranunculus macranthus Vigna radiata Nuphar adv ena Pinus attenuata Spinacia oleracea Pinus lambertiana O enot her a parvi f lor a Leptosira terrestris Hesperaloe parvif lora Pelargonium x sp. P inus canar iens i s F i c u s sp. Maihuenia poeppigii Chara vulgaris Tro c hodendr on ar alioides Lobularia maritima Zygnema circumcarinatum D avi d ia involucra t a Glycine max Bra c h y podium dista c h y o n Cic e r ar iet inum Gnetum parvifolium Populus trichocarpa Joinvillea ascendens Panicum virgatum E h r e t ia ac u m inat a Lat h yru s sa t i v u s O ryza nivara A n t i rrhinum majus Nelumbo lut e a Lepidium vi r ginic u m Pteridium aquilinum P edinom onas minor Citrus sinensis Z ea ma y s Pereskia sacharosa Psilot um nudum Wolffiella lingulata Pinus flexilis Oryza australiensis Abies firma Abolboda macrostachya Passif lora bif lora Cedrus deodara G ossypium must elinum Alsophila spinulosa Hydrocotyle sp. Hordeum vulgare Gossypium hirsutum Euonymus americanus Bryopsis hypnoides Puelia olyriformis Nolina atopocarpa G o ssypium raim ondii Cuscuta exaltata Populus alba Oxypolis greenmanii Typha latifolia Indocalamus longiauritus Leersia tisserantii Ximenia americana Tri t i c u m aesti v u m Rhynchoryza subulata Gossypium darwinii Tra c helium caer uleum Staurastrum punctulatum Cucumis melo Picea sitchensis Aucuba japonica S o r ghum bic olor Nic o t iana tabac u m Jatropha curcas Portulaca oleracea S t aphylea colchica Ostreococcus tauri Oxalis latifolia G e r anium palm a t u m Lotus japonicus Micromonas pusilla Gossypium barbadense Iris virginica Oryza meridionalis E phedr a equis e t ina Oltmannsiellopsis viridis Pentactina rupicola Jacobaea vulgaris P o t a m ophila parvi f lor a Pinus banksiana Ravenea hildebrandt i i Flagellaria indica Olea woodiana Solanum bulbocastanum Lilium superbum Pinus parvif lora var. pent aphylla Nelumbo nucifera Pinus armandii J a sminum nudif lor u m Dunaliella salina H e licospori d i um sp. Pandanus utilis Pinus cembra Chlorokybus atmophyticus Acorus calamus Cheilanthes lindheimeri Rhizanthella gardneri Pinus albicaulis Pseudotsuga sinensis G i nkgo biloba Aneura mirabilis Chlorella var. iabilis Prunus persica Daucus carota Port ulacaria af r a Pinus leiophylla var. chihuahuana Pseudendoclonium akinetum Sparganium eurycarpum Silene latifolia Acidosasa purpurea Anethum graveolens S t igeoclonium helvet icum Gossypium tomentosum Pyrus pyri folia Cryptomeria japonica Cycas tait ungensis Syntrichia ruralis Ageratina adenophora Cycas micronesica Helianthus annuus Berberidopsis corallina Meliosma a ff. c uneif olia F ranklinia alat amaha Phyllostachys propinqua Millettia pinnata Pinus nelsonii Hevea brasiliensis Phoenix dactylifera Ket eleeria davidiana Carica papaya Festuca arundinacea Gossypium arboreum Lactuca sativa Anredera baselloides Ric i nus communi s Microlaena stipoides Sesamum indicum S elaginella unc inat a Silene conica Pinus monticola Pinus taeda Castanea mollissima Pinus aristata Pinus pinaster Strept o c haet a angusti f olia Cerat ophyllum demersum Nerium oleander Oryza rufipogon A Oryza sativa var. indica Platanus occidentalis Anthriscus cerefolium Medicago truncatula Saccharum hybridus Solanum tuberosum Monsonia speciosa Dillenia indica Heuchera sanguinea Renealmia alpinia Neottia nidus Ferrocalamus rimosivaginus Lolium per enne Coccomyxa sp. Phalaenopsis aphrodite Magnolia kwangsiensis Aethionema cordifolium E u c aly p t u s gr andis Q uercus nigra Halocarpus kirkii Phyllostachys edulis Atropa belladonna Crithmum maritimum Apostasia wallichii Phoradendron serotinum Coix lacryma-jobi Scenedesmus obliquus Pot arophyt um riparium Dasypogon bromeliifolius Capsella bursa-pastoris Hosta ventricosa Chlamydomonas reinhardt i i F ragaria vesca Scaevola aemula Piper cenocladum Pyramimonas parkeae Draba nemorosa Aethionema grandiflorum Pinus koraiensis Arabidops i s thaliana Anomochloa marantoidea Ilex cornuta J unc u s effu s u s Rhododendron simsii Oocystis solitaria Nicotiana sylvestris Blossfeldia liliputana Pinus merkusii P inus ger a r diana Taiwania cryptomerioides Barbarea verna Elaeis oleifera G ossypium thurberi Pinus peuce Nephroselmis olivacea 0.4 Silene noctiflora Marchantia polymorpha Puya laxa Centrolepis monogyna Equiset um arvense Monomastix sp. Liriodendron tulipifera Mayaca fluviatilis Kingia australis Nicot iana toment osif ormis Arbut u s unedo Pinus squamata Didierea madagascariensis Mesostigma viride Lonicera japonica Coffea arabica O limarabidopsis pumila Drimys granadensis Gunnera manicata Pinus cont ort a Petroselinum crispum F loydiella terrest ris Erodium texanum Cuscut a ref lexa Navia saxicola Curculigo capit ulat a Nandina domest ica Pinus monophylla Trifolium subterraneum Cuscuta obtusiflora P inus to rre y ana subsp. ins ular i s Tradescant ia ohiensis Solanum lycopersicum G uizot ia abyssinica Phormium tenax Eucalyptus globulus Ptilidi um pul cherri mum Chlorophytum rhizopendulum Mollugo verti c illata Dioscorea elephantipes Theobroma cacao Isoetes flaccida O n c idium sp. Oenothera glazioviana Neoastelia spectabilis Pinus krempfii Pycnococcus provasolii Nicotiana undulata Silene vulgaris Agapant hus praecox Larix decidua Picea morrisonicola P inus thunber gii Oryza sativa var. japonica Angiopteris evecta Cucumis sativus Chloranthus spicatus Crucihimalaya wallichii Thurnia sphaerocephala Georgeantha hexandra Pisum sativum Lem na minor Arabis hirsuta Physcomitrella patens F o ste r ella caulescens Epifagus virginiana Calycanthus floridus Panax ginseng Aco r u s am e r i c anus Podocarpus totara Chamaedorea seifrizii Lar i x occident alis B oea hy g r o m e tri c a Adi antum capillu s Morus indica Ecdeiocolea monostachya Neoregelia carolinae G o ssypium her bac eum Oryza rufipogon B Erodium carvifolium Cephalotaxus wilsoniana Bambusa emeiensis Nasturtium officinale Albuca kirkii Cuscuta gronovii Asparagus officinalis Agathis australis Parachlorella kessleri Part henium argent a t u m O punt ia dec u m bens Volvox cart eri Vitis vinifera T hamnochort us insignis Agrostis stolonifera Y u cca schidiger a Cathaya argyrophylla Bulnesia arborea B elosynaps i s ciliat a Musa acuminata Lomandra longifolia Pinus torreyana subsp. t orreyana Huperzia luc idula E l eusi ne coracana Micromonas sp. Spirodela polyrhiza Amborella trichopoda Pitcairnia feliciana Chae t osphaeridium globosum Plumbago auriculata Manihot esculenta Dendr o c alam u s lat i f lor u s Schizomeris leibleinii N ymphaea alba Anthoceros formosae Pinus rzedowskii W eingart ia kargliana Chlorella vulgaris Wolffia australiana P inus sibir i c a Buxus microphylla Fagopyrum esculentum Bambusa ol dhami i Pinus resinosa Oenothera biennis Phaseolus vulgaris Eleutherococcus senticosus Colocasia esculenta Pinus ponderosa Liquidambar styraciflua Brocchi n i a mi crantha Cornus florida Cyperus alternifolius Pinus ayacahuite Pereskiopsis diguetii Illicium oligandrum Ipomoea purpurea Phyllost achys nigra Oenothera elata Oedogonium cardiacum O enot her a ar gillic ola Welwitschia mirabilis Syngonanthus chrysanthus Corynocarpus laevigata Selaginella moellendorffii Megaleranthis saniculifolia Pinus strobus Ranunculus macranthus Vigna radiata Nuphar adv ena Pinus attenuata Spinacia oleracea Pinus lambertiana O enot her a parvi f lor a Leptosira terrestris Hesperaloe parvif lora Pelargonium x sp. P inus canar iens i s F i c u s sp. Maihuenia poeppigii Chara vulgaris Tro c hodendr on ar alioides Lobularia maritima Zygnema circumcarinatum Dav idia inv olucra t a Glycine max Bra c h y podium dista c h y o n Cic e r ar iet inum Gnetum parvifolium Populus trichocarpa Joinvillea ascendens Panicum virgatum E h r e t ia ac u m inat a Lat h yru s sa t i v u s O ryza nivara A n t i rrhinum majus Nelumbo lut e a Lepidium vi r ginic u m Pteridium aquilinum P edinom onas minor Citrus sinensis Z ea ma y s Pereskia sacharosa Psilot um nudum Wolffiella lingulata Pinus flexilis Oryza australiensis Abies firma Abolboda macrostachya Passif lora bif lora Cedrus deodara G ossypium must elinum Alsophila spinulosa Hydrocotyle sp. Hordeum vulgare Gossypium hirsutum Euonymus americanus Bryopsis hypnoides Puelia olyriformis Nolina atopocarpa G o ssypium raim ondii Cuscuta exaltata Populus alba Oxypolis greenmanii Typha latifolia Indocalamus longiauritus Leersia tisserantii Ximenia americana Tri t i c u m aesti v u m Rhynchoryza subulata Gossypium darwinii Tra c helium caer uleu m Staurastrum punctulatum Cucumis melo Picea sitchensis Aucuba japonica S o r ghum bic olor Nic o t iana tabac u m Jatropha curcas Portulaca oleracea S t aphylea colchica Ostreococcus tauri Oxalis latifolia G e r anium palm a t u m Lotus japonicus Micromonas pusilla Gossypium barbadense Iris virginica Oryza meridionalis E phedr a equis e t ina Oltmannsiellopsis viridis Pentactina rupicola Jacobaea vulgaris P o t a m ophila parvi f lor a Pinus banksiana Ravenea hildebrandt i i Flagellaria indica Olea woodiana Solanum bulbocastanum Lilium superbum Pinus parvif lora var. pent aphylla Nelumbo nucifera Pinus armandii J a sminum nudif lor u m Dunaliella salina H e licospori d i um sp. Pandanus utilis Pinus cembra C h l orokybus atmophyti cus Acorus calamus Cheilanthes lindheimeri Rhizanthella gardneri Pinus albicaulis Pseudotsuga sinensis G i nkgo biloba Aneura mirabilis Chlorella var.iabilis Prunus persica Daucus carota Port ulacaria af r a Pinus leiophylla var. chihuahuana Pseudendoclonium akinetum Sparganium eurycarpum Silene latifolia Acidosasa purpurea Anethum graveolens S t igeoclonium helvet icum Gossypium tomentosum Pyru s pyri folia Cryptomeria japonica Cycas tait ungensis Syntrichia ruralis Ageratina adenophora Cycas micronesica Helianthus annuus Berberidopsis corallina Meliosma a ff. cuneif olia F ranklinia alat amaha Phyllostachys propinqua Millettia pinnata Pinus nelsonii Hevea brasiliensis Phoenix dactylifera Ket eleeria davidiana Carica papaya Festuca arundinacea Gossypium arboreum Lactuca sativa Anredera baselloides Ric i nus communi s Microlaena stipoides Sesamum indicum S elaginella unc inat a Silene conica Pinus monticola Pinus taeda Castanea mollissima Pinus aristata Pinus pinaster Strept o c haet a angusti f olia Cerat ophyllum demersum Nerium oleander Oryza rufipogon A Oryza sativaIndica Platanus occidentalis Anthriscus cerefolium Medicago truncatula Saccharum hybridus Solanum tuberosum Monsonia speciosa Dillenia indica Heuchera sanguinea Renealmia alpinia Neottia nidus Ferrocalamus rimosivaginus Lolium per enne Coccomyxa sp. Phalaenopsis aphrodite Magnolia kwangsiensis Aethionema cordifolium E u c aly p t u s gr andis Q uercus nigra Halocarpus kirkii Phyllostachys edulis Atropa belladonna Crithmum maritimum Apostasia wallichii Phoradendron serotinum Coix lacryma-jobi Scenedesmus obliquus Pot arophyt um riparium Dasypogon bromeliifolius Hosta ventricosa Chlamydomonas reinhardt i i F ragaria vesc a Scaevola aemula Piper cenocladum Pyramimonas parkeae Draba nemorosa Aethionema grandiflorum Pinus koraiensis Arabidops i s thaliana Anomochloa marantoidea Ilex cornuta J unc u s effu s u s Rhododendron simsii Oocystis solitaria Nicotiana sylvestris Blossfeldia liliputana Pinus merkusii P inus ger a r diana Taiwania cryptomerioides Barbarea verna Elaeis oleifera G ossypium thurberi Pinus peuce Nephroselmis olivacea Capsella bursa-pastoris O lea eur opaea ssp. m a r occana O l ea europaea ssp. europaea Olea europaea ssp. cuspidata O lea eur opaea ssp. m a r occana O l ea europaea ssp. europaea Olea europaea ssp. cuspidata



PAGE 1

RESEARCHARTICLEOpenAccessFromalgaetoangiosperms – inferringthe phylogenyofgreenplants( Viridiplantae )from 360plastidgenomesBradRRuhfel1*,MatthewAGitzendanner2,3,4,PamelaSSoltis3,4,DouglasESoltis2,3,4andJGordonBurleigh2,4AbstractBackground: Next-generationsequencinghasprovidedawealthofplastidgenomesequencedatafroman increasinglydiversesetofgreenplants( Viridiplantae ).Althoughthesedatahavehelpedresolvethephylogenyof numerousclades(e.g.,greenalgae,angiosperms,andgymnosperms),theirutilityforinferringrelationshipsacrossall greenplantsisuncertain. Viridiplantae originated700-1500millionyearsagoandmaycompriseasmanyas500,000 species.Thiscladerepresentsamajorsourceofphotosyntheticcarbonandcontainsanimmensediversityoflife forms,includingsomeofthesmallestandlargesteukaryotes.Hereweexplorethelimitsandchallengesofinferring acomprehensivegreenplantphylogenyfromavailablecompleteornearlycompleteplastidgenomesequencedata. Results: Weassembledprotein-codingsequencedatafor78genesfrom360diversegreenplanttaxawithcomplete ornearlycompleteplastidgenomesequencesavailablefromG enBank.Phylogeneticanalysesoftheplastiddatarecovered well-supportedbackbonerelationshipsandstrongsupportforrelationshipsthatwerenotobservedinpreviousanalyses ofmajorsubcladeswithin Viridiplantae .However,therealsoisevidenceofsystematicerrorinsomeanalyses.In severalinstancesweobtainedstronglysupportedbutconflictingtopologiesfromanalysesofnucleotidesversus aminoacidcharacters,andtheconsiderablevariationi nGCcontentamonglineagesandwithinsinglegenomes affectedthephylogeneticplacementofseveraltaxa. Conclusions: Analysesoftheplastidsequencedatarecoveredastronglysupportedframeworkofrelationshipsfor greenplants.Thisframeworkincludes:i)theplacementof Zygnematophyceace assistertolandplants( Embryophyta ),ii) acladeofextantgymnosperms( Acrogymnospermae )withcycads+ Ginkgo sistertoremainingextantgymnosperms andwithgnetophytes( Gnetophyta )sistertononPinaceae conifers(Gnecuptrees),andiii)withinthemonilophyteclade ( Monilophyta ), Equisetales + Psilotales aresisterto Marattiales +leptosporangiateferns.Ouranalysesalsohighlightthe challengesofusingplastidgenomesequencesindeep-levelphylogenomicanalyses,andweprovidesuggestionsfor futureanalysesthatwilllikelyincorporateplastidgenomesequencedataforthousandsofspecies.Weparticularly emphasizetheimportanceofexploringtheeffectsofdifferentpartitioningandcharactercodingstrategies. Keywords: Compositionbias,Phylogenomics,Plastidgenomesequences,Plastomes,RY-coding, ViridiplantaeBackgroundViridiplantae ,orgreenplants,areacladeofperhaps 500,000species[1-6]thatexhibitanastoundingdiversity oflifeforms,includingsomeofthesmallestandlargest eukaryotes[3,7].Fossilevidencesuggeststhecladeisat least750millionyearsold[8-10],whiledivergencetime estimatesfrommoleculardatasuggestitmaybemore thanonebillionyearsold[11-14].Reconstructingthe phylogeneticrelationshipsacrossgreenplantsischallengingbecauseoftheageoftheclade,theextinctionof majorlineages[15-17],andextrememolecularrateand compositionalheterogeneity[18-22].Mostphylogenetic analysesof Viridiplantae haverecoveredtwowellsupportedsubclades, Chlorophyta and Streptophyta [23,24]. Chlorophyta containmostofthetraditionally recognized “ greenalgae, ” and Streptophyta containthe landplants( Embryophyta ),aswellasseveralother lineagesalsoconsidered “ greenalgae ” .Landplants *Correspondence: brad.ruhfel@eku.edu1DepartmentofBiologicalSciences,EasternKentuckyUniversity,Richmond, KY40475,USA Fulllistofauthorinformationisavailableattheendofthearticle 2014Ruhfeletal.;licenseeBioMedCentralLtd.ThisisanOpenAccessarticledistributedunderthetermsoftheCreative CommonsAttributionLicense(http://creativecommons.org/licenses/by/2.0),whichpermitsunrestricteduse,distribution,and reproductioninanymedium,providedtheoriginalworkisproperlycredited.Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 http://www.biomedcentral.com/1471-2148/14/23

PAGE 2

includetheseedplants(gymnospermsandangiosperms; Spermatophyta ),whichconsistof~270,000to~450,000 species[1,3]. Whilemanyofthemajorgreenplantcladesarewell defined,questionsremainregardingtherelationships amongthem.Forexample,theclosestrelativesofland plantshavevariedamonganalyses[23,25-29],ashave therelationshipsamongthethreebryophytelineages (mosses,liverworts,andhornworts)[29-35].Therelationshipsamongextantgymnospermsalsoremaincontentious,particularlywithrespecttotheplacementof Gnetophyta [20,36-43]. Mostbroadanalysesofgreenplantrelationshipsbased onnucleargenesequencedatahavereliedlargelyon 18S/26SrDNAsequences[30,37,44,45],althoughrecent analyseshaveemployednumerousnucleargenes[40,46]. Somestudieshaveusedmitochondrialgenesequence data,oftenincombinationwithotherdata[29,47,48]. However,investigationsofgreenplantphylogenytypicallyhaveeitherlargelyorexclusivelyemployedchloroplastgenes(e.g.,[29,49-52]).Sequencedatafromthe plastidgenomehavetransformedplantsystematicsand contributedgreatlytothecurrentviewofplantrelationships.Withtheplastidgenomepresentinhighcopy numbersineachcellinmostplants,andwithrelatively littlevariationingenecontentandorder[53],aswellas fewreportedinstancesofgeneduplicationorhorizontal genetransfer[54,55],theplastidgenomeprovidesa wealthofphylogeneticallyinformativedatathatarerelativelyeasytoobtainanduse[56,57].Althoughearly phylogeneticstudiesusingoneorafewchloroplastloci providedfundamentalinsightsintorelationshipswithin andamonggreenplantclades,theseanalysesfailedto resolvesomebackbonerelationships[56-59].These remainingenigmaticportionsofthegreenplanttreeoflife ultimatelymotivatedtheuseofentire,ornearlyentire, plastidgenomesequencesforphylogeneticinference. Completesequencingoftherelativelysmall(~150kb) plastidgenomehasbeentechnicallyfeasiblesincethe mid-1980s[60,61],althoughfewplastidgenomeswere sequencedpriorto2000(see[62,63]).Next-generation sequencing(NGS)technologies,suchas454[62]and Illumina[64-67],greatlyreducedthecostanddifficulty ofsequencingplastidgenomes,andconsequently,the numberofplastidgenomesavailableonGenBankincreasednearlysix-foldfrom2006to2012[68].Phylogeneticanalysesbasedoncompleteplastidgenomesequences haveprovidedvaluableinsightsintorelationshipsamong andwithinsubcladesacrossthegreenplanttreeoflife(recentlyreviewedin[26,35,68,69]).Still,studiesemploying completeplastidgenomesgenerallyhaveeitherfocused onsubcladesofgreenplantsorhavehadrelativelylow taxonsampling.Thus,theyhavenotaddressedthemajor relationshipsacrossallgreenplantssimultaneously. Weassembledavailableplastidgenomesequencesto buildaphylogeneticframeworkfor Viridiplantae that reflectsthewealthofnewplastidgenomesequencedata. Furthermore,wehighlightanalyticalchallengesforresolvingthegreenplanttreeoflifewiththistypeofdata. Weperformedphylogeneticanalysesofprotein-coding dataon78genesfrom360taxa,exploringtheeffectsof differentpartitioningandcharacter-codingprotocolsfor theentiredatasetaswellassubsetsofthedata.While ouranalysesrecovermanywell-supportedrelationships andrevealstrongsupportforsomecontentiousrelationships,severalfactors,includingbasecompositionbiases, canaffecttheresults.Wealsohighlightthechallenges ofusingplastidgenomedataindeep-levelphylogenomic analysesandprovidesuggestionsforfutureanalysesthat willincorporateplastidgenomedataforthousandsof species.ResultsDatasetWeassembledplastidprotein-codingsequencesfrom360 species(Additionalfile1)forwhichcompleteornearly completeplastidgenomesequenceswereavailableonGenBank.Ofthe360species,therewere258angiosperms ( Angiospermae ),53gymnosperms( Acrogymnospermae ,includingthree Gnetophyta ),sevenmonilophytes( Monilophyta ),fourlycophytes( Lycopodiophyta ),threeliverworts ( Marchantiophyta ),onehornwort( Anthocerotophyta ),two mosses( Bryophyta ),sixtaxafromtheparaphyleticstreptophyticalgae,and26chlorophyticalgae( Chlorophyta ).The phylogeneticcharactermatricescontainedsequencesfrom 78genesandthefollowingnumberofalignmentpositions: 58,347bpforthematrixcontainingallnucleotidepositions (ntAll)andtheRY-coded(RY)versionofthentAllmatrix; 38,898bpinthematrixcontainingonlythefirstandsecondcodonpositions(ntNo3rd),and19,449aminoacids (AA).Thenumberofgenespresentpertaxonvariedfrom 18to78(mean=70),whilethenumberoftaxapresentper generangedfrom228to356(mean=322;seeAdditional file2).Taxawithfewgenespresent,suchas Helicosporidium (18genes)and Rhizanthella (19genes),represent highlymodifiedcompleteplastidgenomesofnonphotosyntheticspecies[70,71].Thepercentageofmissing data(gapsandambiguouscharacters)was~15.6%for eachofthefourdatasets.Thepatternofdataacrosseach ofthefourmatricesisdecisive,meaningthatitcan uniquelydefineasingletreeforalltaxa[72].Thedata contain100%ofallpossibletripletsoftaxa,andaredecisivefor100%ofallpossibletrees.Allalignmentshave beendepositedintheDryadDataRepository[73].GCbiasGCcontentvariedconsiderablybothamonglineages andalsowithinsinglegenomes,andchi-squaretestsRuhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page2of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 3

rejectedthenullhypothesisofhomogeneousbasefrequencies(Table1).TheaverageGCcontentinthentAll matrixwas38.9%,anditrangedfrom54.3%in Selaginellauncinata to27.5%in Helicosporidium sp.(Figure1, Additionalfile3).Also,theaverageGCcontentvaried amongfirst,second,andthirdcodonpositions,withby farthemostvariationamonglineagesatthethirdcodon position(Figure1,Additionalfile3).Althoughtherewas extensiveheterogeneityinGCcontentacrossallspecies, therewasrelativelylittlevariationamongtheseedplant taxa(Figure2).Therealsowassignificantcorrelation betweennucleotidecompositionandaminoacidcomposition.PlastidgenomesthatareGC-richhadasignificantlyhigherpercentage(F igure3;p<0.001)ofamino acidsthatareencodedbyGC-richcodons(i.e.,G,A,R, andP).Similarly,GC-richplastidgenomeshadasignificantlylowerpercentage(Figur e4;p<0.001)ofaminoacids thatarecodedbyAT-richcodons(i.e.,F,Y,M,I,N,andK).PhylogeneticanalysesInthephylogeneticanalysesofalldatasetsandpartitioningschemes,thepartitioningstrategywiththemost partitionsconsistentlyfitthedatabestbasedonthe AICc(Table2).Thesebest-fitmodelspartitionedthe AAmatrixbygene(78partitions)andthenucleotide (ntAll,ntNo3rd)andRYmatricesbycodonpositionand gene(234partitions).Allaposterioribootstoppinganalysesindicatedthatconvergenceofsupportvalueshad beenreachedafter100replicates,andthusourchoiceof 200replicateswasmorethansufficienttoobtainreliable bootstrapvalues. Wewillfocusonreportingtherelationshipsofmajor cladesof Viridiplantae showninthe50%maximumlikelihood(ML)majority-rulebootstrapconsensussummary treesforeachdataset:ntAll(Figure5),ntNo3rd(Figure6), RY(Figure7),andAA(Figure8).Thesesummarytrees collapsesomecladesforeaseofviewingthemajorrelationshipswithin Viridiplantae .Asummaryofimportant resultsandconflictsamongthesefourdatasetsisgivenin Table3.Weprovidefullmajority-rulebootstrapconsensustreesforthentAll(Figures9,10,11,12,13,and14), ntNo3rd(Additionalfile4),RY(Additionalfile5),andAA (Additionalfile6)datasets.MLtreeswithbranchlengths andBSvaluesarealsoprovided:ntAll(Additionalfile7), ntNo3rd(Additionalfile8) ,RY(Additionalfile9),and AA(Additionalfile10).Averagesupportvaluesamong allinternalnodesintheMLtreeswereslightlyhigher inthentAllphylogeny(~94%bootstrapsupport[BS]; Additionalfile7)comparedtotheotherdatasets (~90-91%BS;Additionalfiles8,9,and10).ThentAll phylogenyalsohadthemostcladesresolvedwith 70%BS(92%;327bipartitionsresolvedoutof357possible)whilethentNo3rd,RY,andAAdatasetshad87%, 87%,and86%ofthepossiblebipartitionsresolvedat 70%BS,respectively.AllresultingtreeshavebeendepositedintheDryadDataRepository[73]. Themonophylyof Chlorophyta receives100%BSin allanalyses. Prasinophyceae areconsistentlynotmonophyletic.Instead,theprasinophyte Nephroselmis issister toallother Chlorophyta (Figure9;Additionalfiles4,5, and6),whileremaining Prasinophyceae formaclade thatisvariouslysupported(ntAll97%BS,ntNo3rd78% BS,RY93%BS,andAA68%BS)andissistertoaclade oftheremaining Chlorophyta.Chlorophyceae are monophyletic(100%BSinallanalyses),but Trebouxiophyceae and Ulvophyceae arenotmonophyletic,andthe relationshipof Chlorophyceae totheselineagesis unresolved. Weconsistentlyrecoveredasinglesetofrelationships amongthestreptophyticalgaesubtendingthelandplant clade. Zygnematophyceae aresistertolandplants, Coleochaetophyceae aresisterto Zygnematophyceae + Embryophyta Charophyceae aresisterto Coleochaetophyceae + ( Zygnematophyceae + Embryophyta ),andacladeof Mesostigmatophyceae + Chlorokybophyceae issistertoall other Streptophyta .Eachoftheserelationshipshas 86% BSsupport(Figures5,6,7,and8). Thebranchingorderofthenon-vascularlandplant lineagesdiffersamonganalyses.InanalysesofthentAll andRYdatasets, Marchantiophyta (liverworts),followed by Bryophyta(mosses),andthen Anthocerotophyta (hornworts)aretheearliest-branchinglandplant lineages,with Anthocerotophyta theimmediatesister tothevascularplants( Tracheophyta ;Figures5and7). InthentAllandRYanalyses,theserelationshipshad 89% BSsupportexceptforthe Bryophyta +( Anthocerophyta + Tracheophyta )relationshipinthentAllanalysis,which receivedonly69%BS(Figure5).Incontrast,inthentNo3rd andAAanalyses, Bryophyta and Marchantiophyta formeda clade(78%BS[Figure6]and99%BS[Figure8],respectively),followedby Anthocerophyta assisterto Tracheophyta (94%[Figure6]and53%BS[Figure8],respectively). Within Tracheophyta ,thentNo3rd,RY,andAAdata setsallplace Lycopodiophyta sistertoa Euphyllophyta clade( Monilophyta + Spermatophyta ; 89%BS,Figures6, 7,and8).However,theanalysisofthentAlldataset places Monilophyta sistertoacladeof Lycopodiophyta + Spermatophyta (75%BS,Figures5,6,7,8,9,and10). Table1Chi-squaretestsofnucleotidecomposition homogeneityamonglineagesData 2dfp ntAll31350.2571851077<0.0001 ntNo3rd11968.0024641077<0.0001 ntAll(Position1)8366.3314391077<0.0001 ntAll(Position2)6003.3380411077<0.0001 ntAll(Position3)46288.2487851077<0.0001 Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page3of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 4

Ouranalysesof Monilophyta generallyrevealstrongsupportforacladeof Equisetales + Psilotales assisterto Marattiales +leptosporangiateferns(representedby Cyatheales and Polypodiales ).Thelowestsupportobtainedwasfor Equisetales + Psilotales inthentNo3rdanalysis(84%BS; Figure6)andntAll(89%BS;Figure5);allothernodes inallanalysesreceived>90%BS,with Marattiales + leptosporangiatefernsreceiving 99%BS. Within Spermatophyta ,allanalysesplacetheextant gymnosperms( Acrogymnospermae )sisterto Angiospermae with100%BS.Withinextantgymnosperms, Cycadales and Ginkgoales formaclade( 98%BSinntAll, ntNo3rd,andAA;51%BSinRY)thatissistertoaclade inwhich Gnetophyta (100%BSinallanalyses)arenested withintheparaphyleticconifers.Thereisgenerallyhigh support(100%BSinntAll[Figure5],ntNo3rd[Figure6], andAA[Figure7];87%BS[Figure8]inRY)placing Gnetophyta assistertoacladeof Araucariales + Cupressales .This “ Gnecup ” clade[sensu16,30,41]isthensisterto Pinales, whichhas100%BSinallanalyses. Inallanalyses, Angiospermae receive100%BS,and Amborella ( Amborellales )issistertoallotherangiosperms,followedby Nymphaeales ,andthen Austrobaileyales .Theserelationshipsaremostlysupportedby 100%BS.However, Nymphaeales +( Austrobaileyales + Mesangiospermae )receives81%BS(Figure6)inthe ntNo3rdanalysesand70%BS(Figure8)intheAAanalyses.Theremainingangiosperms( Mesangiospermae )receive100%BSinallanalyses.Within Mesangiospermae, therelationshipsamong Monocotyledoneae Magnoliidae Eudicotyledoneae ,and Ceratophyllum ( Ceratophyllales ) arenotwellsupportedandvarydependingontheanalysis. Thestrongestsupportfortheplacementof Ceratophyllales is75%BSassisterto Eudicotyledoneae intheRYanalysis (Figure7). Chloranthales receive61-69%BSassistertothewellsupported(100%BSinntAll,RY;83%BSinntNo3rd) Magnoliidae .However, Magnoliidae arenotmonophyleticintheAAanalyses,where Piperales aresisterto Ceratophyllales (67%BS;Figure8). Figure1 BoxplotsofpercentGCcontentinthentAllandntNo3rddatasetsaswellasinthefirst,second,andthirdcodonpositions ofthentAlldataset. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page4of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 5

Figure3 CorrelationbetweenpercentGCnucleotidecontentinthentAllmatrixandpercentofaminoacidsintheAAmatrixthatare codedforbyGC-richcodons(G,A,R,andP). Figure2 BoxplotsofpercentGCcontentinseedplants( Spermatophyta; onleft)andthedatasetasawhole( Viridiplantae; onright)in thentAllandntNo3rddatasetsaswellasthefirst,second,andthirdcodonpositionsofthentAlldataset. Foreachpairofboxplots, valuesforseedplants( Spermatophyta )areontheleft,andvaluesforallgreenplanttaxa( Viridiplantae )areontheright. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page5of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 6

Withinthemonocotclade( Monocotyledoneae ), Acorales followedby Alismatales ,have100%BSinallanalysesas subsequentsisterstotheremainingmonocots.Inthreeof ouranalyses(ntAll,ntNo3rd,andAA),avariouslysupportedclade(72%,69%,and80%BS,respectively)of Liliales +( Pandanales + Dioscoreales )issistertoaclade (>95%BSinthesethreeanalyses)oftheremaining monocots( Asparagales + Commelinidae ).However,inthe RY-codedanalysis, Pandanales + Dioscoreales (100%BS)is sistertoacladeof Liliales +( Asparagales + Commelinidae ), whichreceives69%BS(Figure7).Here Asparagales + Commelinidae issupportedby80%BS. Withintheeudicots( Eudicotyledoneae ),whichreceive 100%BSinallanalyses, Ranunculales aresistertothe Figure4 CorrelationbetweenpercentGCnucleotidecontentinthentAllmatrixandpercentofaminoacidsintheAAmatrixthatare codedforbyAT-richcodons(F,Y,M,I,N,andK). Table2AICcscoresforeachofthephylogeneticmatrixpartitioningstrategies MatrixNumberof characters PartitioningstrategyNumberof partitions Log-likelihoodAICc AICc ntAll58,347OnePart1 3135739.5441166272952.811161114533.884536 CodonPart3 3099273.0996396200056.46846241637.541838 GenePart78 3120195.0773166243312.24176684893.315142 CodonGenePart234 3076219.4267926158418.9266240 RY58,347OnePart1 1239354.4534022480173.24648021572.787069 CodonPart3 1235533.3680702472537.85440113937.394990 GenePart78 1234706.1788992471197.31131412596.851903 CodonGenePart234 1228081.1599862458600.4594110 ntNo3rd38,898OnePart1 1387913.0348302777313.72111730326.016847 CodonPart2 1385570.0861542772645.57081625657.866546 GenePart78 1376158.2630232755293.7879168306.083646 CodonGenePart156 1371218.7164502746987.7042700 AA19,449OnePart1 1418038.1520842837614.1017178353.616354 GenePart78 1413039.6604962829260.4853630 PartitioningstrategiesjudgedtobethebestbytheAICcareinbold. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page6of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 7

Figure5 (Seelegendonnextpage.) Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page7of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 8

remainingtaxa.InthentAll,ntNo3rd,RY,andAAanalyses,thecladeoftheseremainingtaxareceives100%, 85%,100%,and62%BS,respectively.Relationshipsvary among Sabiaceae Proteales ,andacladeoftheremaining taxa,dependingontheanalysis.InthentAllandntNo3rd analyses, Proteales + Sabiaceae aresupportedasaclade, althoughwithonly63%and60%BS,respectively.However,intheRYanalysis, Proteales aresistertoacladecontaining Sabiaceae plustheremainingtaxa,whichhas79% BS.IntheAAanalysis,relationshipsamongthesethree cladesareunresolved. Amongtheremainingeudicots,weconsistentlyrecovered Trochodendrales assisterto Buxales + Pentapetalae and Gunnerales assistertotheremaininglineagesof Pentapetalae : Dilleniaceae Superrosidae ,and Superasteridae .Theplacementof Dilleniaceae remainsuncertain.Thefamilyissisterto Superrosidae inthentAll (95%BS),ntNo3rd(77%BS),andRY(57%BS)analyses, butappearsassisterto Superasteridae (70%BS)inthe AAanalysis. Within Superrosidae ,acladeof Vitales + Saxifragales issupportedinthentAll(75%BS),ntNo3rd(70%BS), andAA(78%BS)analyses.IntheRYanalysis,therelationshipamong Saxifragales Vitales ,andremaining Rosidae ( Fabidae + Malvidae )isunresolved. Fabidae and Malvidae arebothrecoveredwith 99%BSinthe ntAllandRYanalyses.However,eachcladereceives only70%BSinthentNo3rdanalysis.IntheAAanalysisneithercladeismonophyletic; Zygophyllales are embedded(68%BS)withinacladeof Malvidae taxa. TheCOMclade( Celastrales Oxalidales Malpighiales )issistertoacladeof Fagales Cucurbitales Rosales ,and Fabales in Fabidae intheAA(69%BS; Figure8),RY(82%BS;Figure7),andntAll(81%BS;Figure5)treesandformsatrichotomywith Zygophyllales andthecladeof Fagales Cucurbitales Rosales ,and Fabales inthentNo3rdtree(70%BS;Figure6). Zygophyllales are sisterto Geraniales (69%BS;Figure8)intheAAtreeand sistertoallother Fabidae inthentAllandRYtrees(with 100%[Figure5]and99%BS[Figure7],respectively). Superasteridae ( Santalales Berberidopsidales Caryophyllales ,and Asteridae )arerecoveredinallanalyses. Thiscladereceives100%BSinthentAllandRYanalyses,95%BSinthentNo3rdanalysis,and66%BSin theAAanalysis. Santalales and Berberidopsidales are stronglysupportedassubsequentsistersto Caryophyllales + Asteridae .Within Asteridae Cornales ,followed by Ericales ,aresubsequentsisterstoastronglysupportedcladethatcomprisesstronglysupported Campanulidae and Lamiidae clades.Within Lamiidae ,the placementof Boraginaceae isweakamongthevarious analyses. Boraginaceae aresisterto Gentianales (59%BS; Figure8)intheAAtree,partofatrichotomy(100%BS; Figure5)with Lamiales and Solanales + Gentianales in thentAlltree,andsistertoaweaklysupportedcladeincluding Gentianales Lamiales ,and Solanales inthe ntNo3rd(Figure6)andRY(Figure7)trees. Analysisofonlythethirdcodonpositions(nt3rdOnly, Additionalfile11)resultedinseveralverystrongconflictsalongthebackboneof Viridiplantae whencomparedtothetopologyfromthentNo3rdanalyses.These conflictsincludethebackbonerelationshipswithin Chlorophyta ,theplacementsof Cycadales and Lycopodiophyta therelationshipsofthethreemajorbryophytelineages, andbackbonerelationshipswithin Poales .Removaloffour taxa( Epifagus,Helicosporidium,Neottia, andRhizanthella) withelevatedratesofmolecularevolutionandfewgenes presentinthedatasetsdidnotsignificantlyaffectthe resultingtopologies.DiscussionWhiletheenormousphylogeneticdatasetsthatresult fromnewgenomeortranscriptomesequencingefforts canamelioratetheeffectsofrandomorstochasticerror, theyalsomayexacerbatetheeffectsofsystematicerror, orerrorresultingfromproblemsintheanalysis,suchas modelinaccuracy.Thehighamountofagreement amongourvariousanalysesandstrongsupportforresultsgenerallyconsistentwithpreviousstudies(manyof whichalsousedplastidgenes)suggestthatplastidgenomesequencedataholdmuchpromiseforresolvingrelationshipsthroughoutthegreenplants.However, severalareasofconflictbetweenanalysesusingdifferent character-codingstrategiesdemonstratethatplastidgenomephylogeneticsisalsosusceptibletosystematicerror. Hereweevaluatethephylogeneticresults,emphasizing areasofagreementandconcern,andthenaddresssome ofthemethodologicalissuesraisedbyourresults.EvaluationofphylogeneticrelationshipsHistorically, Chlorophyta havebeendividedinto Prasinophyceae Trebouxiophyceae Chlorophyceae ,and Ulvophyceae basedontheultrastructureoftheflagellarapparatusand featuresrelatedtocytokinesis [74,75].Thecurrentstatusof (Seefigureonpreviouspage.) Figure5 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensussummarytreeof Viridiplantae inferredfromtheall nucleotidepositions(ntAll)analysis. Datasetderivedfrom78protein-codinggenesoftheplastidgenome(ntax=360;58,347bp;missingdata~15.6%). Bootstrapsupportvalues 50%areindicated.Terminalswithatrianglerepresentcollapsedcladeswith>2taxa.Notepositionof Lycopodiophyta as sisterto Spermatophyta islikelycausedbybasecompositionbias(seetext).SeeFigures9,10,11,12,13,and14forthecompletetreeand Additionalfile1fortaxonomy. Lami .= Lamiidae ; Campanuli .= Campanulidae ; Lyco .= Lycopodiophyta Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page8of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 9

Figure6 (Seelegendonnextpage.) Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page9of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 10

greenalgaephylogenetics( Chlorophyta andstreptophytic algae)hasbeenreviewedrecently[26,76,77].Themostcomparablestudytooursintermsofdataandtaxonsamplingis byLangandNedelcu[26],whoconstructedaphylogenyof greenalgaewithplastidgenomesequencedata.However, theyanalyzedonlyanaminoaciddatasetusingBayesianinferenceandtheCATmodel[78,79].Wefoundaparaphyletic Prasinophyceae (notincluding Pedinomnas ;Figures5, 6,7and8),whichagreeswithpreviousmolecularanalyses [26,76,77].However,LangandNedelcu[26]recovereda monophyletic Prasinophyceae ,albeitwithlittlesupport. Chlorophyceae aremonophyletic(100%BSinallofouranalyses),whichagreeswiththeresultsofLangandNedelcu [26].Wealsofindthat Trebouxiophyceae and Ulvophyceae arenotmonophyletic,andthattherelationshipof Chlorophyceae totheselineagesisunresolved.Thebranchingorder ofthevarious Trebouxiophyceae Ulvophyceae ,and Chlorophyceae lineageswithin Chlorophyta ,unresolvedinouranalyses,wasalsouncertaininearlieranalyses(reviewedin [26,76,77]).SimilarlyinLangandNedelcu[26], Trebouxiophyceae and Ulvophyceae werenotsupportedasmonophyletic,althoughunlikeourresults,almostallnodesintheir phylogenyweremaximallysupported. Ouranalysesprovideconsistent,strongsupportforthe relationshipsofstreptophyticalgaetolandplants,andall analysessupport Zygnematophyceae asthesistertoland plants(Figures5,6,7,and8).Relationshipsamongthese lineagesandtheclosestrelativesoflandplantshavevaried inpreviousstudiesdependingontaxonsamplingandgene choice.Somestudiesagreewithourresultsplacing Zygnematophyceae assistertolandplants[25,27,80-82],while otherphylogeneticanalysesindicatethat Charophyceae [23,83,84]or Coleochaetophyceae [26,40,85,86]occupythis position.Dependingontheanalysis,Zhongetal.[87] foundeither Zygnematophyceae aloneoracladeof Zygnematophyceae + Coleochaetophyceae assistertolandplants. Inparticular,theresultsofLangandNedelcu[26]conflict withourresultsregardingthesistergroupto Embryophyta Whilewefindacladeof Coleochaetophyceae +( Zygnematophyceae + Embryophyta ),theirresultsstronglysupport Zygnematophyceae +( Coleochaetophyceae + Embryophyta ). Phylogeneticrelationshipsamongbryophytes(mosses, hornworts,andliverworts)arealsocontentious,and nearlyeverypossiblerelationshipamongtheselineages hasbeenreported,oftenwithstrongsupport.Most studieshaveshownthebryophytesasparaphyleticwith respectto Tracheophyta ratherthanasaclade[30-33]. AsrecoveredinourntAllandRYanalyses(Figures5 and7),liverworts( Marchantiophyta )oftenareplaced sistertoallotherlandplants,followedbymosses( Bryophyta ),andwithhornworts( Anthocerotophyta ) sisterto Tracheophyta [29,34,47,50,88,89].Asisterrelationshipbetweenmossesandliverworts,foundin ourntNo3rdandAAanalyses(Figures6and8),was proposedpreviouslybasedonmorphological[90-93] andmoleculardata[27,30,94,95]andhasbeenrecoveredwithnumerousnucleargenes(Wickettetal.,in review).ThisrelationshipwasalsorecoveredinanalysesofcompleteplastidgenomedatabyKaroletal. [34]whendivergenttaxa(i.e., Selaginella spp.)were excludedfromphylogeneticanalysesandalsobyWolf andKarol[35]whenthirdp ositionswereexcluded. Ourresultsplacing Lycopodiophyta sisterto Euphyllophyta inallbutthentAllanalysisagreewithmostmolecularphylogeneticanalyses[29,96,97].Thissplitisalso supportedbyanalysesofmorphologicalcharactersin fossil[15]andextanttaxa[98]. Monilophyta and Spermatophyta alsopossessa30-kbinversioninthelarge single-copyregionoftheplastidgenomenotfoundin Lycopodiophyta andthethreebryophyteclades[99].In thentAllanalysis, Euphyllophyta arenotmonophyletic (Figure5); Lycopodiophyta ,ratherthan Monilophyta ,are sisterto Spermatophyta .Thisrelationshiphasbeenreportedpreviously[34];however,itlikelyisaphylogeneticartifact,perhapsrelatedtobasecompositionbias (seebelow).Theplastidgenomeofthelycophyte Selaginella hasanespeciallyhighGCcontent[21],with Selaginellaunicata havingthehighestGCcontentin ourntAlldataset(54.3%;Figure1). Insomepreviousstudies,relationshipsamonglineages of Monilophyta havenotbeenwellresolvedorsupported (e.g.,[29,89,96-98]).Asaresult,therelationshipsamong Equisetales Psilotales Marattiales ,andleptosporangiate fernsareoftenrepresentedasapolytomy(e.g.,[35]).In contrast,mostofouranalysesrecoveredstrongsupportfor acladeof Equisetales + Psilotales assisterto Marattiales + leptosporangiateferns(representedhereby Cyatheales and Polypodiales ).Theserelationshipsagreewithrecentstudies ofmonilophyterelationshipsbasedonplastidgenomesequencedata[34,35],althoughsupportisstrongerhere.Unfortunately, Ophioglossales ,whichoftenappearassisterto Psilotales ,lackedasequencedplastomeatthetimeofour analyses.However,plastidgenomedatafor Ophioglossales havesubsequentlybeenpublishedandanalyzedinaphylogeneticcontext[100],withstrongsupportfor Ophioglossales assisterto Psilotales andweaksupportforthisclade (Seefigureonpreviouspage.) Figure6 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensussummarytreeof Viridiplantae inferredfromthefirstand secondcodonpositions(ntNo3rd)analysis. Datasetderivedfrom78protein-codinggenesoftheplastidgenome(ntax= 360;38,898bp; missingdata~15.6%).Bootstrapsupportvalues 50%areindicated.Terminalswithatrianglere presentcollapsedcladeswith>2taxa.See Additionalfile4forthecompletetree andAdditionalfile1fortaxonomy. Lami .= Lamiidae ; Campanuli .= Campanulidae Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page10of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 11

Figure7 (Seelegendonnextpage.) Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page11of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 12

assisterto Equisetales .Resultsfromthatstudywithregard to Marattiales andleptosporangiatefernsagreewiththe relationshipspresentedhere. Relationshipsamongthelineagesofextantseedplants, andespeciallytheplacementof Gnetophyta ,havelong beendebated[38,39,43,51,89,101].Gnecuptrees,found inallofouranalyses,wereinitiallyrecoveredbyNickrent etal.[30],andthenmorerecentlybyZhongetal.[41]. However,Zhongetal.[41]suggestedthatthesupportfor Gnecupmaybetheresultoflong-branchattraction;by removinghighlyvariableproteins,supportforGnecup decreased.Furthermore,byremovingwhattheyconsideredparallelsubstitutionsbetweenlineagesleadingto Gnetophyta andto Cryptomeria (thesole Cupressales in theiranalyses),aGnepinetopologywasrecovered.Althoughseveraldifferentplacementsfor Gnetophyta have beenrecoveredandstronglysupported,manystudiesinvolvingmultiplegeneshaveplaced Gnetophyta sisterto Pinales (Gnepine;[38,39,43,89],Wickettetal.,inreview). Usingbothcoalescentandconcatenationanalyses,Xi etal.[102]foundthatthephylogeneticplacementof Gnetophyta differsbetweenthenuclearandplastidgenomes.Intheiranalysesusingnucleardata,theGnepine hypothesisissupported,whiletheiranalysesofplastid datasupporttheGnecuphypothesis.Incontrast,Leeetal. [46]foundstrongsupportfor Gnetophyta sistertothe remaininggymnosperms[( Cycadales + Ginkgoales )+ conifers)]inanMLanalysisof22,833setsofnuclear geneorthologsfrom101landplantgenera. Thebackbonerelationshipsamongangiosperm( Angiospermae )lineagesgenerallyagreewithresultsfromrecent analyses,includinga17-geneanalysisof632angiosperms [103]andpreviousanalysesofplastidgenomedatasets [63,104-106].Thepositionof Ceratophyllum ( Ceratophyllales ),andthustherelationshipsamong Monocotyledoneae Eudicotyledoneae ,and Magnoliidae, variesamong ouranalyses,althoughwithoutstrongsupport.Thiscontrastswithseveralotherlarge,multi-geneanalysesin which Monocotyledoneae aresisterto Ceratophyllales + Eudicotyledoneae [63,103,106].Interestingly,thestrongest supportfortheplacementof Ceratophyllales sisterto Eudicotyledoneae isintheRYanalysis(75%BS;Figure7). However,inthatanalysis,therelationshipsamong Ceratophyllales + Eudicotyledoneae Monocotyledoneae and Magnoliidae areunresolved Withintheangiosperms,somerelationshipsthathave beenuncertain,particularlyatdeeplevels(reviewedin [103,107]),receivemoderatetostrongsupportinatleast someofouranalyses.Forexample,theplacementof Myrtales and Geraniales inthe Malvidae issupported with70%BS(Figure6)inthentNo3rdtreeand 99% BSintheRY(Figure7)andntAll(Figure5)trees.Myrtales and Geraniales arealsoplacedinacladewiththe Malvidae taxaintheAAanalysis(68%BS;Figure8); however, Zygophyllales arealsoincludedwithinthis clade,making Malvidae non-monophyletic.Likewise, Chloranthales aresisterto Magnoliidae inalltrees,but withweakersupport(61%BSforRYandntNo3rd,68% BSforntAll,and69%BSforAA,butwith Piperales removedfrom Magnoliidae inthelatter).Intwocases, allanalysesbutRYresolverelationships(althoughoften withonlymoderatesupport),withRYproducinga polytomythatdoesnotconflictwiththeresolutions foundintheotheranalyses.Thesetwocasesareas follows:(1) Vitales + Saxifragales supportedby 70%BS inallanalysesbutRY,with Saxifragales Vitales ,and remaining Rosidae formingapolytomyintheRYtree (Figure7);(2) Dasypogonaceae + Arecales inallbutRY (52%,78%,and80%BSinthentNo3rd,AA,andntAll trees,respectively)andatrichotomyof Dasypogonaceae Arecales ,and Poales +( Zingiberales + Commelinales )in theRYtree(Figure7).IntwoadditionalcaseswhenRY iscomparedtotheotherthreeanalyses,theRYanalysis producedeitherstrongersupportfortheplacementofa taxonoradifferentplacementaltogether.First,inthe ntAll,ntNo3rd,andAAana lyses,thepositionof Sabiaceace amongtheearly-diverginglineagesof Eudicotyledoneae isweaklysupported.However,intheRY analysis, Sabiaceae receivemoderatesupport(79%BS; Figure7)assistertoastronglysupported(100%BS; Figure7)cladeof Trochodendrales +( Buxales ( Gunnerales + Pentapetalae )).Thiscontrastswithpreviousstudiesthat oftenplace Sabiaceae assisterto Proteales [103].An exampleofadifferentplacementofataxonintheRYanalysiswhencomparedtotheotheranalysesinvolves Liliales ThentAll,ntNo3rd,andtheAAanalysessupport Liliales as sistertoacladeof Dioscoreales + Pandanales with72%,69%, and80%BS,respectively.Thisplacementof Liliales wasalso recoveredinBarrettetal.[108].Incontrast,intheRYanalysis, Lilialesareplacedinacladewith Asparagales + Commelinidae withmoderatesupport(69%BS;Figure7).This latterplacementof Liliales wasstronglysupportedinananalysiswithmuchbettertaxonsampling[103]. Sometaxathathavebeenproblematicinprevious studies(e.g., Boraginaceae,Ceratophyllales ,theCOM clade, Dilleniaceae ,and Zygophyllaceae )continuetodefy (Seefigureonpreviouspage.) Figure7 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensussummarytreeof Viridiplantae inferredfromtheRY-coded (RY)analysis. Datasetderivedfrom78protein-codinggenesoftheplastidgenome(ntax=360;58,347bp;missingdata~15.6%).Bootstrapsupport values 50%areindicated.Terminalswithatrianglerepresentcollapsedcladeswith>2taxa.SeeAdditionalfile5forthecompletetreeand Additionalfile1fortaxonomy. Lami .= Lamiidae ; Campanuli .= Campanulidae Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page12of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 13

Figure8 (Seelegendonnextpage.) Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page13of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 14

definitiveplacement.Theirpositionsvaryamongour analyses,althoughtheyaregenerallynotwellsupported insome,orall,ofthetrees.DespiteitsgeneralplacementoftheCOMcladein Fabidae intheseandother plastidanalyses,thiscladeismorecloselyrelatedto Malvidae insomeanalyses,particularlythoseusing mitochondrialgenesequences(reviewedin[103]).Recentanalysesofplastid,mitochondrial,andnucleardata suggestthattheCOMclademayrepresentancientreticulationinvolving Fabidae and Malvidae duringthe rapidradiationof Rosidae (Sunetal.,inprep.).MethodologicalissuesofplastidphylogenomicanalysesToaddresspotentialsystematicerrorinlarge-scale phylogeneticanalyses,scientistsofteneithertrytoimprove thefitofmodelstothedataorchangeorremoveproblematicdata.Withincreasingsequencelengthandnumberof genes,itismorelikelythatasequencealignmentwillcontainregionswithheterogeneousprocessesofmolecular evolution.Weseeevidenceofthishighheterogeneitywith ourmodel-fittingexperiments,whichalwaysfavorthe mostparameter-richmodels(Table2).Thus,definingpartitioningschemesandmodelsthatcanaccuratelyreflect thetrueprocessesofmolecularevolutionwhilenotoverparameterizingtheanalysisremainscriticallyimportantfor phylogeneticanalysesoflargeplastiddatasets.Although weassessedmodelsthataccountforheterogeneityinpatternsofmolecularevolutionamonggenesandinsome casescodonpositions,ourmodelselectiontestsonlyevaluatedasmallselectionofpossiblemodelsandpartitioning (Seefigureonpreviouspage.) Figure8 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensussummarytreeof Viridiplantae inferredfromtheamino acid(AA)analysis. Datasetderivedfrom78protein-codinggenesoftheplastidgenome(ntax=360;19,449AAs;missingdata~15.6%).Bootstrap supportvalues 50%areindicated.Terminalswithatrianglerepresentcollapsedcladeswith>2taxa.SeeAdditionalfile6forthecompletetreeand Additionalfile1fortaxonomy. Lami .= Lamiidae ; Campanuli .= Campanulidae Table3Summaryofselectedsimilaritiesandconflictsbetweenbootstrapconsensustopologiesderivedfromthefour datasetsTaxonntAllntNo3rdRYAA Amborellales sistertoallother Angiospermae (100%/100%) sistertoallother Angiospermae (100%/81%) sistertoallother Angiospermae (100%/100%) sistertoallother Angiospermae (100%/70%) Anthocerotophyta sisterto Tracheophyta (100%/100%) sisterto Tracheophyta (94%/100%) sisterto Tracheophyta (95%/100%) sisterto Tracheophyta (53%/90%) Ceratophyllales sisterto Eudicotyledoneae (52%/100%) sisterto Monocotyledoneae + Eudicotyledoneae (52%/54%) sisterto Eudicotyledoneae (75%/100%) sisterto Piperales (67%) COMcladewithin Fabidae (100%)within Fabidae (70%)within Fabidae (99%)sistertoacladeincluding Cucurbitales,Rosales,Fabales, Fagales (69%/100%; Fabidae notmonophyletic) Dilleniales sisterto Superrosidae (95%/100%) sisterto Superrosidae (77%/100%) sisterto Superrosidae (57%/100%) sisterto Superasteridae (70%/66%) Ginkgoales sisterto Cycadales (98%/100%) sisterto Cycadales (100%/100%) sisterto Cycadales (51%/100%) sisterto Cycadales (100%/100%) Gnetophyta sisterto Cupressales + Araucariales (100%/100%) sisterto Cupressales + Araucariales (100%/100%) sisterto Cupressales + Araucariales (87%/100%) sisterto Cupressales + Araucariales (100%/100%)Marchantiophyta sistertoallother Embryophyta (100%/69%) sisterto Bryophyta (78%/100%)sistertoallother Embryophyta (100%/89%) sisterto Bryophyta (99%/100%) Monilophyta sisterto Lycopodiophyta + Spermatophyta (100%/75%) sisterto Spermatophyta (93%/100%) sisterto Spermatophyta (100%/100%) sisterto Spermatophyta (89%/100%) Prasinophyceae notmonophyletic; Nephroselmis sistertoallother Chlorophyta (100%/87%) notmonophyletic; Nephroselmis sistertoallother Chlorophyta (100%/78%) notmonophyletic; Nephroselmis sistertoall other Chlorophyta (100%/92%) notmonophyletic; Nephroselmis sistertoallother Chlorophyta (100%/96%) Zygnematophyceae sisterto Embryophyta (97%/100%) sisterto Embryophyta (99%/100%) sisterto Embryophyta (86%/100%) sisterto Embryophyta (93%/100%)Bootstrapsupport(BS)values>50%areshownaspercentages.Whensistergroupsforthetaxonofinterestarelisted,bootstrapsupport(BS)valueson theleft areforthecladeincludingthetaxonofinterestanditssistergroupwithin Viridiplantae, whileBSvaluesontherightareforthemoreinclusivecladeexcluding thetaxonofinterest.IfonlyoneBSvalueisgivenforasisterrelationship,onlytwoterminalsareinvolved(seealsoFigures 5 6 7 ,and 8 ).Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page14of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 15

schemes.Itispossiblethatotherpartitioningschemes couldenablesimplermodels. Mostconventionalphylogeneticmodels,likethoseused inouranalyses,alsoassumehomogeneousprocessesof evolutionthroughoutthetree.Yetwhenthebranchesof thephylogenyencompassoveronebillionyearsofevolutionaryhistory,aslikelydothoseinthegreenplants,the patternsofevolutionalmostcertainlydifferamong lineagesandthroughtime.Thisisapparentfromtheoften goodfitofcovarionmodels(whichmaybetterdescribe rateshiftsthroughtime)toplastidgenes[109,110]and thepresenceofnucleotidecompositionalheterogeneity, whichcanconfoundconventionalphylogeneticanalyses (e.g.,[111,112]).Also,ourmodelsdonotaccountforshifts inselectivepressureorinstancesofpositiveselectionthat willaffectnucleotideandaminoacidsubstitutionpatterns (e.g.,[113,114]). Nucleotidecompositionalheterogeneityremainsaconcernforgreenplantplastidgenomeanalyses.Thisvariationismostevidentinnon-seedplanttaxa(Figure2),and thusithasnotbeenafocusofmanypreviousphylogenetic analysesofplastidgenomesequences.AGCbiasinitselfis notnecessarilyproblematicforphylogeneticanalyses,but nearlyallcommonlyusedmodelsforlikelihood-based phylogeneticanalysesassumesingleequilibriumnucleotide frequencies.GiventhatGCcontentappearstovaryby Figure9 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensustreeof Viridiplantae inferredfromtheallnucleotide positions(ntAll)analysis.Portionoftreeshowing Chlorophyta,Chlorokybophyceae,Mesostigmatophyceae,Charophyceae, Coleochaetophyceae,Zygnematophyceae,Marchantiophyta,Bryophyta, and Anthocerotophyta. Datasetderivedfrom78protein-coding genesoftheplastidgenome(ntax=360;58,347bp;missingdata~15.6%).Bootstrapsupportvalues 50%areindicated.SeealsoFigure5fora summarytreeofmajor Viridiplantae cladesandAdditionalfile1fortaxonomy.TreecontinuedinFigure10. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page15of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 16

codonpositioninplants(Figures1and2)[115-117],apartitioningschemethatestimatesseparatenucleotidefrequenciesforeachcodonpositionmayaccountforsomeof thespatialheterogeneityinGCcontentintheplastidgenome,butitdoesnotaddressthedifferencesinGCfrequencyamonglineages. AcommonlyusedstrategytoreducetheeffectsofGC heterogeneityacrosslineagesisRY-coding,inwhichthe purines(AandG)arecodedasRsandthepyrimidines (CandT)arecodedasYs[118].RY-codingcanreduce thecompositionalvariabilityamonglineages,improvethe fitofmodels,andincreasethesignalforinternalbranches [118-121].AnobviousdisadvantagetoRY-codingisthat bycodingthesequenceswithtwocharacterstatesinstead offour,itreducestheamountofinformationinthesequences.Ingeneral,weseelittleoverallreduction,and evensomegains,inbootstrapsupportwhenusingRYcodingcomparedtotheuseofallnucleotidedata(ntAll), Figure10 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensustreeof Viridiplantae inferredfromtheallnucleotide positions(ntAll)analysis.Portionoftreeshowing Monilophyta Lycopodiophyta ,and Acrogymnospermae. Datasetderivedfrom78 protein-codinggenesoftheplastidgenome(ntax=360;58,347bp;missingdata~15.6%).Bootstrapsupportvalues 50%areindicated.Seealso Figure5forasummarytreeofmajor Viridiplantae cladesandAdditionalfile1fortaxonomy.Notepositionof Lycopodiophyta assisterto Spermatophyta islikelycausedbybasecompositionbias(seetext).TreecontinuedinFigures9and11. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page16of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 17

suggestingthatthebenefitsofRY-codingmakeupforany potentialcostsofinformationloss.Perhapsthebiggest topologicaldifferenceintheRYphylogeny(Figure7)comparedtontAll(Figure5)istheplacementof Monilophyta ratherthan Lycopodiophyta assistertoseedplants.The unexpectedplacementof Lycopodiophyta asthesisterto seedplantsinthentAllanalysis(Figure5)isalmostcertainlyanartifactofsystematicerror;severalotherlinesof evidencesupport Monilophyta asthesistergroupofseed plants(seeabove). Approachestoreducingsystematicerrorsbyexcluding problematicdata,whichoftenincludefast-evolvingor saturatedsites,alsohavebeensuggestedforplastidgenomeanalyses[20,41,80,110,122].Withthepropermodel ofmolecularevolutionandadequatetaxonsampling, fastsitesarenotnecessarilyproblematic;theyareonly problematicinsofarastheyaredifficulttomodel.Yetwith heterogeneousprocessesofmolecularevolutionthroughoutthetree,thefast-evolvingorsaturatedsitescanproduceasignificantnon-phylogeneticsignal(e.g.,[123]). Indeed,thethirdcodonpositionsappeartohaveespecially highlevelsofcompositionalheterogeneity,potentially causingsystematicerror(Figures1and2),andananalysis ofjustthethirdcodonpositions(nt3rdOnly)conflicts withtheanalysesofotherdatasetsinseveralcriticalparts ofthetree(Additionalfile11).However,thirdcodonpositionsalsorepresentalargeproportionofthevariablesites inthealignment,andremovingthemmayexcludemuch ofthephylogeneticinformationinsomepartsofthetree. Withregardtobackbonerelationshipsinourphylogeny, excludingthethirdpositionsites(ntNo3rd)producesseveralinterestingchangesincontrasttontAll:1)itsupports thesisterrelationshipofmossesandliverworts,2)monilophytes,notlycophytes,areplacedsistertoseedplantsas expected,and3)supportforsomeofthebackboneangiospermrelationshipsisreduced.Thus,theeffectsofremovingthethirdcodonpositionsitesappeartovaryin differentpartsofthetree. Anotherstrategyforovercomingpotentialerrorassociatedwithfast-evolvingsitesistocodethesequencesas aminoacidsratherthannucleotides.Thisdoesnotnecessarilyeliminateproblemsofcompositionalheterogeneity, astheGCbiasalsomaybiasaminoacidcomposition (Figures3and4)[124].Regardingbackbonegreen plantrelationships,theAAanalysisprovidedsimilar resultstoanalysesofonlyfirstandsecondcodonpositions.AAanalysisalsoproducedsomeweaklysupported,questionablerelat ionshipsamongangiosperm lineages(i.e., Piperales + Ceratophyllales ;Figure8).In previousdeep-levelplantanalyses,analysesofamino aciddatahaveresultedinarguablymoreproblematic orquestionablerelationsh ipsthananalysesofnucleotidedata[29,80].However,theseresultsarelikelydue toinappropriatemodelsofaminoacidevolution[125], andwithbettermodels,optimizedforplastidevolution,aminoaciddatamaybeavaluablesourceof phylogeneticinformation. Taxonsamplingisalsoimportantforplastidphylogenomicstudies,especiallywhenthemodelofevolutionis inadequate[56,58,126-131],andgenome-scaleanalyses Figure11 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensustreeof Viridiplantae inferredfromtheallnucleotide positions(ntAll)analysis.Portionoftreeshowing Amborellales,Nymphaeales,Austrobaileyales,Chloranthales, and Magnoliidae. Dataset derivedfrom78protein-codinggenesoftheplastidgenome(ntax=360;58,347bp;missingdata~15.6%).Bootstrapsupportvalues 50%are indicated.SeealsoFigure5forasummarytreeofmajor Viridiplantae cladesandAdditionalfile1fortaxonomy.TreecontinuedinFigures10and12. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page17of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 18

Iris virginica Neoastelia spectabilis Agrostis stolonifera Phalaenopsis aphrodite Rhynchoryza subulata Acorus calamus Puelia olyriformis Curculigo capitulata Thamnochortus insignis Spirodela polyrhiza Sorghum bicolor Georgeantha hexandra Musa acuminata Fosterella caulescens Potarophytum riparium Asparagus officinalis Ecdeiocolea monostachya Elaeis oleifera Lolium perenne Oryza australiensis Sparganium eurycarpum Belosynapsis ciliata Flagellaria indica Ravenea hildebrandtii Oryza sativa var. japonica Chlorophytum rhizopendulu m Hesperaloe parviflora Joinvillea ascendens Brachypodium distachyon Mayaca fluviatilis Renealmia alpinia Saccharum hybridus Colocasia esculenta Hordeum vulgare Acidosasa purpurea Chamaedorea seifrizii Streptochaeta angustifolia Syngonanthus chrysanthus Eleusine coracana Phyllostachys propinqua Pandanus utilis Oryza rufipogon B Nolina atopocarpa Albuca kirkii Apostasia wallichii Puya laxa Coix lacryma-jobi Potamophila parviflora Oncidium sp. Centrolepis monogyna Phyllostachys nigra Dioscorea elephantipes Bambusa emeiensis Panicum virgatum Phyllostachys edulis Rhizanthella gardneri Wolffia australiana Navia saxicola Dasypogon bromeliifolius Tradescantia ohiensis Cyperus alternifolius Wolffiella lingulata Pitcairnia feliciana Phormium tenax Leersia tisserantii Dendrocalamus latiflorus Anomochloa marantoidea Ferrocalamus rimosivaginus Thurnia sphaerocephala Lomandra longifolia Oryza meridionalis Lilium superbum Microlaena stipoides Yucca schidigera Neottia nidus-avis Juncus effusus Acorus americanus Typha latifolia Lemna minor Festuca arundinacea Agapanthus praecox Oryza nivara Phoenix dactylifera Bambusa oldhamii Abolboda macrostachya Indocalamus longiauritus Zea mays Oryza sativa var. indica Kingia australis Hosta ventricosa Triticum aestivum Brocchinia micrantha Oryza rufipogon A Neoregelia carolinae 88 100 100 100 100 100 70 100 100 100 100 100 100 100 100 100 100 87 100 100 100 100 92 100 100 72 100 98100 100 100 100 100 93 100 100 100 100 100 100 100 100 100 94 100 100 88 100 100 100 55 100 100 59 100 96 100 100 100 75 100 80 100 100 83 100 100 100 100 100 100 53 100 100 100 100 100 100 100 100 100 100 100 100 100 100 93 100 100 100 100 100 76 To Fi g 11: Amborellales, N y mphaeales, Austrobaile y ales, and Ma g noliidae To Fig. 13: Ceratophyllales, Ranunculales, Sabiaceae, Proteales, Trochodendrales, Buxales, Gunnerales, and Superasteridae Figure12 (Seelegendonnextpage.) Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page18of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 19

oftenhavelimitedtaxonsampling.Newmethodsforrapid andinexpensiveplastidgenomesequencing(e.g.,[132]) mayamelioratetheeffectsofinsufficientsamplingofextanttaxa;however,manymajorlineagesofgreenplants arenowextinct,precludingtheirinclusioninanalysesof moleculardata(butsee[133-136]).Inaddition,ancient, rapidradiationsaboundwithinportionsofthegreenplant treeoflife,creatingextremelydifficultphylogeneticproblemsnomatterthetaxonsampling[63,69,107,137]. Furthermore,evenintheabsenceofsystematicerror, itispossiblethatatreebuiltfromplastidgenomedata willnotreflectspeciesrelationships.Theplastidgenome representsasinglelocusoflinkedgenes(i.e.,asinglecoalescenthistory).Forphylogeneticanalyses,thiscanbe beneficialbecausecombininggeneswithdifferentevolutionaryhistoriesintoasinglecharactermatrixcanlead tophylogeneticerror[138-140].However,incomplete lineagesortingorancientreticulationcouldleadtoconflictbetweentheplastidgenetreeandthespeciesphylogeny[141].Forthisreason,itwillbeinterestingto comparephylogenetichypothesesfromtheplastidgenomewithindependentphylogeneticestimatesfromnumerousnuclearandmitochondrialloci. Finally,whilefullplastidgenomesequencedataprovidemuchpowerforresolvingdifficultphylogeneticrelationships,itisnotclearthattheycanresolveallplant relationships.Theoreticalworksuggeststhatextremely largedatasetsmaybenecessarytoresolvesomerelationshipswhentheinternalnodesareseparatedbyvery shortbranches[142],andrecentanalysesindicatethat fullplastidgenomesarenotsufficienttorejectalternativetopologiesamongmonocots[108].Indeed,theunresolvedorconflictingpartsofthegreenplantphylogeny inouranalysesaregenerallyassociatedwithshortinternalbranchlengths(seeAdditionalfiles7,8,9,10, and11).Thus,evenifthemodelofevolutionaccurately reflectsthetrueprocessofmolecularevolution,and thereisnosystematicerror,plastidgenomedataalone maynotbesufficienttoresolveallpartsofthegreen planttreeoflife.Thatis,thetopologymaynotbeidentifiablewiththeplastiddataalone.Arecentanalysisusing anewdiagnostictestforphylogeneticidentifiability basedondatacloningsuggestedthatabackbonetopologyofangiospermswasidentifiablefromplastidsequencedatausingtheGTR+ model[143],butthetree inthispaperismuchlargerandthemodelsmorecomplex.Inanycase,itwillbenecessarytoincludeperspectivesfromthenucleargenomeandphenotypicdata beforeweareconfidentaboutalldeep-levelrelationships amonggreenplants.ConclusionsOurdiverseanalysesprovideafirstapproachtoaddressingsomeofthedifficultissuesassociatedwithplastid phylogeneticanalysesatthisevolutionarydepthand leveloftaxonsampling.Theresultsoftheanalysesusing differentmodels,character-codingstrategies,andcharactersubsetssuggestthatmuchofthetreeisrobustto manydifferentphylogeneticapproaches,andtheyhighlightregionsofthetreethatneedmorescrutiny(i.e., thoserelationshipsnotconsistentacrossanalyses).More sophisticatedmodellingapproachesmaymoreaccurately characterizetheheterogeneousprocessesofmolecular evolution,butitisalsocrucialthattheparametersofthese complexmodelscanbeestimatedbythedataathand [143].Whileitmaybeimpossibleforanymodeltoreflect perfectlythecomplexitiesofmolecularevolution,aswe bettercharacterizetheseprocessesitwillbepossibleto examinethroughsimulationstheirpossibleeffectson phylogeneticanalysesandtorecognizephylogeneticerror causedbymodelmisspecification.MethodsTaxonandsequencesamplingProtein-codingdata,includingnucleotidesandtheircorrespondingaminoacidsequences,forall Viridiplantae taxathathadcompleteornearlycompleteplastidgenomesequencesweredownloadedfromGenBankon February28,2012.Ifthereweremultiplegenomesequencesfromthesametaxon,weincludedthesequencewiththemostdata.Oursamplingincluded mostmajorlineagesof Viridiplantae .Acompletelist oftaxaandGenBankaccessionnumbersisavailablein Additionalfile1. Taxonomicnames(Additionalfile1)followvarious references.Fourclassesofchlorophyticalgae( Chlorophyta )arerecognizedfollowingatraditionalclassification[26,76].Classesofstreptophyticalgaeandorders forbothchlorophyticandstreptophyticalgaefollow Leliaertetal.[76].Namesforthethreemainbryophyte cladesfollowrecentclassifications:mosses( Bryophyta [144]),hornworts( Anthocerotophyta [145]),andliverworts( Marchantiophyta [146]).MajorcladesoftracheophytesfollowCantinoetal.[147]andSoltisetal.[103]. Familialandordinalnameswithinmajorcladesofland plantsfollowthesereferences: Bryophyta [144]; (Seefigureonpreviouspage.) Figure12 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensustreeof Viridiplantae inferredfromtheallnucleotide positions(ntAll)analysis.Portionoftreeshowing Monocotyledoneae. Datasetderivedfrom78protein-codinggenesoftheplastidgenome (ntax=360;58,347bp;missingdata~15.6%).Bootstrapsupportvalues 50%areindicated.SeealsoFigure5forasummarytreeofmajor Viridiplantae cladesandAdditionalfile1fortaxonomy.TreecontinuedinFigures11and13. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page19of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 20

Figure13 (Seelegendonnextpage.) Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page20of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 21

Anthocerotophyta [145]; Marchantiophyta [146];lycophytes ( Lycopodiophyta )andferns( Monilophyta )[148];gymnosperms( Acrogymnospermae [149]);andangiosperms ( Angiospermae [150]).Allscientificnamesareitalicizedto distinguishcommonnamesfromscientificnames[147,151].BuildingthephylogeneticcharactermatrixTobuildthephylogeneticmatrix,firstweusedaclusteringapproachtoidentifyhomologousgenesequences. Aminoacidsequencesfromalldownloadedgenomes werecomparedtoeachotherusingBLASTPv.2.2.26 [152].SignificantBLASThitsweredefinedasthosehavingamaximum e -valueof1.0e-5andhavingthehitregioncoveratleast40%ofthetargetandquery sequences.BasedontheBLASThits,weformedclusters ofputativehomologsusingsingle-linkageclustering. Thisapproachidentifiedgroupsofsequencesthathada significantBLASThitwithatleastoneothersequence intheclusterandwereconnectedtoeachotherbya pathofsignificantBLASThits.Theresultingclusters weremodifiedintwoways.First,clustersthatcontained twoormoredifferentgenesfromasingletaxonwerereclusteredatamorestringent e -valuetoseparatethe genes.Second,whenitappearedthatasinglegenewas splitintomultipleclusters,wecombinedthem.Some clusterscontainedmultiplesequencesfromthesame specieswhenthegenewaspresentintheinvertedrepeat regionintheplastidgenome.Ifthesequenceswere identical,onlyonewasretainedforanalysis.Incases wherethetwosequencesdifferedslightly,weremoved bothsequences.Onlyclusterscontainingsequences fromatleast50%ofthe360taxawereretainedforthe phylogeneticanalyses. Eachremainingaminoacidcluster(78total)was alignedwithMAFFTv.6.859[153]usingtheL-INS-i algorithm,andsubsequently,poorlyalignedregionswere removedusingtrimAlv.1.2rev59[154].Afterusing trimAl,wealsovisuallyinspectedthetrimmedalignmentsandremovedpoorlyalignedregions.Thenucleotidesequencesforeachclusterwerealignedwith PAL2NALv.14[155]tocorrespondtothetrimmed aminoacidalignmentandensurethatthecorrectreadingframewasmaintained.Wecheckedforanomalous sequencesbybuildingMLtreesfromeachofthealigned clusterswithRAxML[156,157]followingthesearchstrategiesoutlinedbelow.Thesetopologieswerevisuallyexamined,andsequencesinobviouslyspuriouslocationsin thetreewereremoved.Ifanysequenceswereremoved fromaclusteralignment,werealignedandeditedthe cluster ’ suntrimmeddataasdescribedabove.Alignments foreachgenewereconcatenatedusingFASconCATv.1.0 [158]. Fromthisdataset,wegeneratedanaminoacid(AA) alignment,twonucleotidealignments,andabinarycharacteralignment.Thefirstnucleotidealignmentcontainedallnucleotidepositions(ntAll),whilethesecond containedonlythefirstandsecondcodonpositions (ntNo3rd).ThebinarycharacteralignmentwasanRYcodedversion(RY)ofthentAlldataset.RY-coding [159]involvesrecodingthenucleotidesasbinarycharacters,eitherpurines(AorG=R)orpyrimidines(CorT= Y).RY-codinghasbeenusedtoamelioratebiasescaused bysaturation,rateheterogeneity,andbasecomposition [119,160,161].Todetermineifthedatasetsweredecisive usingourselectedpartitioningschemes(seebelow),we followedtheapproachusedinSandersonetal.[72]. Weassessedbasecompositionbiasinthenucleotide dataset(ntAll)byconductingachi-squaretestusing PAUP*v.4.0b10[162]todetermineifthebasefrequenciesacrosstaxawerehomogeneous.Todetermineif basecompositionofthenucleotidesequencesinthe ntAllmatrixcouldaffectthecompositionofaminoacid sequencesintheAAmatrix,weconductedlinearregressionsinR[163].WeexaminedtherelationshipofpercentGCcontenttothepercentofaminoacidsthatare codedforbyGC-richcodons(i.e.,G,A,R,andP)as wellastherelationshipofpercentGCcontenttothe percentofaminoacidsthatarecodedforbyAT-rich codons(i.e.,F,Y,M,I,N,andK).PhylogeneticanalysesAllMLphylogeneticanalyseswereimplementedwith RAxMLv.7.3.0[156,157].Theoptimalpartitioning schemeforeachalignmentwaschosenfromamongseveralcommonlyusedpartitioningstrategiesusingthe correctedAkaikeinformationcriterion(AICc)[164,165]. Thispenalizesmodelsforadditionalparametersand shouldaccountforthetrade-offbetweenincreasedmodel fitandover-parameterizationwhenchoosingthebest model.Forthenucleotide(ntAllandntNo3rd)and RY-codeddata,weexaminedfourpossiblepartitioning strategies:1)nopartitioning,2)partitioningbyeach codonposition(threepartitions),3)partitioningby gene(78partitions),and4)partitioningbyeachcodon (Seefigureonpreviouspage.) Figure13 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensustreeof Viridiplantae inferredfromtheallnucleotide positions(ntAll)analysis.Portionoftreeshowing Ceratophyllales,Ranunculales,Sabiaceae,Proteales,Trochodendrales,Buxales, Gunnerales, and Superasteridae. Datasetderivedfrom78protein-codinggenesoftheplastidgenome(ntax=360;58,347bp;missing data~15.6%).Bootstrapsupportvalues 50%areindicated.SeealsoFigure5forasummarytreeofmajor Viridiplantae cladesand Additionalfile1fortaxonomy.T reecontinuedinFigures12and14. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page21of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 22

Figure14 (Seelegendonnextpage.) Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page22of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 23

positionwithineachgene(234partitions).FortheAA data,wetestedtwopartitioningstrategies:1)nopartitioning,and2)partitioningbygene(78partitions).A novelapproachfordeterminingpartitionsofphylogenomicdatasetsaposterioriusingaBayesianmixture modelhasrecentlybeenproposed[69].Additionally, theprogramPartitionFinder[166]allowsforthestatisticalcomparisonofmultipleaprioripartitioning schemes.Weexploredbothofthesemethods,butwe wereunabletocompletetheanalysesduetocomputationallimitationsresultingfromthelargesizeofour dataset. Todeterminewhichpartitioningschemewasoptimal foreachdataset,wefirstobtainedtheoptimalMLtree foreachdatasetundereachpartitioningschemeasfollows.Forthenucleotide(ntAll,ntNo3rd)andRY-coded data,weran10MLsearchesfromdifferentstarting trees.WeusedtheGTR+ modelofevolutionforeach partitioninthenucleotidedatasetandthebinarymodel ofevolution(BINGAMMA)fortheRYdataset.Forthe AAdata,weran3MLsearchesfromdifferentstarting trees.Toselectthebestaminoacidsubstitutionmodel foreachpartitionoftheAAdataset,weusedthePerl script(ProteinModelSelection.pl)includedintheRAxML distributionpackage.ForeachMLsearch,weestimateda separatesubstitutionratematrixforeachpartitionbuta singlesetofbranchlengthparametersforallpartitions. Wethenoptimizedthemodelandbranchlengthsoneach resultingMLtreeusingRAxML(-fe).AICcvaluesfor eachpartitioningschemewerethencalculatedbyusing thelog-likelihood,numberofestimableparameters,and samplesizegivenbyRAxML.Theoptimalpartitioning strategyforeachdatasetwasthenusedinsubsequentML bootstrapanalyses.Bootstrapsearches(200replicatesfor eachmatrix)wereexecutedseparatelyfromthesearchfor thebestMLtreeusingthestandardbootstrapoptionin RAxML.Todetermineif200replicateswereadequatefor estimatingbootstrapvalues,weconductedaposteriori bootstoppinganalyses(-IautoMRE)asimplementedin RAxMLanddescribedinPattengaleetal.[167].Alltrees wererootedatthebranchbetween Chlorophyta and Streptophyta [23,24]. Tofurtherexploreourdata,weconductedthefollowingphylogeneticanalysesusingthemethodsdescribed aboveunlessotherwisenoted.Todetermineifthereis conflictbetweenthephylogeneticsignalinthentNo3rd datasetandthedatasetcontainingonlythirdpositions (nt3rdOnly),weanalyzedthent3rdOnlydatapartitioned bygeneregion.Wealsoconductedphylogeneticanalysesoneachofthefourmaindatasets(ntAll,ntNo3rd, RY,andAA)withfourtaxaremoved: Neottianidus-avis and Rhizanthellagardneri (mycoheterotrophicorchids), Epifagusvirginiana (aparasiticfloweringplant),and Helicosporidium sp.(aparasiticgreenalga).Thesetaxa haveelevatedratesofmolecularevolutionandrelatively fewgenespresentinthedatasets(seeAdditionalfile2). Weremovedthemtoensurethattheirinclusiondidnot causeanyphylogeneticartifacts.AvailabilityofsupportingdataThedatasetssupportingtheresultsofthisarticleare availableintheDryadDigitalRepository:http://doi.org/ 10.5061/dryad.k1t1f.AdditionalfilesAdditionalfile1: Taxonsampling. Taxaincludedinthisstudy,their GenBankaccessionnumbers,originalpu blications,andtheirhighertaxonomy. Additionalfile2: Genessampledandmissingdataforeachtaxon. Informationontaxasampledforeachgeneincluded,andthepercentof missingdataforeachtaxonineachdataset.Numberofgenespresent pertaxonandnumberoftaxapresentpergenearealsogiven. Additionalfile3: GCcontentforeachtaxoninthentAlland ntNo3rddatasetsaswellasinthefirst,second,andthirdcodon positionsofthentAlldataset. Additionalfile4: Fiftypercentmaximumlikelihoodmajority-rule bootstrapconsensussummarytreeof Viridiplantae inferredfrom thefirstandsecondcodonpositions(ntNo3rd)analysis. Seealso Figure6forasummarytreeofmajor Viridiplantae cladesand Additionalfile1fortaxonomy.Datasetderivedfrom78protein-coding genesoftheplastidgenome(ntax=360,38,898bp,missingdata~15.6%,). Bootstrapsupportvalues 50%areindicated. Additionalfile5: Fiftypercentmaximumlikelihoodmajority-rule bootstrapconsensustreeof Viridiplantae inferredfromtheRYcoded(RY)analysis. SeealsoFigure7forasummarytreeofmajor Viridiplantae cladesandAdditionalfile1fortax onomy.Datasetderived from78protein-codinggenesoftheplastidgenome(ntax=360, 58,347bp,missingdata~15.6%,).Bootstrapsupportvalues 50%are indicated. Additionalfile6: Fiftypercentmaximumlikelihoodmajority-rule bootstrapconsensustreeof Viridiplantae inferredfromtheamino acid(AA)analysis. SeealsoFigure8forasummarytreeofmajor Viridiplantae cladesandAdditionalfile1fortaxonomy.Datasetderived from78protein-codinggenesoftheplastidgenome(ntax=360,19,449 AAs,missingdata~15.6%,).Bootstrapsupportvalues 50%are indicated. Additionalfile7: Maximumlikelihoodtreeof Viridiplantae inferred fromtheallnucleotidepositions(ntAll)analysis. Cladogramofthe maximumlikelihoodbipartitiontreeisshownontheleftwithbootstrap valuesindicatedabovethebranches.Thephylogramofsametreeis shownontheright.Datasetderivedfrom78protein-codinggenesof theplastidgenome(ntax=360;58,347bp;missingdata~15.6%).Bootstrap supportvalues 50%areindicated. (Seefigureonpreviouspage.) Figure14 Fiftypercentmaximumlikelihoodmajority-rulebootstrapconsensustreeof Viridiplantae inferredfromtheallnucleotide positions(ntAll)analysis.Portionoftreeshowing Dilleniaceae and Superrosidae. Datasetderivedfrom78protein-codinggenesofthe plastidgenome(ntax=360;58,347bp;missingdata~15.6%).Bootstrapsupportvalues 50%areindicated.SeealsoFigure5forasummarytree ofmajor Viridiplantae cladesandAdditionalfile1fortaxonomy.TreecontinuedinFigure13. Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page23of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 24

Additionalfile8: Maximumlikelihoodtreeof Viridiplantae inferred fromthefirstandsecondcodonpositions(ntNo3rd)analysis. Cladogramofthemaximumlikelihoodbipartitiontreeisshownonthe leftwithbootstrapvaluesindicatedabovethebranches.Thephylogram ofsametreeisshownontheright.Datasetderivedfrom78protein-coding genesoftheplastidgenome(ntax=360,38,898bp,missingdata~15.6%,). Bootstrapsupportvalues 50%areindicated. Additionalfile9: Maximumlikelihoodtreeof Viridiplantae inferred fromtheRY-coded(RY)analysis. Cladogramofthemaximum likelihoodbipartitiontreeisshownontheleftwithbootstrapvalues indicatedabovethebranches.Thephylogramofsametreeisshownon theright.Datasetderivedfrom78protein-codinggenesoftheplastid genome(ntax=360,58,347bp,missingdata~15.6%,).Bootstrapsupport values 50%areindicated. Additionalfile10: Maximumlikelihoodtreeof Viridiplantae inferredfromtheaminoacid(AA)analysis. Cladogramofthe maximumlikelihoodbipartitiontreeisshownontheleftwithbootstrap valuesindicatedabovethebranches.Thephylogramofsametreeis shownontheright.Datasetderivedfrom78protein-codinggenesof theplastidgenome(ntax= 360,19,449AAs,missingdata~15.6%,). Bootstrapsupportvalues 50%areindicated. Additionalfile11: Maximumlikelihoodtreeof Viridiplantae inferredfromthethirdcodonposition(nt3rdOnly)analysis. Cladogramofthemaximumlikelihoodbipartitiontreeisshownonthe leftwithbootstrapvaluesindicatedabovethebranches.Thephylogram ofsametreeisshownontheright.Datasetderivedfrom78protein-coding genesoftheplastidgenome(ntax=360,19,449bp,missingdata~15.6%,). Bootstrapsupportvalues 50%areindicated. Competinginterests Theauthorsdeclarethattheyhavenocompetinginterests. Authors ’ contributions BRRconceivedthestudy.BRR,PSS,DES,andJGBparticipatedinthedesign ofthestudy.BRR,MAG,andJGBanalyzedthedata.BRR,PSS,DES,andJGB wrotethepaper.Allauthorsreadandapprovedthefinalmanuscript. Acknowledgements ThisresearchwassupportedinpartbytheiPlantTreeofLifeProject(iPlant Collaborative,fundedbyNSFgrantDBI-0735191)andtheOpenTreeofLife Project(NSFgrant#DEB-12008809).WewouldalsoliketothankE.L.Braun andZ.XifortheirinputregardingaspectsofourdataanalysesandE.V. Mavrodievforhelpwiththefigures. Authordetails1DepartmentofBiologicalSciences,EasternKentuckyUniversity,Richmond, KY40475,USA.2DepartmentofBiology,UniversityofFlorida,Gainesville,FL 32611-8525,USA.3FloridaMuseumofNaturalHistory,UniversityofFlorida, Gainesville,FL32611-7800,USA.4GeneticsInstitute,UniversityofFlorida, Gainesville,FL32610,USA. Received:21June2013Accepted:13January2014 Published:17February2014 References1.GovaertsR: Howmanyspeciesofseedplantsarethere?-aresponse. Taxon 2003, 52 (3):583 – 584. 2.GovaertsR: Howmanyspeciesofseedplantsarethere? Taxon 2001, 50 (4):1085 – 1090. 3.JuddWS,CampbellCS,KelloggEA,StevensPF,DonoghueMJ: Plant systematics:aphylogeneticapproach. 3rdedition.Sunderland,MA:Sinauer Associates;2008. 4. Charophyceangreenalgae. [http://www.life.umd.edu/labs/delwiche/ Charophyte.html] 5. AlgaeBase. [http://www.algaebase.org] 6.GuiryMD: Howmanyspeciesofalgaearethere? JPhycol 2012, 48 (5):1057 – 1063. 7.CourtiesC,VaquerA,TroussellierM,LautierJ,Chretiennot-DinetMJ,NeveuxJ, MachadoC,ClaustreH: Smallesteukaryoticorganism. Nature 1994, 370 (6487):255. 8.ButterfieldNJ: Modesofpre-Ediacaranmulticellularity. PrecambrianRes 2009, 173 (1 – 4):201 – 211. 9.ButterfieldNJ,KnollAH,SwettK: PaleobiologyoftheNeoproterozoic SvanbergfjelletFormation,Spitsbergen. FossilsStrata 1994, 34: 1 – 84. 10.HalversonGP,MaloofAC,SchragDP,DudasFO,HurtgenM: Stratigraphy andgeochemistryofaca800Manegativecarbonisotopeintervalin northeasternSvalbard. ChemGeol 2007, 237 (1 – 2):5 – 27. 11.YoonHS,HackettJD,CinigliaC,PintoG,BhattacharyaD: Amolecular timelinefortheoriginofphotosyntheticeukaryotes. MolBiolEvol 2004, 21 (5):809 – 818. 12.HedgesSB,BlairJE,VenturiML,ShoeJL: Amoleculartimescaleof eukaryoteevolutionandtheriseofcomplexmulticellularlife. BMCEvol Biol 2004, 4: 2. 13.HerronMD,HackettJD,AylwardFO,MichodRE: Triassicoriginandearly radiationofmulticellularvolvocinealgae. ProcNatlAcadSciUSA 2009, 106 (9):3254 – 3258. 14.ParfreyLW,LahrDJG,KnollAH,KatzLA:Estimatingthetimingofearly eukaryoticdiversificationwithmultigenemolecularclocks. ProcNatlAcad SciUSA 2011, 108 (33):13624 – 13629. 15.KenrickP,CranePR: Theoriginandearlyevolutionofplantsonland. Nature 1997, 389: 33 – 39. 16.DoyleJA: Seedfernsandtheoriginofangiosperms. JTorreyBotSoc 2006, 133 (1):169 – 209. 17.HiltonJ,BatemanRM: Pteridospermsarethebackboneofseed-plant phylogeny. JTorreyBotSoc 2006, 133 (1):119 – 168. 18.RothfelsCJ,LarssonA,KuoLY,KorallP,ChiouWL,PryerKM: Overcoming deeproots,fastrates,andshortinternodestoresolvetheancientrapid radiationofeupolypodIIferns. SystBiol 2012, 61 (3):490 – 509. 19.SoltisPS,SoltisDE,SavolainenV,CranePR,BarracloughTG: Rate heterogeneityamonglineagesoftracheophytes:integrationof molecularandfossildataandevidenceformolecularlivingfossils. ProcNatlAcadSciUSA 2002, 99 (7):4430 – 4435. 20.ZhongB,DeuschO,GoremykinVV,PennyD,BiggsPJ,AthertonRA, NikiforovaSV,LockhartPJ: Systematicerrorinseedplantphylogenomics. GenomeBiolEvol 2011, 3: 1340 – 1348. 21.SmithDR: UnparalleledGCcontentintheplastidDNAof Selaginella PlantMolBiol 2009, 71 (6):627 – 639. 22.SmithSA,DonoghueMJ: Ratesofmolecularevolutionarelinkedtolife historyinfloweringplants. Science 2008, 322 (5898):86 – 89. 23.KarolKG,McCourtRM,CiminoMT,DelwicheCF: Theclosestlivingrelatives oflandplants. Science 2001, 294: 2351 – 2353. 24.LemieuxC,OtisC,TurmelM: Ancestralchloroplastgenomein Mesostigma viride revealsanearlybranchofgreenplantevolution. Nature 2000, 403 (6770):649 – 652. 25.WodniokS,BrinkmannH,GlocknerG,HeidelAJ,PhilippeH,MelkonianM,BeckerB: Originoflandplants:doconjugatinggreenalgaeholdthekey? BMCEvolBiol 2011, 11: 104. 26.LangBF,NedelcuAM: Plastidgenomesofalgae. In Genomicsof ChloroplastsandMitochondria ,Volume35.EditedbyBockR,KnoopV. Netherlands:Springer;2012:59 – 87. 27.TurmelM,OtisC,LemieuxC: Thechloroplastgenomesequenceof Chara vulgaris shedsnewlightintotheclosestgreenalgalrelativesofland plants. MolBiolEvol 2006, 23 (6):1324 – 1338. 28.TurmelM,PombertJ,CharleboisP,OtisC,LemieuxC: Thegreenalgal ancestryoflandplantsasrevealedbythechloroplastgenome. IntJPl Sci 2007, 168 (5):679 – 689. 29.QiuYL,LiL,WangB,ChenZ,KnoopV,Groth-MalonekM,DombrovskaO, LeeJ,KentL,RestJ, etal : Thedeepestdivergencesinlandplantsinferred fromphylogenomicevidence. ProcNatlAcadSciUSA 2006, 103 (42):15511 – 15516. 30.NickrentDL,ParkinsonCL,PalmerJD,DuffRJ: Multigenephylogenyof landplantswithspecialreferencetobryophytesandtheearliestland plants. MolBiolEvol 2000, 17: 1885 – 1895. 31.RenzagliaKS,SchuetteS,DuffRJ,LigroneR,ShawAJ,MishlerBD,Duckett JG: Bryophytephylogeny:advancingthemolecularandmorphological frontiers. Bryologist 2007, 110 (2):179 – 213. 32.MishlerBD,ChurchillSP: Acladisticapproachtothephylogenyofthe “ bryophytes ” Brittonia 1984, 36: 406 – 424.Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page24of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 25

33.ShawJ,RenzagliaK: Phylogenyanddiversificationofbryophytes. AmerJ Bot 2004, 91 (10):1557 – 1581. 34.KarolKG,ArumuganathanK,BooreJL,DuffyAM,EverettKDE,HallJD, HansenSK,KuehlJV,MandoliDF,MishlerBD, etal : Completeplastome sequencesof Equisetumarvense and Isoetesflaccida :implicationsfor phylogenyandplastidgenomeevolutionofearlylandplantlineages. BMCEvolBiol 2010, 10: 321. 35.WolfPG,KarolKG: Plastomesofbryophytes,lycophytesandferns. In GenomicsofChloroplastsandMitochondria ,Volume35.EditedbyBockR, KnoopV.Netherlands:Springer;2012:89 – 102. 36.CranePR: Phylogeneticanalysisofseedplantsandtheoriginof angiosperms. AnnMissouriBotGard 1985, 72: 716 – 793. 37.ChawSM,ZharkikhA,SungHM,LauTC,LiWH: Molecularphylogenyof extantgymnospermsandseedplantevolution:analysisofnuclear18S rRNAsequences. MolBiolEvol 1997, 14 (1):56 – 68. 38.BoweLM,CoatG,dePamphilisCW: Phylogenyofseedplantsbasedonall threegenomiccompartments:extantgymnospermsaremonophyletic andGnetales ’ closestrelativesareconifers. ProcNatlAcadSciUSA 2000, 97 (8):4092 – 4097. 39.ChawSM,ParkinsonCL,ChengYC,VincentTM,PalmerJD: Seedplant phylogenyinferredfromallthreeplantgenomes:monophylyofextant gymnospermsandoriginofGnetalesfromconifers. ProcNatlAcadSci USA 2000, 97 (8):4086 – 4091. 40.FinetC,TimmeRE,DelwicheCF,MarletaF: Multigenephylogenyofthe greenlineagerevealstheoriginanddiversificationoflandplants. Curr Biol 2010, 20 (24):2217 – 2222. 41.ZhongB,YonezawaT,ZhongY,HasegawaM: ThepositionofGnetales amongseedplants:overcomingpitfallsofchloroplastphylogenomics. MolBiolEvol 2010, 27 (12):2855 – 2863. 42.MathewsS: Phylogeneticrelationshipsamongseedplants:persistent questionsandthelimitsofmoleculardata. AmerJBot 2009, 96 (1):228 – 236. 43.BurleighJG,MathewsS: Phylogeneticsignalinnucleotidedatafromseedplants:implicationsforresolvingtheseedplanttreeoflife. AmerJBot 2004, 91 (10):1599 – 1613. 44.BhattacharyaD,MedlinL: Algalphylogenyandtheoriginoflandplants. PlantPhysiol 1998, 116 (1):9 – 15. 45.SoltisPS,SoltisDE,WolfPG,NickrentDL,ChawS-M,ChapmanRL: The phylogenyoflandplantsinferredfrom18SrDNAsequences:pushing thelimitsofrDNAsignal? MolBiolEvol 1999, 16: 1774 – 1784. 46.LeeEK,Cibrian-JaramilloA,KolokotronisS-O,KatariMS,StamatakisA,OttM, ChiuJC,LittleDP,StevensonDW,McCombieWR, etal : Afunctional phylogenomicviewoftheseedplants. PLoSGenet 2011, 7 (12):e1002411. 47.QiuYL,ChoY,CoxJC,PalmerJD: Thegainofthreemitochondrialintrons identifiesliverwortsastheearliestlandplants. Nature 1998, 394: 671 – 674. 48.DuffRJ,NickrentDL: Phylogeneticrelationshipsoflandplantsusing mitochondrialsmall-subunitrDNAsequences. AmerJBot 1999, 86: 372 – 386. 49.QiuYL,PalmerJD: Phylogenyofearlylandplants:insightsfromgenes andgenomes. TrendsPlantSci 1999, 4 (1):26 – 30. 50.QiuYL: Phylogenyandevolutionofcharophyticalgaeandlandplants. JSystEvol 2008, 46 (3):287 – 306. 51.MagallonS,SandersonMJ: Relationshipsamongseedplantsinferredfrom highlyconservedgenes:Sortingconflictingphylogeneticsignalsamong ancientlineages. AmerJBot 2002, 89 (12):1991 – 2006. 52.SmithS,BeaulieuJ,DonoghueM: Mega-phylogenyapproachfor comparativebiology:analternativetosupertreeandsupermatrix approaches. BMCEvolBiol 2009, 9 (1):37. 53.WickeS,SchneeweissG,dePamphilisC,MllerK,QuandtD: Theevolution oftheplastidchromosomeinlandplants:genecontent,geneorder, genefunction. PlantMolBiol 2011, 76 (3):273 – 297. 54.PalmerJD,NugentJM,HerbonLA: Unusualstructureofgeranium chloroplastdna-atriple-sizedinvertedrepeat,extensivegeneduplications, multipleinversions,and2repeatfamilies. ProcNatlAcadSciUSA 1987, 84(3):769 – 773. 55.StegemannS,KeutheM,GreinerS,BockR: Horizontaltransferof chloroplastgenomesbetweenplantspecies. ProcNatlAcadSciUSA 2012, 109 (7):2434 – 2438. 56.SoltisDE,SoltisPM: Choosinganapproachandanappropriategenefor phylogeneticanalysis. In MolecularSystematicsofPlantsII. EditedbySoltis DE,SoltisPM,DoyleJ.Boston:Kluwer;1998:1 – 42. 57.OlmsteadRG,PalmerJD: ChloroplastDNAsystematics-areviewof methodsanddata-analysis. AmerJBot 1994, 81 (9):1205 – 1224. 58.ChaseMW,SoltisDE,OlmsteadRG,MorganD,LesDH,MishlerBD,DuvallMR, PriceRA,HillsHG,QiuY-L, etal : Phylogeneticsofseedplants:Ananalysisof nucleotidesequencesfromtheplastidgene rbcL AnnMissouriBotGard 1993, 80: 528 – 580. 59.SavolainenV,ChaseMW: Adecadeofprogressinplantmolecular phylogenetics. TrendsGen 2003, 19 (12):717 – 724. 60.ShinozakiK, etal : Thecompletenucleotidesequenceoftobaccochloroplast genome:itsgeneorganizationandexpression. EMBOJ 1986, 5: 2043 – 2049. 61.OhyamaK,FukuzawaH,KohchiT,ShiraiH,SanoT,SanoS,UmesonoK, ShikiY,TakeuchiM,ChangZ, etal : Chloroplastgeneorganization deducedfromcompletesequenceofliverwort Marchantiapolymorpha chloroplastDNA. Nature 1986, 322 (6079):572 – 574. 62.MooreMJ,DhingraA,SoltisPS,ShawR,FarmerieWG,FoltaKM,SoltisDE: Rapidandaccuratepyrosequencingofangiospermplastidgenomes. BMCPlantBiol 2006, 6: 17. 63.MooreMJ,SoltisPS,BellCD,BurleighJG,SoltisDE: Phylogeneticanalysisof 83plastidgenesfurtherresolvestheearlydiversificationofeudicots. ProcNatlAcadSciUSA 2010, 107 (10):4623 – 4628. 64.CronnR,KnausBJ,ListonA,MaughanPJ,ParksM,SyringJV,UdallJ: Targetedenrichmentstrategiesfornext-generationplantbiology. AmerJ Bot 2012, 99 (2):291 –311. 65.CronnR,ListonA,ParksM,GernandtDS,ShenR,MocklerT: Multiplex sequencingofplantchloroplast genomesusingSolexasequencingby-synthesistechnology. NucleicAcidsRes 2008, 36 (19):1 – 11. 66.ParksM,CronnR,ListonA: Increasingphylogeneticresolutionatlow taxonomiclevelsusingmassivelyparallelsequencingofchloroplast genomes. BMCBiol 2009, 7: 84. 67.StraubSCK,ParksM,WeitemierK,FishbeinM,CronnRC,ListonA: Navigatingthetipofthegenomiciceberg:next-generationsequencing forplantsystematics. AmerJBot 2012, 99 (2):349 – 364. 68.JansenRK,RuhlmanTA: Plastidgenomesofseedplants. In Genomicsof ChloroplastsandMitochondria ,Volume35.EditedbyBockR,KnoopV. Netherlands:Springer;2012. 69.XiZ,RuhfelBR,SchaeferH,AmorimAM,SugumaranM,WurdackKJ,EndressPK, MatthewsML,StevensPF,MathewsS, etal : Phylogenomicsandaposteriori datapartitioningresolvetheCretaceousangiospermradiationMalpighiales. ProcNatlAcadSciUSA 2012, 109 (43):17519 – 17524. 70.deKoningAP,KeelingPJ: Thecompleteplastidgenomesequenceofthe parasiticgreenalga Helicosporidium sp.ishighlyreducedandstructured. BMCBiol 2006, 4: 10. 71.DelannoyE,FujiiS,ColasdesFrancs-SmallC,BrundrettM,SmallI: Rampant genelossintheundergroundorchid Rhizanthellagardneri highlights evolutionaryconstraintsonplastidgenomes. MolBiolEvol 2011, 28 (7):2077 – 2086. 72.SandersonMJ,McMahonMM,SteelM: Phylogenomicswithincomplete taxoncoverage:thelimitstoinference. BMCEvolBiol 2010, 10: 13. 73.RuhfelBR,GitzendannerMA,SoltisPS,SoltisDE,BurleighJG: Datafrom: fromalgaetoangiosperms: – inferringthephylogenyofgreenplants ( Viridiplantae )from360plastidgenomes. DryadDataRepository 2014 : doi:10.5061/dryad.k1t1f. 74.LewisLA,McCourtRM: Greenalgaeandtheoriginoflandplants. AmerJ Bot 2004, 91 (10):1535 – 1556. 75.MattoxKR,StewartKD: Classificationofthegreenalgae:aconceptbased oncomparativecytology. In TheSystematicsofGreenAlgae.EditedbyIrvin DEG,JohnDM.London,UK:AcademicPress;1984:29 – 72. 76.LeliaertF,SmithDR,MoreauH,HerronMD,VerbruggenH,DelwicheCF,De ClerckO: Phylogenyandmolecularevolutionofthegreenalgae. CRCCrit RevPlantSci 2012, 31 (1):1 – 46. 77.LeliaertF,VerbruggenH,ZechmanFW: Intothedeep:Newdiscoveriesat thebaseofthegreenplantphylogeny. Bioessays 2011, 33 (9):683 – 692. 78.LartillotN,BrinkmannH,PhilippeH: Suppressionoflong-branchattraction artefactsintheanimalphylogenyusingasite-heterogeneousmodel. BMCEvolBiol 2007, 7: 14. 79.LartillotN,PhilippeH: ABayesianmixturemodelforacross-siteheterogeneities intheamino-acidreplacementprocess. MolBiolEvol 2004, 21: 1095. 80.LemieuxC,OtisC,TurmelM: Acladeunitingthegreenalgae Mesostigma viride and Chlorokybusatmophyticus representsthedeepestbranchof theStreptophytainchloroplastgenome-basedphylogenies. BMCBiol 2007, 5: 2. 81.Rodriguez-EzpeletaN,PhilippeH,BrinkmannH,BeckerB,MelkonianM: Phylogeneticanalysesofnuclear,mitochondrial,andplastidmultigeneRuhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page25of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 26

datasetssupporttheplacementof Mesostigma intheStreptophyta. Mol BiolEvol 2007, 24 (3):723 – 731. 82.TimmeRE,BachvaroffTR,DelwicheCF: Broadphylogenomicsamplingand thesisterlineageoflandplants. PLoSONE 2012, 7 (1):e29696. 83.TurmelM,OtisC,LemieuxC: Anunexpectedlylargeandlooselypacked mitochondrialgenomeinthecharophyceangreenalga Chlorokybus atmophyticus BMCGenomics 2007, 8: 12. 84.CocquytE,VerbruggenH,LeliaertF,DeClerckO: Evolutionandcytological diversificationofthegreenseaweeds(Ulvophyceae). MolBiolEvol 2010, 27 (9):2052 – 2061. 85.TurmelM,GagnonM-C,O ’ KellyCJ,OtisC,LemieuxC: Thechloroplast genomesofthegreenalgae Pyramimonas Monomastix ,and Pycnococcus shednewlightontheevolutionaryhistoryofprasinophytesandthe originofthesecondarychloroplastsofeuglenids. MolBiolEvol 2009, 26 (3):631 – 648. 86.TurmelM,OtisC,LemieuxC: Thechloroplastgenomesofthegreenalgae Pedinomonasminor Parachlorellakessleri ,and Oocystissolitatia reveala sharedancestrybetweenthePedinomonadalesandChlorellales. MolBiol Evol 2009, 26 (10):2317 – 2331. 87.ZhongB,XiZ,GoremykinVV,FongR,MclenachanPA,NovisPM,DavisCC, PennyD: Streptophytealgaeandtheoriginoflandplantsrevisitedusing heterogeneousmodelswiththreenewalgalchloroplastgenomes. Mol BiolEvol 2014, 31 (1):177 – 183. 88.Groth-MalonekM,PruchnerD,GreweF,KnoopV: Ancestorsoftrans-splicing mitochondrialintronssupportserialsistergrouprelationshipsofhornworts andmosseswithvascularplants. MolBiolEvol 2005, 22 (1):117 – 125. 89.QiuYL,LiL,WangB,ChenZ,DombrovskaO,LeeJH,KentL,LiRQ,Jobson RW,HendryTA, etal : Anonfloweringlandplantphylogenyinferredfrom nucleotidesequencesofsevenchloroplast,mitochondrial,andnuclear genes. IntJPlSci 2007, 168 (5):691 –708. 90.RenzagliaKS,DuffRJ,NickrentDL,GarbaryDJ: Vegetativeand reproductiveinnovationsofearlylandplants:implicationsforaunified phylogeny. PhilosTranssRSocLonB 2000, 355: 769 – 793. 91.RenzagliaKS,GarbaryDJ: Motilegametesoflandplants:diversity, development,andevolution. CRCCritRevPlantSci 2001, 20 (2): 107 – 213. 92.GarbaryDJ,RenzagliaKS,DuckettJG: Thephylogenyoflandplants-a cladisticanalysisbasedonmalegametogenesis. PlSystEvol 1993, 188: 237 – 269. 93.GarbaryDJ,RenzagliaKS: Bryophytephylogenyandtheevolutionof landplants:evidencefromdevelopmentandultrastructure. In Bryologyforthetwenty-firstcentury. EditedbyBatesJW,AshtonNW, DuckettJG.Leeds,U.K:ManeyPublishingandBritishBryologicalSociety; 1998:45 – 63. 94.NishiyamaT,WolfPG,KugitaM,SinclairRB,SugitaM,SugiuraC,WakasugiT, YamadaK,YoshinagaK,YamaguchiK, etal : Chloroplastphylogeny indicatesthatbryophytesaremonophyletic. MolBiolEvol 2004, 21 (10):1813 – 1819. 95.GoremykinVV,HellwigFH: Evidenceforthemostbasalsplitinland plantsdividingbryophyteandtracheophytelineages. PlSystEvol 2005, 254 (1 – 2):93 – 103. 96.PryerKM,SchneiderH,SmithAR,CranfillR,WolfPG,HuntJS,SipesSD: Horsetailsandfernsareamonophyleticgroupandtheclosestliving relativestoseedplants. Nature 2001, 409: 618 – 622. 97.PryerKM,SchneiderH,MagallnS: Theradiationofvascularplants .In AssemblingtheTreeofLife. EditedbyCracraftJ,DonoghueMJ.NewYork: UniversityPress;2004:138 – 153. 98.KranzHD,HussVAR: Molecularevolutionofpteridophytesandtheir relationshiptoseedplants:evidencefromcomplete18SrRNAgene sequences. PlSystEvol 1996, 202 (1 – 2):1 – 11. 99.RaubesonLA,JansenRK: ChloroplastDNAevidenceontheancient evolutionarysplitinvascularlandplants. Science 1992, 255 (5052):1697 – 1699. 100.GreweF,GuoW,GubbelsE,HansenAK,MowerJ: Completeplastidgenomesfrom Ophioglossumcalifornicum Psilotumnudum ,and Equisetumhyemale revealanancestrallandplantgenomestructureand resolvethepositionofEquisetalesamongmonilophytes. BMCEvolBiol 2013, 13 (1):8. 101.SoltisDE,SoltisPS,ZanisMJ: Phylogenyofseedplantsbasedonevidence fromeightgenes. AmerJBot 2002, 89 (10):1670 – 1681. 102.XiZ,RestJ,DavisCC: Phylogenomicsandcoalescentanalysesresolve extantseedplantrelationships. PLoSONE 2013, 8 (11):e80870. 103.SoltisDE,SmithSA,CellineseN,WurdackKJ,TankDC,BrockingtonSF, Refulio-RodriguezNF,WalkerJB,MooreMJ,CarlswardBS, etal : Angiosperm phylogeny:17genes,640taxa. AmJBot 2011, 98 (4):704 – 730. 104.JansenRK,SaskiC,LeeSB,HansenAK,DaniellH: Completeplastidgenome sequencesofthreerosids( Castanea Prunus Theobroma ):evidenceforat leasttwoindependenttransfersof rpl22 tothenucleus. MolBiolEvol 2011, 28 (1):835 – 847. 105.JansenRK,CaiZ,RaubesonLA,DaniellH,DepamphilisCW,Leebens-MackJ, MullerKF,Guisinger-BellianM,HaberleRC,HansenAK, etal : Analysisof81 genesfrom64plastidgenomesresolvesrelationshipsinangiosperms andidentifiesgenome-scaleevolutionarypatterns. ProcNatlAcadSciUSA 2007, 104: 19369 – 19374. 106.MooreMJ,BellCD,SoltisPS,SoltisDE: Usingplastidgenome-scaledatato resolveenigmaticrelationshipsamongbasalangiosperms. ProcNatlAcad SciUSA 2007, 104 (49):19363 – 19368. 107.SoltisDE,SoltisPS,EndressPK,ChaseMW: Phylogenyandevolutionof angiosperms. Sunderland,Mass:SinauerAssociates;2005. 108.BarrettCF,DavisJI,Leebens-MackJ,ConranJG,StevensonDW: Plastid genomesanddeeprelationshipsamongthecommelinidmonocot angiosperms. Cladistics 2013, 29 (1):65 – 87. 109.AneC,BurleighJG,McMahonMM,SandersonMJ: Covarionstructurein plastidgenomeevolution:anewstatisticaltest. MolBiolEvol 2005, 22 (4):914– 924. 110.GoremykinVV,NikiforovaSV,BiggsPJ,ZhongBJ,DelangeP,MartinW, WoetzelS,AthertonRA,McLenachanPA,LockhartPJ: Theevolutionary rootoffloweringplants. SystBiol 2013, 62 (1):50 – 61. 111.FosterPG: Modelingcompositionalheterogeneity. SystBiol 2004, 53 (3):485 – 495. 112.JermiinLS,HoSYW,AbabnehF,RobinsonJ,LarkumAWD: Thebiasing effectofcompositionalheterogeneityonphylogeneticestimatesmay beunderestimated. SystBiol 2004, 53 (4):638 – 643. 113.ErixonP,OxelmanB: Whole-genepositiveselection,elevated synonymoussubstitutionrates,duplication,andindelevolutionofthe chloroplast clpP1 gene. PLoSONE 2008, 3 (1):10. 114.GuisingerMM,KuehlJV,BooreJL,JansenRK: Genome-wideanalysesof GeraniaceaeplastidDNArevealunprecedentedpatternsofincreased nucleotidesubstitutions. ProcNatlAcadSciUSA 2008, 105 (47):18424 – 18429. 115.CaiZQ,PenaflorC,KuehlJV,Leebens-MackJ,CarlsonJE,dePamphilisCW, BooreJL,JansenRK: Completeplastidgenomesequencesof Drimys Liriodendron ,and Piper :implicationsforthephylogeneticrelationships ofmagnoliids. BMCEvolBiol 2006, 6: 20. 116.RaubesonLA,PeeryR,ChumleyTW,DziubekC,FourcadeHM,BooreJL, JansenRK: Comparativechloroplastgenomics:analysesincludingnew sequencesfromtheangiosperms Nupharadvena and Ranunculus macranthus BMCGenomics 2007, 8: 27. 117.GuisingerMM,KuehlJV,BooreJL,JansenRK: Extremereconfigurationof plastidgenomesintheangiospermfamilyGeraniaceae:rearrangements, repeats,andcodonusage. MolBiolEvol 2011, 28 (1):583 – 600. 118.PhillipsMJ,PennyD: Therootofthemammaliantreeinferredfrom wholemitochondrialgenomes. MolPhylogenetandEvol 2003, 28 (2):171 – 185. 119.PhillipsMJ,DelsucF,PennyD: Genome-scalephylogenyandthe detectionofsystematicbiases. MolBiolEvol 2004,21: 1455. 120.IshikawaSA,InagakiY,HashimotoT: RY-codingandnon-homogeneous modelscanamelioratethemaximum-likelihoodinferencesfrom nucleotidesequencedatawithparallelcompositionalheterogeneity. EvolBioinform 2012, 8: 357 – 371. 121.DelsucF,PhillipsMJ,PennyD: Commenton “ Hexapodorigins: monophyleticorparaphyletic? ” Science 2003, 301 (5639):1482. 122.ParksM,CronnR,ListonA: Separatingthewheatfromthechaff: mitigatingtheeffectsofnoiseinaplastomephylogenomicdataset from Pinus L.(Pinaceae). BMCEvolBiol 2012, 12 (1):100. 123.JeffroyO,BrinkmannH,DelsucF,PhilippeH: Phylogenomics:the beginningofincongruence? TrendsGenet 2006, 22 (4):225 – 231. 124.FosterPG,HickeyDA: CompositionalbiasmayaffectbothDNA-based andprotein-basedphylogeneticreconstructions. JMolEvol 1999, 48 (3):284 – 290. 125.MathewsS,ClementsMD,BeilsteinMA: Aduplicategenerootingofseed plantsandthephylogeneticpositionoffloweringplants. PhilosTransR SocB-BiolSci 2010, 365 (1539):383 – 395. 126.SoltisDE,AlbertVA,SavolainenV,HiluK,QiuYL,ChaseMW,FarrisJS, StefanovicS,RiceDW,PalmerJD, etal : Genome-scaledata,angiospermRuhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page26of27 http://www.biomedcentral.com/1471-2148/14/23

PAGE 27

relationships,and “ endingincongruence ” :acautionarytalein phylogenetics. TrendsPlantSci 2004, 9 (10):477 – 483. 127.GraybealA: Isitbettertoaddtaxaorcharacterstoadifficult phylogeneticproblem? SystBiol 1998, 47: 9 – 17. 128.HillisDM: Taxonomicsampling,phylogeneticaccuracy,andinvestigator bias. SystBiol 1998, 47 (1):3 – 8. 129.ZwicklDJ,HillisDM: Increasedtaxonsamplinggreatlyreduces phylogeneticerror. SystBiol 2002, 51: 588 – 598. 130.HillisDM,PollockDD,McGuireJA,ZwicklDJ: Issparsetaxonsamplinga problemforphylogeneticinference? SystBiol 2003, 52: 124 – 126. 131.Leebens-MackJ,RaubesonLA,CuiL,KuehlJV,FourcadeMH,ChumleyTW, BooreJL,JansenRK,dePamphilisCW: Identifyingthebasalangiosperm nodeinchloroplastgenomephylogenies:samplingone ’ swayoutofthe FelsensteinZone. MolBiolEvol 2005, 22 (10):1948 – 1963. 132.StullGW,MooreMJ,MandalaVS,DouglasNA,KatesH-R,QiX,Brockington SF,SoltisPS,SoltisDE,GitzendannerMA: Atargetedenrichmentstrategy formassivelyparallelsequencingofangiospermplastidgenomes. Appl PlantSci 2013, 1 (2):1200497. 133.WiensJJ: Missingdata,incompletetaxa,andphylogeneticaccuracy. Syst Biol 2003, 52 (4):528 – 538. 134.WiensJJ,MoenDS: MissingdataandtheaccuracyofBayesian phylogenetics. JSystEvol 2008, 46 (3):307 – 314. 135.RuhfelBR,StevensPF,DavisCC: Combinedmorphologicalandmolecular phylogenyoftheclusioidclade(Malpighiales)andtheplacementofthe ancientrosidmacrofossil Paleoclusia IntJPlSci 2013, 174 (6):910 – 936. 136.WiensJJ:Paleontology,genomics,andcombined-dataphylogenetics: canmoleculardataimprovephylogenyestimationforfossiltaxa? Syst Biol 2009, 58 (1):87 – 99. 137.WangH,MooreMJ,SoltisPS,BellCD,BrockingtonSF,AlexandreR,Davis CC,LatvisM,ManchesterSR,SoltisDE: Rosidradiationandtherapidrise ofangiosperm-dominatedforests. ProcNatlAcadSciUSA 2009, 106 (10):3853 – 3858. 138.KubatkoLS,DegnanJH: Inconsistencyofphylogeneticestimatesfrom concatenateddataundercoalescence. SystBiol 2007, 56 (1):17 – 24. 139.MatsenFA,SteelM: Phylogeneticmixturesonasingletreecanmimica treeofanothertopology. SystBiol 2007, 56 (5):767 – 775. 140.PennyD,WhiteWT,HendyMD,PhillipsMJ: AbiasinMLestimatesof branchlengthsinthepresenceofmultiplesignals. MolBiolEvol 2008, 25 (2):239 – 242. 141.MaddisonWP: Genetreesinspeciestrees. SystBiol 1997, 46 (3):523 – 536. 142.MosselE,SteelM: Howmuchcanevolvedcharacterstellusaboutthe treethatgeneratedthem? In MathematicsofEvolutionandPhylogeny. EditedbyGascuelO,SteelM.Oxford:OxfordUniversityPress;2005:384 – 412. 143.PoncianoJM,BurleighJG,BraunEL,TaperML: Assessingparameter identifiabilityinphylogeneticmodelsusingdatacloning. SystBiol 2012, 61 (6):955 – 972. 144.GoffinetB,BuckWR,ShawAJ: Morphologyandclassificationofthe Bryophyta. In BryophyteBiology. 2ndedition.EditedbyGoffinetB,ShawAJ. Cambridge,UK:CambridgeUniversityPress;2008:55 – 138. 145.StotlerRE,Crandall-StotlerB: ArevisedclassificationoftheAnthocerotophyta andachecklistofthehornwortsofNorthAmerica,northofMexico. Bryologist 2005, 108 (1):16 – 26. 146.Crandall-StotlerB,StotlerRE,LongDG: Phylogenyandclassificationofthe Marchantiophyta. EdinbJBot 2009, 66 (1):155 – 198. 147.CantinoPD,DoyleJA,GrahamSW,JuddWS,OlmsteadRG,SoltisDE,Soltis PS,DonoghueMJ: TowardsaphylogeneticnomenclatureofTracheophyta. Taxon 2007, 56 (3):1E – 44E. 148.ChristenhuszMJM,ZhangX-C,SchneiderH: Alinearsequenceofextant familiesandgeneraoflycophytesandferns. Phytotaxa 2011, 19: 7 – 54. 149.ChristenhuszMJM,RevealJL,FarjonA,GardnerMF,MillRR,ChaseMW: A newclassificationandlinearsequenceofextantgymnosperms. Phytotaxa 2011, 19: 55 – 70. 150.IIIA: AnupdateoftheAngiospermPhylogenyGroupclassificationfor theordersandfamiliesoffloweringplants:APGIII. BotJLinnSoc 2009, 161 (2):105 – 121. 151.McNeillJ,BarrieFR,BuckWR,DemoulinV,GreuterW,HawkworthDL, HerendeenPS,KnappS,MarholdK,PradoJ, etal : Internationalcodeof nomenclatureforalgae,fungi,andplants(Melbournecode);adoptedbythe EighteenthInternationalBotanicalCongress,Melbourne,Australia,July2011. Knigstein,Germany:KoeltzScientificBooks;2012. 152.AltschulSF,MaddenTL,SchafferAA,ZhangJH,ZhangZ,MillerW,LipmanDJ: GappedBLASTandPSI-BLAST:anewgenerationofproteindatabase searchprograms. NucleicAcidsRes 1997, 25 (17):3389 – 3402. 153.KatohK,MisawaK,KumaK,MiyataT: MAFFT:anovelmethodforrapid multiplesequencealignmentbasedonfastFouriertransform. Nucleic AcidsRes 2002, 30 (14):3059 – 3066. 154.Capella-GutierrezS,Silla-MartinezJM,GabaldonT: trimAl:atoolfor automatedalignmenttrimminginlarge-scalephylogeneticanalyses. Bioinformatics 2009, 25 (15):1972 – 1973. 155.SuyamaM,TorrentsD,BorkP: PAL2NAL:robustconversionofprotein sequencealignmentsintothecorrespondingcodonalignments. Nucleic AcidsRes 2006, 34 (suppl2):W609 – W612. 156.StamatakisA: RAxML-VI-HPC:Maximumlikelihood-basedphylogenetic analyseswiththousandsoftaxaandmixedmodels. Bioinformatics 2006, 22 (21):2688 – 2690. 157.OttM,ZolaJ,AluruS,StamatakisA: Large-scalemaximumlikelihoodbasedphylogeneticanalysisontheIBMBlueGene/L. In Proceedingsof IEEE/ACMSupercomputing(SC2007)conference:2007. Reno,Nevada,USA: ACM;2007. 158.KuckP,MeusemannK: FASconCAT:Convenienthandlingofdatamatrices. MolPhylogenetEvol 2010, 56 (3):1115 – 1118.159.WoeseCR,AchenbachL,RouviereP,MandelcoL: Archaealphylogeny: reexaminationofthephylogeneticpositionof Archaeoglobusfulgidus in lightofcertaincomposition-inducedartifacts. SystApplMicrobiol 1991, 14: 364. 160.DelsucF,BrinkmannH,PhilippeH: Phylogenomicsandthereconstruction ofthetreeoflife. NatRevGenet 2005, 6 (5):361 – 375. 161.PhilippeH,DelsucF,BrinkmannH,LartillotN: Phylogenomics. AnnuRev EcolEvolSyst 2005, 36 (1):541 – 562. 162.SwoffordDL: PAUP*:PhylogeneticAnalysisUsingParsimony(*andOther Methods).Version4b10. Sunderland,MA:SinauerAssociates;2003. 163.TeamRC: R:Alanguageandenvironmentforstatisticalcomputing. Vienna, Austria:RFoundationforStatisticalComputing;2012. 164.HurvichCM,TsaiCL: Regressionandtime-seriesmodelselectioninsmall samples. Biometrika 1989, 76 (2):297 – 307. 165.PosadaD,BuckleyTR: Modelselectionandmodelaveragingin phylogenetics:advantagesofAkaikeInformationCriterionandBayesian approachesoverlikelihoodratiotests. SystBiol 2004, 53 (5):793 – 808. 166.LanfearR,CalcottB,HoSYW,GuindonS: PartitionFinder:combined selectionofpartitioningschemesandsubstitutionmodelsfor phylogeneticanalyses. MolBiolEvol 2012, 29 (6):1695 – 1701. 167.PattengaleND,AlipourM,Bininda-EmondsORP,MoretBME,StamatakisA: How manybootstrapreplicatesarenecessary? JComputBiol 2010, 17 (3):337 – 354.doi:10.1186/1471-2148-14-23 Citethisarticleas: Ruhfel etal. : Fromalgaetoangiosperms – inferring thephylogenyofgreenplants( Viridiplantae )from360plastidgenomes. BMCEvolutionaryBiology 2014 14 :23. Submit your next manuscript to BioMed Central and take full advantage of: € Convenient online submission € Thorough peer review € No space constraints or color “gure charges € Immediate publication on acceptance € Inclusion in PubMed, CAS, Scopus and Google Scholar € Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Ruhfel etal.BMCEvolutionaryBiology 2014, 14 :23 Page27of27 http://www.biomedcentral.com/1471-2148/14/23



PAGE 1

Liriodendron tulipifera Nandina domest ica Olea woodiana Kingia australis Anomochloa marantoidea Larix decidua Phyllostachys edulis Anredera baselloides P inus thunber gii G i nkgo biloba Aethionema grandiflorum Gossypium tomentosum Plumbago auriculata B elosynaps i s ciliat a Citrus sinensis E phedr a equis e t ina Phyllost achys nigra Rhizanthella gardneri J a sminum nudif lor u m Puya laxa Cheilanthes lindheimeri Welwitschia mirabilis Abolboda macrostachya E l eusi ne coracana Oltmannsiellopsis viridis Theobroma cacao Gossypium arboreum Bulnesia arborea Blossfeldia liliputana Dunaliella salina P o t a m ophila parvi f lor a Atropa belladonna F loydiella t errest ris Arabidops i s thaliana G ossypium must elinum Phormium tenax Lar i x o ccident alis Zygnema circumcarinatum Ilex cornuta Didierea madagascariensis Euonymus americanus Nicotiana sylvestris Silene noctiflora Barbarea verna Oryza sativa var. indica Pinus monophylla Lomandra longifolia H e licospori d i um s p. Z ea m a y s Gnetum parvifolium Adi antum capillu s Erodium carvifolium Chamaedorea seifrizii Sparganium eurycarpum Pinus nelsonii Eucalyptus globulus Oryza rufipogon B Elaeis oleifera S t aphylea colchica Coffea arabica F ragaria vesca Anthoceros formosae Meliosma a ff. c uneif olia Ravenea hildebrandt i i Ageratina adenophora O n c idium sp. Asparagus officinalis Anthriscus cerefolium Oryza sativa var. japonica Scaevola aemula Spirodela polyrhiza Oxypolis greenmanii Pinus koraiensis Bambusa ol dhami i O l ea europaea ssp. europaea Millettia pinnata Dillenia indica Vigna radiata Ipomoea purpurea Oryza meridionalis Huperzia luc idula Thurnia sphaerocephala Volvox cart eri Cerat ophyllum demersum Pentactina rupicola G e r anium palm a t u m Pereskiopsis diguetii Wolffiella lingulata Picea sitchensis Syntrichia ruralis Pinus t orreyana ssp. t orreyana Lepidium vi r ginic u m Pitcairnia feliciana Cedrus deodara Nelumbo lut e a Micromonas s p. Neoregelia carolinae Solanum tuberosum Equiset um arvense Pinus armandii Aucuba japonica Rhododendron simsii F ranklinia alat amaha Pinus ponderosa Tri t i c u m aesti v u m Iris virginica Mayaca fluviatilis Cuscut a ref lexa Y u cca schidiger a Saccharum hybridus Phalaenopsis aphrodite Oenothera elata Oedogonium cardiacum Draba nemorosa O enot her a parv i f lor a Lolium per enne Cycas t ait ungensis Berberidopsis corallina J unc u s e ffu s u s Agathis australis Halocarpus kirkii G ossypium t hurberi Pisum sativum Cucumis sativus W eingart ia k argliana Leersia tisserantii Morus indica Olea europaea ssp. cuspidata Prunus persica G o ssypium raim ondii Pinus t aeda Crithmum maritimum Georgeantha hexandra Cuscuta obtusiflora E h r e t ia ac u m inat a Ferrocalamus rimosivaginus Physcomitrella patens Ptilid i um pul cherri mum Pereskia sacharosa Calycanthus floridus Illicium oligandrum Solanum bulbocastanum Albuca kirkii Nic o t iana t abac u m Epifagus virginiana Cycas micronesica Passif lora bif lora Navia saxicola Cucumis melo Anethum graveolens Silene latifolia Leptosira terrestris Q uercus nigra Port ulacaria af r a Castanea mollissima Chlamydomonas reinhardt i i Chaet osphaeridium globosum G o ssypium her bac eum Alsophila spinulosa Gossypium darwinii C h l orokybus atmophyticus Panax ginseng P inus ger a r diana Hesperaloe parvif lora Vitis vinifera Aco r u s a m e r i c anus Centrolepis monogyna Lobularia maritima Strept o c haet a angusti f olia Silene vulgaris Lat h yru s sa t i v u s Pinus leiophylla var. chihuahuana Ximenia americana Marchantia polymorpha Pseudendoclonium akinetum Trifolium subterraneum Chloranthus spicatus Parachlorella kessleri O punt ia dec u m bens Pinus aristata Cic e r a r iet inum Musa acuminata Corynocarpus laevigata G uizot ia abyssinic a Apostasia wallichii E u c aly p t u s g r andis Agapant hus praecox Nolina atopocarpa Pot arophyt um riparium Pinus merkusii Fagopyrum esculentum Amborella trichopoda Pinus krempfii Cathaya argyrophylla Acorus calamus Dioscorea elephantipes Lotus japonicus Tro c hodendr on ar alioides Bambusa emeiensis Tradescant ia ohiensis Bryopsis hypnoides Glycine max Chlorella variabilis Nicotiana undulata Silene conica Pinus lambertiana Pycnococcus provasolii Acidosasa purpurea Pinus banksiana Pinus ayacahuite Crucihimalaya wallichii Mollugo verti c illata Psilot um nudum Pyramimonas parkeae Piper cenocladum Staurastrum punctulatum Nuphar adv ena Liquidambar styraciflua S o r ghum bic olor Medicago truncatula O ryza nivara Daucus carota Carica papaya Microlaena stipoides Pinus attenuata Platanus occidentalis T hamnochort us insignis Micromonas pusilla Monsonia speciosa Rhynchoryza subulata Cornus florida S elaginella unc inat a Nephroselmis olivacea Oocystis solitaria Pelargonium x sp. Portulaca oleracea Ecdeiocolea monostachya Pinus monticola Nicot iana t oment osif ormis O limarabidopsis pumila Oenothera biennis Scenedesmus obliquus Typha latifolia Monomastix s p. Hydrocotyle s p. Capsella bursa-pastoris Abies firma Dav idia inv olucra t a Mesostigma viride Taiwania cryptomerioides Phaseolus vulgaris Cuscuta exaltata Indocalamus longiauritus Brocchi n i a mi crantha Pinus cembra Pinus pinaster Chara vulgaris Aethionema cordifolium A n t i rrhinum majus F i c u s s p. Pandanus utilis Colocasia esculenta Curculigo c apit ulat a Populus trichocarpa Cuscuta gronovii Part henium argent a t u m Drimys granadensis Pinus parvif lora var. pent aphylla Hevea brasiliensis Puelia olyriformis Helianthus annuus Pinus f lexilis Jacobaea vulgaris Gunnera manicata Renealmia alpinia Cephalotaxus wilsoniana Coix lacryma-jobi Chlorophytum rhizopendulum Heuchera sanguinea Isoetes flaccida Pinus peuce Joinvillea ascendens Ostreococcus tauri Cyperus alternifolius Pteridium aquilinum Pseudotsuga sinensis Arbut u s unedo Picea morrisonicola Maihuenia poeppigii Oryza australiensis Erodium texanum S t igeoclonium helvet icum P inus canar iens i s P edinom onas minor Gossypium barbadense O lea eur opaea ssp. m a r occana Coccomyxa s p. Pinus albicaulis Podocarpus totara Oxalis latifolia Pinus squamata Eleutherococcus senticosus O enot her a ar gillic ola Agrostis stolonifera Gossypium hirsutum Hordeum vulgare Pinus rzedowskii Schizomeris leibleinii Oenothera glazioviana Petroselinum crispum Pinus resinosa Cryptomeria japonica Nelumbo nucifera Aneura mirabilis Dendr o c alam u s lat i f lor u s Ranunculus macranthus Oryza rufipogon A Pinus strobus Ket eleeria davidiana Ric i nus communi s Pyru s p yri folia B oea hy g r o m e tri c a Syngonanthus chrysanthus P inus sibir i c a Buxus microphylla Phoenix dactylifera Selaginella moellendorffii P inus to rre y ana s sp. ins ular i s Tra c helium caer uleum Lonicera japonica Jatropha curcas Arabis hirsut a Phoradendron serotinum Bra c h y podium dista c h y o n Chlorella vulgaris Neottia nidus Lem na m inor Phyllostachys propinqua Lactuca sativa F o ste r ella c aulescens Magnolia kwangsiensis Sesamum indicum Populus alba Nerium oleander Dasypogon bromeliifolius Pinus cont ort a Panicum virgatum Hosta ventricosa Nasturtium officinale Festuca arundinacea Megaleranthis saniculifolia Manihot esculenta Flagellaria indica N ymphaea alba Spinacia oleracea Wolffia australiana Lilium superbum Neoastelia spectabilis Solanum lycopersicum Angiopteris evecta7 8 8 9 100 9 9 100 100 9 8 7 8 100 8 2 9 0 100 6 9 100 100 7 8 9 3 100 8 0 8 8 5 0 100 100 100 6 4 100 100 5 2 100 100 100 100 9 3 100 100 100 8 2 100 9 9 9 7 5 2 100 5 2 100 100 100 100 100 100 9 0 100 100 100 100 7 0 9 6 100 100 100 100 100 100 100 8 2 9 2 7 5 100 100 100 100 100 8 5 100 100 9 9 100 5 5 100 100 100 8 1 100 100 100 6 6 8 1 100 6 0 9 9 6 7 100 100 7 2 100 100 100 7 8 9 9 100 9 1 100 5 9 100 100 100 8 3 100 9 6 100 100 100 100 8 8 6 0 5 5 100 100 7 0 100 100 100 100 100 9 2 8 8 100 100 100 5 4 100 100 5 2 100 7 8 100 8 8 100 100 100 100 8 2 7 0 100 100 100 100 100 100 7 7 9 6 100 9 2 100 100 100 5 9 8 9 8 1 6 2 9 5 100 100 9 9 100 100 9 8 100 100 7 8 100 100 100 100 8 9 100 9 9 100 6 1 100 100 8 4 100 9 4 100 100 100 100 100 9 8 100 100 100 8 4 100 100 100 9 8 100 100 100 9 2 100 100 100 100 5 6 100 100 100 9 9 7 3 9 7 100 100 100 9 9 100 8 9 100 100 100 100 100 100 7 0 100 100 5 1 100 100 100 100 9 9 100 100 100 100 6 9 100 100 8 4 100 100 100 100 100 9 7 100 100 100 100 8 5 100 100 100 100 7 5 100 100 100 9 3 100 100 100 100 100 9 4 100 100 100 100 100 4 7 100 100 100 100 100 100 8 5 100 8 4 100 100 100 9 2 100 100 100 100 100 100 7 4 100 100 9 9 100 100 100 100 100 5 3 100 9 3 100 100 100 100 100 100 100 100 5 2 100 100 100 100 100 8 0 100 100 100 100 100 100 100 100 9 9 100 5 9 9 6 6 5 100 100 100 100 0.2 Liriodendron tulipifera Nandina domest ica Olea woodiana Kingia australis Anomochloa marantoidea Larix decidua Phyllostachys edulis Anredera baselloides P inus thunber gii G i nkgo biloba Aethionema grandiflorum Gossypium tomentosum Plumbago auriculata B elosynaps i s ciliat a Citrus sinensis E phedr a equis e t ina Phyllost achys nigra Rhizanthella gardneri J a sminum nudif lor u m Puya laxa Cheilanthes lindheimeri Welwitschia mirabilis Abolboda macrostachya E l eusi ne coracana Oltmannsiellopsis viridis Theobroma cacao Gossypium arboreum Bulnesia arborea Blossfeldia liliputana Dunaliella salina P o t a m ophila parvi f lor a Atropa belladonna F loydiella t errest ris Arabidops i s thaliana G ossypium must elinum Phormium tenax Lar i x o ccident alis Zygnema circumcarinatum Ilex cornuta Didierea madagascariensis Euonymus americanus Nicotiana sylvestris Silene noctiflora Barbarea verna Oryza sativa var. indica Pinus monophylla Lomandra longifolia H e licospori d i um s p. Z ea m a y s Gnetum parvifolium Adi antum capillu s Erodium carvifolium Chamaedorea seifrizii Sparganium eurycarpum Pinus nelsonii Eucalyptus globulus Oryza rufipogon B Elaeis oleifera S t aphylea colchica Coffea arabica F ragaria vesca Anthoceros formosae Meliosma a ff. cuneif olia Ravenea hildebrandt i i Ageratina adenophora O n c idium s p. Asparagus officinalis Anthriscus cerefolium Oryza sativa var. japonica Scaevola aemula Spirodela polyrhiza Oxypolis greenmanii Pinus koraiensis Bambusa ol dhami i O l ea europaea ssp. europaea Millettia pinnata Dillenia indica Vigna radiata Ipomoea purpurea Oryza meridionalis Huperzia luc idula Thurnia sphaerocephala Volvox cart eri Cerat ophyllum demersum Pentactina rupicola G e r anium palm a t u m Pereskiopsis diguetii Wolffiella lingulata Picea sitchensis Syntrichia ruralis Pinus t orreyana ssp. t orreyana Lepidium vi r ginic u m Pitcairnia feliciana Cedrus deodara Nelumbo lut e a Micromonas s p. Neoregelia carolinae Solanum tuberosum Equiset um arvense Pinus armandii Aucuba japonica Rhododendron simsii F ranklinia alat amaha Pinus ponderosa Tri t i c u m aesti v u m Iris virginica Mayaca fluviatilis Cuscut a ref lexa Y u cca schidiger a Saccharum hybridus Phalaenopsis aphrodite Oenothera elata Oedogonium cardiacum Draba nemorosa O enot her a parv i f lor a Lolium per enne Cycas t ait ungensis Berberidopsis corallina J unc u s e ffu s u s Agathis australis Halocarpus kirkii G ossypium t hurberi Pisum sativum Cucumis sativus W eingart ia k argliana Leersia tisserantii Morus indica Olea europaea ssp. cuspidata Prunus persica G o ssypium raim ondii Pinus t aeda Crithmum maritimum Georgeantha hexandra Cuscuta obtusiflora E h r e t ia ac u m inat a Ferrocalamus rimosivaginus Physcomitrella patens Ptilid i um pul cherri mum Pereskia sacharosa Calycanthus floridus Illicium oligandrum Solanum bulbocastanum Albuca kirkii Nic o t iana t abac u m Epifagus virginiana Cycas micronesica Passif lora bif lora Navia saxicola Cucumis melo Anethum graveolens Silene latifolia Leptosira terrestris Q uercus nigra Port ulacaria af r a Castanea mollissima Chlamydomonas reinhardt i i Chaet osphaeridium globosum G o ssypium her bac eum Alsophila spinulosa Gossypium darwinii C h l orokybus atmophyti cus Panax ginseng P inus ger a r diana Hesperaloe parvif lora Vitis vinifera Aco r u s a m e r i c anus Centrolepis monogyna Lobularia maritima Strept o c haet a angusti f olia Silene vulgaris Lat h yru s sa t i v u s Pinus leiophylla var. chihuahuana Ximenia americana Marchantia polymorpha Pseudendoclonium akinetum Trifolium subterraneum Chloranthus spicatus Parachlorella kessleri O punt ia dec u m bens Pinus aristata Cic e r a r iet inum Musa acuminata Corynocarpus laevigata G uizot ia abyssinica Apostasia wallichii E u c aly p t u s g r andis Agapant hus praecox Nolina atopocarpa Pot arophyt um riparium Pinus merkusii Fagopyrum esculentum Amborella trichopoda Pinus krempfii Cathaya argyrophylla Acorus calamus Dioscorea elephantipes Lotus japonicus Tro c hodendr on ar alioides Bambusa emeiensis Tradescant ia ohiensis Bryopsis hypnoides Glycine max Chlorella variabilis Nicotiana undulata Silene conica Pinus lambertiana Pycnococcus provasolii Acidosasa purpurea Pinus banksiana Pinus ayacahuite Crucihimalaya wallichii Mollugo verti c illata Psilot um nudum Pyramimonas parkeae Piper cenocladum Staurastrum punctulatum Nuphar adv ena Liquidambar styraciflua S o r ghum bic olor Medicago truncatula O ryza nivara Daucus carota Carica papaya Microlaena stipoides Pinus attenuata Platanus occidentalis T hamnochort us insignis Micromonas pusilla Monsonia speciosa Rhynchoryza subulata Cornus florida S elaginella unc inat a Nephroselmis olivacea Oocystis solitaria Pelargonium x sp. Portulaca oleracea Ecdeiocolea monostachya Pinus monticola Nicot iana t oment osif ormis O limarabidopsis pumila Oenothera biennis Scenedesmus obliquus Typha latifolia Monomastix s p. Hydrocotyle s p. Capsella bursa-pastoris Abies firma Dav idia inv olucra t a Mesostigma viride Taiwania cryptomerioides Phaseolus vulgaris Cuscuta exaltata Indocalamus longiauritus Brocchi n i a mi crantha Pinus cembra Pinus pinaster Chara vulgaris Aethionema cordifolium A n t i rrhinum majus F i c u s s p. Pandanus utilis Colocasia esculenta Curculigo c apit ulat a Populus trichocarpa Cuscuta gronovii Part henium argent a t u m Drimys granadensis Pinus parvif lora var. pent aphylla Hevea brasiliensis Puelia olyriformis Helianthus annuus Pinus f lexilis Jacobaea vulgaris Gunnera manicata Renealmia alpinia Cephalotaxus wilsoniana Coix lacryma-jobi Chlorophytum rhizopendulum Heuchera sanguinea Isoetes flaccida Pinus peuce Joinvillea ascendens Ostreococcus tauri Cyperus alternifolius Pteridium aquilinum Pseudotsuga sinensis Arbut u s unedo Picea morrisonicola Maihuenia poeppigii Oryza australiensis Erodium texanum S t igeoclonium helvet icum P inus canar iens i s P edinom onas minor Gossypium barbadense O lea eur opaea ssp. m a r occana Coccomyxa s p. Pinus albicaulis Podocarpus totara Oxalis latifolia Pinus squamata Eleutherococcus senticosus O enot her a argillic ola Agrostis stolonifera Gossypium hirsutum Hordeum vulgare Pinus rzedowskii Schizomeris leibleinii Oenothera glazioviana Petroselinum crispum Pinus resinosa Cryptomeria japonica Nelumbo nucifera Aneura mirabilis Dendr o c alam u s lat i f lor u s Ranunculus macranthus Oryza rufipogon A Pinus strobus Ket eleeria davidiana Ric i nus communi s Pyrus pyri folia B oea hy g r o m e tri c a Syngonanthus chrysanthus P inus sibir i c a Buxus microphylla Phoenix dactylifera Selaginella moellendorffii P inus to rre y ana s sp. ins ular i s Tra c helium caer uleum Lonicera japonica Jatropha curcas Arabis hirsuta Phoradendron serotinum Bra c h y podium dista c h y o n Chlorella vulgaris Neottia nidus Lem na m inor Phyllostachys propinqua Lactuca sativa F o ste r ella c aulescens Magnolia kwangsiensis Sesamum indicum Populus alba Nerium oleander Dasypogon bromeliifolius Pinus cont ort a Panicum virgatum Hosta ventricosa Nasturtium officinale Festuca arundinacea Megaleranthis saniculifolia Manihot esculenta Flagellaria indica N ymphaea alba Spinacia oleracea Wolffia australiana Lilium superbum Neoastelia spectabilis Solanum lycopersicum Angiopteris evecta



PAGE 1

Olea europaea ssp. cuspidata Antirrhinum majus Hev ea br a s iliens i s Larix occidentalis Pycnoc o ccu s pr o v a s olii Daucus carota Nastu rtium offi c inale Oryza meridionalis P ent a ctina rupic ola Pinus canariensis Didierea madagascariensis P inus ay a c ahuit e P o rtulac a r ia afra Eleutherococcus senticosus A t ropa belladonna Jasminum nudiflorum Fragaria vesca Heliant hus annuus Helicosporidium sp. Bambusa emeiensis Equisetum arvense Petroselinum crisp.um Erodium te x anum Chlorophytum rhizopendulum C h l amydomona s rei nha r d t i i Franklinia alatamaha Crucihimalaya wallichii Chloranthus spicatus Mesostigma viride Wolffia australiana Gunnera manicata Draba nemorosa Gossypium tomentosum Pinus torreyana subsp. t orreyana Typha latifolia Potamophila parviflora T heobroma cacao Manihot esculenta Vigna radiata Passiflora biflora Calycanthus floridus G eorgeant ha hexandra C occomyxa sp. Citrus sinensis Coix lacryma-jobi Magn o lia kwangsiensi s Pinus banksiana Fagopyrum esculentum F i c u s sp. G uizot ia abyssinica Nymphaea alba Lemna minor Cornus florida Puelia olyrif ormis Dunaliella salina Mollugo verticillata Silene latifolia Agrostis stolonifera A n t hoc e r o s fo rmo s a e Gossypium barbadense Neottia nidus-avis Dasypogon bromeliifolius Oedogonium cardiacum Nuphar advena Hydrocotyle sp. O ryza aust raliensis Pinus krempf i i Cuscuta reflexa Saccharum hybridus Joinvillea ascendens Parthenium argentatum Adiantum capillus-veneris Cycas taitungensis Panicum virgat u m Ferrocalamus rimosivaginus Megaleranthis saniculifolia Triticum aestivum Populus trichocarpa Puya laxa Tradescantia ohiensis Gossypium mustelinum Crithmum maritimum Phalaenopsis aphrodite Meliosma aff. cuneifolia Silene conica Asparagus officinalis Pandanus utilis Phyllostachys propinqua Hordeum vulgare Heuchera sanguinea F lagellaria indica Lilium superbum Marchantia polymorpha Ricinus communis Oryza rufipogon Lathyrus sativus Gossypium hirsutum Pereskia sacharosa Syntrichia ruralis P inus peuc e Cicer ar iet i n u m Cuscu t a gr o n o v i i O enot her a parvi f lor a Jacobaea vulgaris Chara vulgaris T rif olium subt erraneum Ximenia americana Selaginella uncinata Oxalis latifolia Nelum bo lut e a Colocasia esculenta Eleusine coracana Agat his aust ralis Cheilanthes lindheimeri Oryza sativa var. indica Solanum lycopersicum Boea hygrometrica Gossypium thurberi O enot hera argillicola Pel argo n ium x sp. Belosynapsis ciliat a Monsonia sp.eciosa Lolium perenne Glycine max Cuscuta obtusiflora Millettia pinnata P inus parvi f lor a v a r. pent aphy lla Pteridium aquilinum Psilotum nudum P i tcairni a felic i ana Wolffiella lingulata Spirodela polyrhiza O l ea europaea ssp. europaea Weingartia kargliana Lotus japonicus Oryza sativa var. japonica P inus pinaste r Jatropha curcas Pinus aristata P anax gins eng Physcomitrella patens Pinus resinosa Geranium palmatum Populus alba Zygnema circumcarinatum Nicotiana undulata Pinus sibirica Chlorella vulgaris Lonicera japonica Piper cenocladum Pinus flexilis Capsella bursa-pastoris Vitis vinifera Keteleeria davidiana Selaginella moellendorffii Abolboda macrostachya Cucumis sat ivus O lea eur opaea ssp. m a r occana P inus armandii Erodium carvif olium Prunus persi c a Pinus thunbergii Thurnia sp. haerocephala Pinus nelsonii Tro c hodendr on ar alioides Phyllostachys edulis Angiopteris evecta Spinacia oleracea Centrolepis monogyna Mayaca fluviatilis Cephalot axus wilsoniana Morus indica Thamnochortus insignis Pinus strobus E u c aly p t u s globulus Opuntia decumbens Drimys granadensis Oocystis solitaria Phyllostachys nigra Albuca kirkii Nic o t iana to m ent o s i f o rmi s Anethum graveolens Acidosasa purpurea Cyperus alternifolius Buxus microphylla Medi cago trunca tul a Alsophila spinulosa Pinus gerardiana Liriodendron tulipifera Chlorokybus at mophyt icus I pomoea purpurea Nandina domestica Bulnesia arborea Nolina at opocarpa Solanum bulbocastanum Anthriscus cerefolium Dioscorea elephantipes Bambusa oldhamii Gossypium raimondii Pinus cembra Pseudotsuga sinensis Scenedesmus obliquus Ilex cornuta Hesperaloe parvif lora P lat anus occident alis I ndoc alam u s longiaur i t u s Phaseolus vulgaris Halocarpus kirkii Barbarea verna Festuca arundinacea Microlaena stipoides Juncus effusus Pinus torreyana subsp. insularis Gossypium herbaceum Sorghum bicolor Chaetosphaeridium globosum Dillenia indica Pinus albicaulis Davidia involucrata F loy diella te rre stri s Podocarpus totara Staurastrum punctulatum Aucuba japonica Lactuca sativa Ranunculus macranthus Cathaya argyrophylla Pedinomonas minor Renealmia alpinia Volvox carter i Chlorella variabilis Lar i x dec idua Neoastelia spectabilis Ehret ia acuminat a Hosta ventricosa Lobularia maritima Nic o t iana tabac u m Castanea mollissi m a Ageratina adenophora Neoregelia carolinae Rhynchoryza subulata Agapanthus praecox Cycas micronesica Leersia tisserantii Maihuenia poeppigii Pinus lambertiana Pinus rzedowskii Yucca schidigera Silene vulgaris Olimarabidopsis pumila Cucumis melo Olea woodiana Schizomeris leibleinii Nelumbo nucifera Syngonanthus chrysanthus Pyrus pyrifolia Pinus attenuata Iris virginica Monomast ix sp. Aethionema grandiflorum Arbutus unedo Apostasia wallichii Isoetes flaccida Epifagus virginiana Acorus americanus Zea mays Phormium tenax Dendrocalamus latiflorus Eucalyptus grandis Oncidium sp. S t igeoclonium helvet icum Ostreococcus tauri Arabidopsis thaliana Pisum sativum Potarophytum riparium I llicium oligandrum Ecdeiocolea monostachya P inus merk u s i i Pyramimonas parkeae Picea morrisonicola Pinus leiophylla var. chihuahuana Musa acuminata Oryza rufipogon Phoradendron serotinum Pinus koraiensis Ptilidium pulcherrimum Nephroselmis olivacea Pereskiopsis diguetii Solanum tuberosum Pinus squamata Navia saxicola Pinus ponderosa Acorus calamus Car i c a papay a Kingia australis S e s a m u m indic u m Scaev ola aem ula P inus monophy lla G net um parvif olium Liquidambar styraciflua Nicotiana sylvestris B rocchinia mic rant h a E phedr a equis e t ina Micromonas pusilla Oryza ni vara Cuscuta exaltata Lept osira terrest ris Gossypium arboreum O l tmanns iellops i s vi r idis Abies firma Picea sitchensis A nom o c hloa ma r ant oidea Corynocarpus laevigata Pinus contorta Anredera baselloides Huperzia lucidula Silene noct i f lora S t aphylea colchica Brach ypodi um di stachyon Sparganium eurycarpum Amborella trichopoda Arabis hirsuta Taiwania cryptomerioides Lomandra longifolia Elaeis oleifera P inus mont i c ola Rhododendron simsii Lepidium virginicum Gossypi um darwi nii Rhizanthella gardneri Plumbago auriculata Coffea arabica Strept o c haet a angusti f olia Pinus taeda O enot her a elat a Trachelium caeruleum P hoenix dactylif e r a Parachlorella kessleri O enot hera biennis Pseudendoclonium akinetum Chamaedorea seifrizii Quercus nigra Ner ium oleander Ravenea hildebrandtii E uonymu s am e r i c anus Ceratophyllum demersum Aethionema cordifolium Micromonas sp. Cedrus deodara Bryops i s hy pnoides Portulaca oleracea Fosterella caulescens Ginkgo biloba Oenothera glazioviana Aneura mirabilis Oxypolis gr eenm anii Blossfeldia liliputana Curculigo capitulata Cryptomeria japonica Berberidopsis corallina Welwitschia mirabilis 100 100 100 100 100 100 100 6 2 100 100 100 100 6 6 100 100 100 8 5 100 9 3 7 0 100 100 100 8 8 100 9 6 100 100 9 9 7 9 100 100 100 100 100 100 100 100 100 100 100 100 100 6 6 6 9 100 100 100 9 1 6 0 100 100 6 2 100 9 9 6 2 100 100 100 9 4 100 100 100 100 100 100 100 5 6 100 9 1 6 9 9 3 8 9 9 3 5 9 100 100 100 100 9 7 100 100 100 100 100 100 9 3 100 100 100 100 9 5 100 100 9 9 9 0 100 100 100 7 8 9 6 100 100 100 7 1 9 9 100 9 9 100 5 3 6 7 100 100 100 100 8 6 100 7 0 9 5 8 6 6 6 100 100 100 100 100 100 9 9 100 9 7 100 100 9 2 100 100 100 100 100 100 9 9 100 100 100 100 8 9 6 8 9 7 100 100 100 100 100 9 1 8 7 100 100 100 100 6 3 5 4 9 4 6 2 100 100 100 100 100 100 100 9 6 5 5 100 100 9 8 100 100 8 5 6 6 100 5 8 5 9 100 100 9 9 100 9 3 100 100 100 100 100 100 100 100 100 6 2 100 100 100 100 100 9 6 9 3 100 5 4 5 3 5 7 100 100 100 9 4 9 1 7 4 7 2 100 100 5 3 100 100 6 8 7 8 100 8 8 100 100 9 4 9 3 5 1 100 100 100 8 6 100 100 100 100 100 9 7 100 100 100 100 5 7 100 100 100 100 100 100 100 100 100 6 3 8 0 7 0 6 9 100 5 6 8 6 100 100 100 100 100 100 9 3 100 8 1 6 9 100 100 6 1 100 100 100 9 9 100 100 100 100 100 100 7 9 100 5 9 7 6 100 100 100 9 2 100 100 8 3 100 100 100 100 100 9 9 100 100 100 6 5 100 9 9 7 7 9 9 100 100 100 100 100 100 100 9 9 9 5 6 9 100 100 9 3 9 8 100 100 100 100 100 8 1 100 100 100 100 100 100 100 100 100 100 100 100 8 0 7 8 9 7 8 7 100



PAGE 1

Maihuenia poeppigii Cerat ophyllum demersum Aethionema grandiflorum Mayaca fluviatilis O lea eur opaea ssp. m a r occana Microlaena stipoides Nasturtium officinale Ximenia americana F o ste r ella c aulescens Pandanus utilis Pinus cont ort a P inus canar iens i s Pteridium aquilinum Aucuba japonica Nolina atopocarpa Piper cenocladum Oocystis solitaria Pinus parvif lora var. pent aphylla Phoradendron serotinum Silene vulgaris Capsella bursa-pastoris Pinus banksiana Dav idia i nvolucrata Chlorella variabilis Lat h yru s sa t i v u s Pereskiopsis diguetii Sparganium eurycarpum Micromonas s p. Gunnera manicata Dillenia indica Scaevola aemula Magnolia k wangsiensis Silene latifolia Tradescant ia ohiensis Coccomyxa s p. Phoenix dactylifera Platanus occidentalis Marchantia polymorpha Castanea mollissima Arabis hirsuta Chloranthus spicatus Panax ginseng Nelumbo lut e a Agathis australis B elosynaps i s ciliat a Neoastelia spectabilis Pinus lambertiana Pinus leiophylla var. chihuahuana Cephalotaxus wilsoniana Liquidambar styraciflua Silene noctiflora Spinacia oleracea Cathaya argyrophylla Corynocarpus laevigata Cuscuta exaltata Buxus microphylla Hevea brasiliensis Nephroselmis olivacea Wolffiella lingulata Psilot um nudum Nicotiana undulata Cuscuta gronovii Bambusa ol dhami i Calycanthus floridus O limarabidopsis pumila Cuscuta obtusiflora Anomochloa marantoidea Leersia tisserantii Gossypium darwinii F ragaria vesca Carica papaya Nicot iana t oment osif ormis Ranunculus macranthus Euonymus americanus Abolboda macrostachya Berberidopsis corallina Scenedesmus obliquus Hydrocotyle s p. Pinus ponderosa Arabidops i s thaliana G ossypium t hurberi Ageratina adenophora Chl orokybus atmophyticus Lilium superbum Chlamydomonas reinhardt i i Rhododendron simsii Passif lora bif lora Petroselinum crispum O ryza nivara Pot arophyt um riparium Tra c helium caer uleum Pinus nelsonii Dendr o c alam u s lat i f lor u s Megaleranthis saniculifolia Z ea m a y s Schizomeris leibleinii Nelumbo nucifera Spirodela polyrhiza Micromonas pusilla Ipomoea purpurea Y u cca schidiger a Staurastrum punctulatum P o t a m ophila parvi f lor a Panicum virgatum Acorus calamus P inus sibir i c a Ravenea hildebrandt i i Pseudotsuga sinensis Dasypogon bromeliifolius Pyrus pyri folia Wolffia australiana Oryza meridionalis Draba nemorosa Gossypium tomentosum Cuscut a ref lexa Syngonanthus chrysanthus Curculigo c api t ulat a T hamnochort us insignis Ric i nus communi s Cornus florida Lar i x o ccident alis E h r e t ia ac u m inat a Plumbago auriculata Chlorophytum rhizopendulum Gossypium barbadense Sesamum indicum Apostasia wallichii Centrolepis monogyna Pinus squamata Pinus krempfii Isoetes flaccida G o ssypium her bac eum Chaet osphaeridium globosum Oenothera glazioviana Typha latifolia G i nkgo biloba Oenothera biennis Alsophila spinulosa Strept o c haet a angusti f olia Hesperaloe parvif lora Crucihimalaya wallichii Pycnococcus provasolii Neoregelia carolinae Pisum sativum Silene conica Pitcairnia feliciana Pinus ayacahuite Crithmum maritimum Helianthus annuus Pinus monticola Erodium texanum O n c idium sp. Medicago truncatula Daucus carota Phalaenopsis aphrodite Picea morrisonicola Iris virginica Cryptomeria japonica Trifolium subterraneum Aco r u s a m e r i c anus Solanum tuberosum Albuca kirkii Anethum graveolens Lactuca sativa Pinus aristata Eucalyptus globulus Angiopteris evecta S t aphylea colchica Coix lacryma-jobi Oenothera elata Prunus persica Populus alba Millettia pinnata Rhynchoryza subulata Oryza rufipogon B Pinus pinaster Cycas micronesica G uiz o t ia abyssinica Monsonia speciosa W eingartia k a r gliana Pinus cembra Epifagus virginiana Cucumis melo Lolium per enne P inus to rre y ana ssp. ins ular i s Dunaliella salina P art henium argent a t u m Eleutherococcus senticosus Olea europaea ssp. cuspidata Ilex cornuta Pinus koraiensis Oryza australiensis Asparagus officinalis G ossypium must elinum P inus thunber gii Festuca arundinacea Georgeantha hexandra Pinus strobus Pinus attenuata Atropa belladonna G e r anium palm a t u m Mesostigma viride E u c aly p t u s g r andis Vigna radiata E l e u s ine coracan a Pinus albicaulis Welwitschia mirabilis Oxalis latifolia N ymphaea alba Jatropha curcas Oryza sativa var. indica Colocasia esculenta Taiwania cryptomerioides Ostreococcus tauri Flagellaria indica Pyramimonas parkeae Pinus armandii Cyperus alternifolius A n t i rrhinum majus Phyllostachys edulis Anthriscus cerefolium E phedr a equis e t ina Arbut u s unedo Hordeum vulgare Tri t i c u m aesti v u m Pinus peuce F ranklinia alat amaha Syntrichia ruralis B oea hy g r o m e tri c a Pinus merkusii Ferrocalamus rimosivaginus Pseudendoclonium akinetum J a sminum nudif lor u m P edinom onas minor Phormium tenax Pinus resinosa Amborella trichopoda Populus trichocarpa P inus ger a r diana Picea sitchensis Tro c hodendr on ar alioides Indocalamus longiauritus Pentactina rupicola Aneura mirabilis Agrostis stolonifera Larix decidua Elaeis oleifera Oxypolis greenmanii Lonicera japonica Anredera baselloides Puya laxa Podocarpus totara Oedogonium cardiacum Phaseolus vulgaris Musa acuminata Bulnesia arborea F loydiella t errest ris Renealmia alpinia Gossypium arboreum Cycas t ait ungensis Heuchera sanguinea Port ulacaria af r a Lobularia maritima Lomandra longifolia Chlorella vulgaris Q uercus nigra Morus indica Joinvillea ascendens Abies firma Blossfeldia liliputana Equiset um arvense O punt ia dec u m bens Thurnia sphaerocephala Mollugo verti c illata H e licospori d i um s p. Solanum bulbocastanum Aethionema cordifolium Nic o t iana t abac u m Chara vulgaris Rhizanthella gardneri Zygnema circumcarinatum Brocchi nia micrantha Cheilanthes lindheimeri Pinus t orreyana ssp. t orreyana Monomastix s p. Dioscorea elephantipes Nicotiana sylvestris S o r ghum bic olor Agapant hus praecox Ptil idium pulcherrimum Anthoceros formosae Pinus t aeda Nuphar adv ena Phyllost achys nigra Volvox cart eri Illicium oligandrum Manihot esculenta Port ulaca oleracea Oryza sativa var. japonica Theobroma cacao Oen othe ra argillic ola Drimys granadensis O l ea europaea ssp. europaea Bambusa emeiensis Cedrus deodara Bra c h y podium dista c h y o n Parachlorella kessleri S t igeoclonium helvet icum Acidosasa purpurea Pinus f lexilis Olea woodiana Lotus japonicus Neottia nidus Ket eleeria davidiana Vitis vinifera Kingia australis Cucumis sativus Solanum lycopersicum Glycine max J unc u s e ffu s u s O enot her a parvi f lor a Saccharum hybridus Barbarea verna G o ssypium raim ondii Pelargonium x sp. Selaginella moellendorffii Pinus monophylla Fagopyrum esculentum Halocarpus kirkii Erodium carvifolium Citrus sinensis Pereskia sacharosa Navia saxicola Cic e r a r iet inum Bryopsis hypnoides Gnetum parvifolium Gossypium hirsutum C offea arabica Phyllostachys propinqua Nandina domest ica Ecdeiocolea monostachya Lem na m inor S elaginella unc inat a Didierea madagascariensis Melios ma a ff. cuneif olia Pinus rzedowskii Lepidium vi r ginic u m Physcomitrella patens Liriodendron tulipifera F i c u s s p. Oryza sativa var. japonica Puelia olyriformis Leptosira terrestris Adi antum capillu s Hosta ventricosa Huperzia luc idula Oltmannsiellopsis viridis Jacobaea vulgaris Chamaedorea seifrizii Nerium oleander100 6 6 6 4 100 100 100 100 100 8 4 100 100 100 100 6 2 100 100 100 7 0 100 100 100 100 100 9 0 100 6 4 100 100 9 0 100 100 100 100 100 100 100 100 100 8 6 8 7 7 6 9 5 100 100 100 100 9 9 100 100 100 100 100 100 100 100 7 0 100 100 100 8 8 100 100 100 8 7 100 100 9 8 100 100 100 100 100 100 100 100 9 9 100 100 100 100 100 100 100 100 100 100 5 6 100 100 9 7 100 100 7 2 100 100 100 100 9 4 100 100 100 100 100 100 6 9 100 100 7 5 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 8 2 7 2 9 4 100 6 1 100 100 100 100 100 100 100 100 9 9 100 7 1 100 100 100 100 100 9 9 100 100 100 100 9 2 9 9 100 100 6 8 100 100 100 8 5 100 6 3 9 6 100 8 8 100 100 100 100 100 6 4 100 100 100 9 4 100 100 100 100 100 100 5 2 9 8 100 100 100 100 6 7 100 7 3 8 0 100 100 100 100 100 100 100 100 100 9 9 100 100 100 100 100 9 4 100 100 100 9 9 100 100 100 100 100 5 9 9 9 100 100 100 9 8 6 8 9 9 100 100 7 5 9 9 6 9 100 100 100 100 100 9 7 9 7 100 100 100 100 100 100 100 100 5 6 100 100 100 100 100 100 100 100 100 100 100 100 8 6 100 100 100 100 8 8 8 9 100 100 100 100 100 100 100 7 4 100 100 100 100 100 100 7 3 7 3 100 100 100 100 100 9 3 100 9 8 100 100 100 100 100 100 100 7 7 100 7 3 100 100 5 5 100 100 100 100 100 100 100 9 7 100 100 100 100 100 100 9 3 100 7 4 9 3 100 100 100 100 100 5 7 100 100 100 100 100 100 100 100 100 100 100 5 6 6 2 0.4 Maihuenia poeppigii Cerat ophyllum demersum Aethionema grandiflorum Mayaca fluviatilis Microlaena stipoides Nasturtium officinale Ximenia americana F o ste r ella c aulescens Pandanus utilis Pinus cont ort a P inus canar iens i s Pteridium aquilinum Aucuba japonica Nolina atopocarpa Piper cenocladum Oocystis solitaria Pinus parvif lora var. pent aphylla Phoradendron serotinum Silene vulgaris Capsella bursa-pastoris Pinus banksiana D avi d ia involucra t a Chlorella variabilis Lat h yru s sa t i v u s Pereskiopsis diguetii Sparganium eurycarpum Micromonas s p. Gunnera manicata Dillenia indica Scaevola aemula Magnolia kwangsiensis Silene latifolia Tradescantia ohiensis Coccomyxa s p. Phoenix dactylifera Platanus occidentalis Marchantia polymorpha Castanea mollissima Arabis hirsuta Chloranthus spicatus Panax ginseng Nelumbo lut e a Agathis australis B elosynaps i s ciliat a Neoastelia spectabilis Pinus lambertiana Pinus leiophylla var. chihuahuana Cephalotaxus wilsoniana Liquidambar styraciflua Silene noctiflora Spinacia oleracea Cathaya argyrophylla Corynocarpus laevigata Cuscuta exaltata Buxus microphylla Hevea brasiliensis Nephroselmis olivacea Wolffiella lingulata Psilot um nudum Nicotiana undulata Cuscuta gronovii Bambusa ol dhami i Calycanthus floridus O limarabidopsis pumila Cuscuta obtusiflora Anomochloa marantoidea Leersia tisserantii Gossypium darwinii F ragaria vesca Carica papaya Nicot iana t oment osif ormis Ranunculus macranthus Euonymus americanus Abolboda macrostachya Berberidopsis corallina Scenedesmus obliquus Hydrocotyle s p. Pinus ponderosa Arabidops i s thaliana G ossypium t hurberi Ageratina adenophora C h l orokybus atmophyticus Lilium superbum Chlamydomonas reinhardt i i Rhododendron simsii Passif lora bif lora Petroselinum crispum Pot arophyt um riparium Tra c helium caer uleum Pinus nelsonii Dendr o c alam u s lat i f lor u s Megaleranthis saniculifolia Z ea m a y s Schizomeris leibleinii Nelumbo nucifera Spirodela polyrhiza Micromonas pusilla Ipomoea purpurea Y u cca schidiger a Staurastrum punctulatum P o t a m ophila parvi f lor a Panicum virgatum Acorus calamus P inus sibir i c a Ravenea hildebrandt i i Pseudotsuga sinensis Dasypogon bromeliifolius Pyrus pyri folia Wolffia australiana Oryza meridionalis Draba nemorosa Gossypium tomentosum Cuscut a ref lexa Syngonanthus chrysanthus Curculigo c apit ulat a T hamnochort us insignis Ric i nus communi s Cornus florida Lar i x o ccident alis E h r e t ia ac u m inat a Plumbago auriculata Chlorophytum rhizopendulum Gossypium barbadense Sesamum indicum Apostasia wallichii Centrolepis monogyna Pinus squamata Pinus krempfii Isoetes flaccida G o ssypium her bac eum Chaet osphaeridium globosum Oenothera glazioviana Typha latifolia G i nkgo biloba Oenothera biennis Alsophila spinulosa Strept o c haet a angusti f olia Hesperaloe parvif lora Crucihimalaya wallichii Pycnococcus provasolii Neoregelia carolinae Pisum sativum Silene conica Pitcairnia feliciana Pinus ayacahuite Crithmum maritimum Helianthus annuus Pinus monticola Erodium texanum O n c idium sp. Medicago truncatula Daucus carota Phalaenopsis aphrodite Picea morrisonicola Iris virginica Cryptomeria japonica Trifolium subterraneum Aco r u s a m e r i c anus Solanum tuberosum Albuca kirkii Anethum graveolens Lactuca sativa Pinus aristata Eucalyptus globulus Angiopteris evecta S t aphylea colchica Coix lacryma-jobi Oenothera elata Prunus persica Populus alba Millettia pinnata Rhynchoryza subulata Pinus pinaster Cycas micronesica G uizot ia abys sinic a Monsonia speciosa W eingart ia k argliana Pinus cembra Epifagus virginiana Cucumis melo Lolium per enne P inus to rre y ana ssp. ins ular i s Dunaliella salina Part henium argent a t u m Eleutherococcus senticosus Ilex cornuta Pinus koraiensis Oryza australiensis Asparagus officinalis G ossypium must elinum P inus thunber gii Festuca arundinacea Georgeantha hexandra Pinus strobus Pinus attenuata Atropa belladonna G e r anium palm a t u m Mesostigma viride E u c aly p t u s g r andis Vigna radiata E l eusi ne coracana Pinus albicaulis Welwitschia mirabilis Oxalis latifolia N ymphaea alba Jatropha curcas Oryza sativa var. indica Colocasia esculenta Taiwania cryptomerioides Ostreococcus tauri Flagellaria indica Pyramimonas parkeae Pinus armandii Cyperus alternifolius A n t i rrhinum majus Phyllostachys edulis Anthriscus cerefolium E phedr a equis e t ina Arbut u s unedo Hordeum vulgare Tri t i c u m aesti v u m Pinus peuce F ranklinia alat amaha Syntrichia ruralis B oea hy g r o m e tri c a Pinus merkusii Ferrocalamus rimosivaginus Pseudendoclonium akinetum J a sminum nudif lor u m P edinom onas minor Phormium tenax Pinus resinosa Amborella trichopoda Populus trichocarpa P inus ger a r diana Picea sitchensis Tro c hodendr on ar alioides Indocalamus longiauritus Pentactina rupicola Aneura mirabilis Agrostis stolonifera Larix decidua Elaeis oleifera Oxypolis greenmanii Lonicera japonica Anredera baselloides Puya laxa Podocarpus totara Oedogonium cardiacum Phaseolus vulgaris Musa acuminata Bulnesia arborea F loydiella t errest ris Renealmia alpinia Gossypium arboreum Cycas t ait ungensis Heuchera sanguinea Port ulacaria af r a Lobularia maritima Lomandra longifolia Chlorella vulgaris Q uercus nigra Morus indica Joinvillea ascendens Abies firma Blossfeldia liliputana Equiset um arvense O punt ia dec u m bens Thurnia sphaerocephala Mollugo verti c illata H e licospori d i um s p. Solanum bulbocastanum Aethionema cordifolium Nic o t iana t abac u m Chara vulgaris Rhizanthella gardneri Zygnema circumcarinatum Brocchini a mi crantha Cheilanthes lindheimeri Pinus t orreyana ssp. t orreyana Monomastix s p. Dioscorea elephantipes Nicotiana sylvestris S o r ghum bic olor Agapant hus praecox Ptilid i um pul cherri mum Anthoceros formosae Pinus t aeda Nuphar adv ena Phyllost achys nigra Volvox cart eri Illicium oligandrum Manihot esculenta Portulaca oleracea Oryza rufipogon A Theobroma cacao O enot her a ar gillic ola Drimys granadensis Bambusa emeiensis Cedrus deodara Bra c h y podium dista c h y o n Parachlorella kessleri S t igeoclonium helvet icum Acidosasa purpurea Pinus f lexilis Olea woodiana Lotus japonicus Neottia nidus Ket eleeria davidiana Vitis vinifera Kingia australis Cucumis sativus Solanum lycopersicum Glycine max J unc u s e ffu s u s O enot her a parvi f lor a Saccharum hybridus Barbarea verna G o ssypium raim ondii Pelargonium x sp. Selaginella moellendorffii Pinus monophylla Fagopyrum esculentum Halocarpus kirkii Erodium carvifolium Citrus sinensis Pereskia sacharosa Navia saxicola Cic e r a r iet inum Bryopsis hypnoides Gnetum parvifolium Gossypium hirsutum Coffea arabica Phyllostachys propinqua Nandina domest ica Ecdeiocolea monostachya Lem na m inor S elaginella unc ina t a Didierea madagascariensis Meliosma a ff. c uneif olia Pinus rzedowskii Lepidium vi r ginic u m Physcomitrella patens Liriodendron tulipifera F i c u s sp Oryza sativa var. japonica Puelia olyriformis Leptosira terrestris Adi antum capillu s Hosta ventricosa Huperzia luc idula Oltmannsiellopsis viridis Jacobaea vulgaris Chamaedorea seifrizii Nerium oleander O lea eur opaea ssp. m a r occana Olea europaea ssp. cuspidata O l ea europaea ssp. europaea O ryza nivara Oryza rufipogon B