What Can We Learn from a Simple Approach for Assessing Substitutional Saturation?

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Material Information

Title:
What Can We Learn from a Simple Approach for Assessing Substitutional Saturation?
Physical Description:
1 online resource (50 p.)
Language:
english
Creator:
Sabo, Jessica L
Publisher:
University of Florida
Place of Publication:
Gainesville, Fla.
Publication Date:

Thesis/Dissertation Information

Degree:
Master's ( M.S.)
Degree Grantor:
University of Florida
Degree Disciplines:
Zoology, Biology
Committee Chair:
BRAUN,EDWARD LOUIS
Committee Co-Chair:
BARBAZUK,WILLIAM BRADLEY
Committee Members:
BURLEIGH,JOHN GORDON

Subjects

Subjects / Keywords:
method -- phylogenetics -- phylogenomics -- saturation
Biology -- Dissertations, Academic -- UF
Genre:
Zoology thesis, M.S.
bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

Notes

Abstract:
Thereare two common sources of phylogenetic error, random error and systematicerror. One type of systematic error that persists with increased taxa/data issubstitutional saturation. Saturation is the point at which sequences haveundergone so many substitutions per site that the observed distance representsa poor estimate of the true genetic distance. Saturation impacts the recoveryof divergent relationships more than for recently diverged taxa. Traditionally,saturation has been measured with qualitative saturation plots. Here we proposethe program EstPhySat that provides a quantitative interpretation ofsaturation plots and a simple metric of saturation using a second-degreepolynomial best-fit line. We use the derivative to find the point (inflectionpoint) when observed distances cease to increase, thus, relaxing the dependenceupon a specific parametric model. The saturation statistics were used to assessmodel fit and phylogenetic accuracy. We found that saturation is unlikely toneither identify model fit deficiencies nor provide predictive power for theaccuracy of phylogenetic analyses. The results of this study indicate thatidentifying and excluding saturated data may not be necessary in order toresolve true phylogenetic relationships.
General Note:
In the series University of Florida Digital Collections.
General Note:
Includes vita.
Bibliography:
Includes bibliographical references.
Source of Description:
Description based on online resource; title from PDF title page.
Source of Description:
This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Statement of Responsibility:
by Jessica L Sabo.
Thesis:
Thesis (M.S.)--University of Florida, 2013.
Local:
Adviser: BRAUN,EDWARD LOUIS.
Local:
Co-adviser: BARBAZUK,WILLIAM BRADLEY.
Electronic Access:
RESTRICTED TO UF STUDENTS, STAFF, FACULTY, AND ON-CAMPUS USE UNTIL 2015-12-31

Record Information

Source Institution:
UFRGP
Rights Management:
Applicable rights reserved.
Classification:
lcc - LD1780 2013
System ID:
UFE0046355:00001