Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees (original) (raw)

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1 Department of Biology, University of Florida, Gainesville, FL 32609, USA

2 NESCent, Durham, NC 27705, USA

* Correspondence to be sent to: Department of Biology, University of Florida, PO Box 118526, Gainesville, FL 32611, USA; E-mail: gburleigh@ufl.edu

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3 Department of Computer Science, Iowa State University, Ames, IA 50011, USA

4 School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel

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3 Department of Computer Science, Iowa State University, Ames, IA 50011, USA

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5 Department of Biology, University of North Carolina, Chapel Hill, NC 27599

6 Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany

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3 Department of Computer Science, Iowa State University, Ames, IA 50011, USA

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2 NESCent, Durham, NC 27705, USA

5 Department of Biology, University of North Carolina, Chapel Hill, NC 27599

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Received:

25 February 2009

Revision received:

03 July 2009

Published:

24 December 2010

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J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Stefanie Hartmann, André Wehe, Todd J. Vision, Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees, Systematic Biology, Volume 60, Issue 2, March 2011, Pages 117–125, https://doi.org/10.1093/sysbio/syq072
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Abstract

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.

© The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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