A comparative study of SVDquartets and other coalescent-based species tree estimation methods

BMC Genomics

Research

Ashu Gupta¹  Shashank Yaduvanshi¹  Tandy Warnow²  Siavash Mirarab³  Ruth Davidson⁴  Jed Chou⁴  Mike Nute⁵ 

[1] Department of Computer Science, University of Illinois Urbana-Champaign, 61801, Urbana, IL, USA;Department of Computer Science, University of Illinois Urbana-Champaign, 61801, Urbana, IL, USA;Department of Computer Science, University of Texas at Austin, 78712, Austin, TX, USA;Department of Electrical and Computer Engineering, University of California San Diego, 92093, La Jolla, CA, USA;Department of Computer Science, University of Texas at Austin, 78712, Austin, TX, USA;Department of Mathematics, University of Illinois Urbana-Champaign, 61801, Urbana, IL, USA;Department of Statistics, University of Illinois Urbana-Champaign, 61820, Champaign, IL, USA;

关键词: species tree inference;    SNP;    multilocus;    SVDquartets;    QMC;    ASTRAL;    NJst;    RAxML;   

DOI  :  10.1186/1471-2164-16-S10-S2

来源: Springer

【 摘 要 】

BackgroundSpecies tree estimation is challenging in the presence of incomplete lineage sorting (ILS), which can make gene trees different from the species tree. Because ILS is expected to occur and the standard concatenation approach can return incorrect trees with high support in the presence of ILS, "coalescent-based" summary methods (which first estimate gene trees and then combine gene trees into a species tree) have been developed that have theoretical guarantees of robustness to arbitrarily high amounts of ILS. Some studies have suggested that summary methods should only be used on "c-genes" (i.e., recombination-free loci) that can be extremely short (sometimes fewer than 100 sites). However, gene trees estimated on short alignments can have high estimation error, and summary methods tend to have high error on short c-genes. To address this problem, Chifman and Kubatko introduced SVDquartets, a new coalescent-based method. SVDquartets takes multi-locus unlinked single-site data, infers the quartet trees for all subsets of four species, and then combines the set of quartet trees into a species tree using a quartet amalgamation heuristic. Yet, the relative accuracy of SVDquartets to leading coalescent-based methods has not been assessed.ResultsWe compared SVDquartets to two leading coalescent-based methods (ASTRAL-2 and NJst), and to concatenation using maximum likelihood. We used a collection of simulated datasets, varying ILS levels, numbers of taxa, and number of sites per locus. Although SVDquartets was sometimes more accurate than ASTRAL-2 and NJst, most often the best results were obtained using ASTRAL-2, even on the shortest gene sequence alignments we explored (with only 10 sites per locus). Finally, concatenation was the most accurate of all methods under low ILS conditions.ConclusionsASTRAL-2 generally had the best accuracy under higher ILS conditions, and concatenation had the best accuracy under the lowest ILS conditions. However, SVDquartets was competitive with the best methods under conditions with low ILS and small numbers of sites per locus. The good performance under many conditions of ASTRAL-2 in comparison to SVDquartets is surprising given the known vulnerability of ASTRAL-2 and similar methods to short gene sequences.

【 授权许可】

Unknown   
© Chou et al. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.