Bayesian species delimitation using multilocus sequence data

Proceedings of the National Academy of Sciences of the United States of America
Ziheng Yang, Bruce Rannala

Abstract

In the absence of recent admixture between species, bipartitions of individuals in gene trees that are shared across loci can potentially be used to infer the presence of two or more species. This approach to species delimitation via molecular sequence data has been constrained by the fact that genealogies for individual loci are often poorly resolved and that ancestral lineage sorting, hybridization, and other population genetic processes can lead to discordant gene trees. Here we use a Bayesian modeling approach to generate the posterior probabilities of species assignments taking account of uncertainties due to unknown gene trees and the ancestral coalescent process. For tractability, we rely on a user-specified guide tree to avoid integrating over all possible species delimitations. The statistical performance of the method is examined using simulations, and the method is illustrated by analyzing sequence data from rotifers, fence lizards, and human populations.

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Citations

Mar 30, 2012·Nature Reviews. Genetics·Ziheng Yang, Bruce Rannala
Aug 31, 2013·Bioinformatics·Jiajie ZhangAlexandros Stamatakis
Jun 4, 2010·Proceedings. Biological Sciences·Adam D Leaché, Matthew K Fujita
Oct 22, 2010·Proceedings. Biological Sciences·Aaron M BauerRobert F Inger
Dec 28, 2012·Proceedings. Biological Sciences·Dioli Ann PayoOlivier De Clerck
Nov 16, 2012·BMC Evolutionary Biology·Ricardo S RamiroDarren J Obbard
Dec 12, 2012·BMC Evolutionary Biology·Maria Tereza C ThoméJoão Alexandrino
Sep 7, 2013·BMC Evolutionary Biology·Yuanyuan Zhang, Shuqiang Li
Oct 1, 2013·Frontiers in Zoology·Katharina M Jörger, Michael Schrödl
May 16, 2012·PloS One·Jennifer Hoyal Cuthill, Michael Charleston
Mar 2, 2013·PloS One·Matthew J PhillipsMichael Bunce
Nov 19, 2013·PloS One·David G Chapple, Peter A Ritchie
Jul 22, 2011·Genetics·Sang Chul Choi, Jody Hey
Dec 24, 2013·Systematic Biology·Melisa OlaveL Lacey Knowles
Jan 10, 2014·Proceedings. Biological Sciences·Danielle L Edwards, L Lacey Knowles
Dec 18, 2013·Systematic Biology·Simon JolyPeter J Lockhart
Mar 15, 2014·Systematic Biology·Adam D LeachéRemco R Bouckaert
Mar 26, 2014·Molecular Phylogenetics and Evolution·Shannon M TorstromBradley J Swanson

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