Improved Reversible Jump Algorithms for Bayesian Species Delimitation
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TLDR
Modifications are introduced to the rjMCMC algorithms that remove the constraint on the new species divergence time when splitting and alter the gene trees to remove incompatibilities, and are found to improve mixing of the Markov chain for both simulated and empirical data sets.Abstract:
Several computational methods have recently been proposed for delimiting species using multilocus sequence data. Among them, the Bayesian method of Yang and Rannala uses the multispecies coalescent model in the likelihood framework to calculate the posterior probabilities for the different species-delimitation models. It has a sound statistical basis and is found to have nice statistical properties in simulation studies, such as low error rates of undersplitting and oversplitting. However, the method suffers from poor mixing of the reversible-jump Markov chain Monte Carlo (rjMCMC) algorithms. Here, we describe several modifications to the algorithms. We propose a flexible prior that allows the user to specify the probability that each node on the guide tree represents a true speciation event. We also introduce modifications to the rjMCMC algorithms that remove the constraint on the new species divergence time when splitting and alter the gene trees to remove incompatibilities. The new algorithms are found to improve mixing of the Markov chain for both simulated and empirical data sets.read more
Citations
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Journal ArticleDOI
How to fail at species delimitation.
TL;DR: Researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Journal ArticleDOI
The BPP program for species tree estimation and species delimitation
Ziheng Yang,Ziheng Yang +1 more
TL;DR: An overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model, is provided.
Journal ArticleDOI
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci
Ziheng Yang,Bruce Rannala +1 more
TL;DR: Simulation results indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci, and of the impact of the prior on population size parameters (θ) on Bayesian species delimitation.
Journal ArticleDOI
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent.
TL;DR: A practical guide to the use of BPP in species tree estimation, a Bayesian program suitable for analyzing multilocus sequence data sets and it accommodates the heterogeneity of gene trees among loci and gene tree uncertainties due to limited phylogenetic information at each locus.
Journal ArticleDOI
Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent.
TL;DR: A Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using molecular sequences from multiple loci by using three new operators for sampling from the posterior using the Markov chain Monte Carlo algorithm.
References
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Journal ArticleDOI
Evolutionary trees from DNA sequences: A maximum likelihood approach
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
Journal ArticleDOI
Bayesian Inference of Species Trees from Multilocus Data
Joseph Heled,Alexei J. Drummond +1 more
TL;DR: It is demonstrated that both BEST and the new Bayesian Markov chain Monte Carlo method for the multispecies coalescent have much better estimation accuracy for species tree topology than concatenation, and the method outperforms BEST in divergence time and population size estimation.
Journal ArticleDOI
Bayesian species delimitation using multilocus sequence data
Ziheng Yang,Bruce Rannala +1 more
TL;DR: A Bayesian modeling approach is used to generate the posterior probabilities of species assignments taking account of uncertainties due to unknown gene trees and the ancestral coalescent process and the method is illustrated by analyzing sequence data from rotifers, fence lizards, and human populations.
Journal ArticleDOI
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
Kanchon K. Dasmahapatra,James R. Walters,Adriana D. Briscoe,John W. Davey,Annabel Whibley,Nicola J. Nadeau,Aleksey V. Zimin,Daniel S.T. Hughes,Laura Ferguson,Simon H. Martin,Camilo Salazar,Camilo Salazar,James J. Lewis,Sebastian Adler,Seung-Joon Ahn,Dean A. Baker,Simon W. Baxter,Nicola Chamberlain,Ritika Chauhan,Brian A. Counterman,Tamas Dalmay,Lawrence E. Gilbert,Karl H.J. Gordon,David G. Heckel,Heather M. Hines,Katharina J. Hoff,Peter W. H. Holland,Emmanuelle Jacquin-Joly,Francis M. Jiggins,Robert T. Jones,Durrell D. Kapan,Durrell D. Kapan,Paul J. Kersey,Gerardo Lamas,Daniel Lawson,Daniel Mapleson,Luana S. Maroja,Arnaud Martin,Simon Moxon,William J. Palmer,Riccardo Papa,Alexie Papanicolaou,Yannick Pauchet,David A. Ray,Neil Rosser,Steven L. Salzberg,Megan A. Supple,Alison K. Surridge,Ayşe Tenger-Trolander,Heiko Vogel,Paul A. Wilkinson,Derek Wilson,James A. Yorke,Furong Yuan,Alexi Balmuth,Cathlene Eland,Karim Gharbi,Marian Thomson,Richard A. Gibbs,Yi Han,Joy Jayaseelan,Christie Kovar,Tittu Mathew,Donna M. Muzny,Fiona Ongeri,Ling-Ling Pu,Jiaxin Qu,Rebecca Thornton,Kim C. Worley,Yuanqing Wu,Mauricio Linares,Mark Blaxter,Richard H. ffrench-Constant,Mathieu Joron,Marcus R. Kronforst,Sean P. Mullen,Robert D. Reed,Steven E. Scherer,Stephen Richards,James Mallet,James Mallet,W. Owen McMillan,Chris D. Jiggins,Chris D. Jiggins +83 more
TL;DR: It is inferred that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.
Journal ArticleDOI
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
Bruce Rannala,Ziheng Yang +1 more
TL;DR: In this article, a Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times.