The influence of gene flow on species tree estimation: a simulation study.
暂无分享,去创建一个
Ziheng Yang | Bruce Rannala | Adam D Leaché | B. Rannala | Ziheng Yang | A. Leaché | Rebecca B Harris | Rebecca B. Harris
[1] C. Moritz,et al. Recent and rapid speciation with limited morphological disparity in the genus Rattus. , 2011, Systematic biology.
[2] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[3] David Gerard,et al. Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling , 2011, BMC Evolutionary Biology.
[4] Liang Liu,et al. Estimating Species Trees Using Multiple-Allele DNA Sequence Data , 2008, Evolution; international journal of organic evolution.
[5] N. Rosenberg,et al. Discordance of Species Trees with Their Most Likely Gene Trees , 2006, PLoS genetics.
[6] A. Drummond,et al. Bayesian Inference of Species Trees from Multilocus Data , 2009, Molecular biology and evolution.
[7] T. Sang,et al. Testing hybridization hypotheses based on incongruent gene trees. , 2000, Systematic biology.
[8] Mariana Morando,et al. Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae). , 2012, Systematic biology.
[9] Montgomery Slatkin,et al. Subdivision in an ancestral species creates asymmetry in gene trees. , 2008, Molecular biology and evolution.
[10] S. Edwards,et al. Genetic Introgression: An Integral but Neglected Component of Speciation in Birds , 2011 .
[11] Bryan C. Carstens,et al. Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats , 2010, Systematic biology.
[12] J. Hey. Isolation with migration models for more than two populations. , 2010, Molecular biology and evolution.
[13] Scott V Edwards,et al. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model , 2010, BMC Evolutionary Biology.
[14] Richard R. Hudson,et al. Generating samples under a Wright-Fisher neutral model of genetic variation , 2002, Bioinform..
[15] B. Rannala,et al. Phylogenetic inference using whole genomes. , 2008, Annual review of genomics and human genetics.
[16] J. Hey,et al. Joint Inference of Population Assignment and Demographic History , 2011, Genetics.
[17] S. Edwards. IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? , 2009, Evolution; international journal of organic evolution.
[18] David Bryant,et al. Simulating gene trees under the multispecies coalescent and time-dependent migration , 2013, BMC Evolutionary Biology.
[19] P. Wirtz. Mother species–father species: unidirectional hybridization in animals with female choice , 1999, Animal Behaviour.
[20] Mary K Kuhner,et al. Coalescent genealogy samplers: windows into population history. , 2009, Trends in ecology & evolution.
[21] Ziheng Yang. A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data , 2010, Genome biology and evolution.
[22] Luay Nakhleh,et al. The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection , 2012, PLoS genetics.
[23] Nicholas Stiffler,et al. Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags , 2010, PLoS genetics.
[24] Laura Salter Kubatko,et al. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. , 2009, Theoretical population biology.
[25] F. Tajima. Evolutionary relationship of DNA sequences in finite populations. , 1983, Genetics.
[26] B. Rannala,et al. Bayesian species delimitation using multilocus sequence data , 2010, Proceedings of the National Academy of Sciences.
[27] S. Jeffery. Evolution of Protein Molecules , 1979 .
[28] T. Glenn. Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.
[29] Noah A Rosenberg,et al. Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.
[30] Tianqi Zhu,et al. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. , 2012, Molecular biology and evolution.
[31] Roland Kays,et al. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. , 2011, Genome research.
[32] John P. Huelsenbeck,et al. MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..
[33] M Slatkin,et al. A cladistic measure of gene flow inferred from the phylogenies of alleles. , 1989, Genetics.
[34] L. Kubatko. Identifying hybridization events in the presence of coalescence via model selection. , 2009, Systematic biology.
[35] Scott V Edwards,et al. Coalescent methods for estimating phylogenetic trees. , 2009, Molecular phylogenetics and evolution.
[36] Jody Hey,et al. Divergence with Gene Flow: Models and Data , 2010 .
[37] Montgomery Slatkin,et al. Gene Flow in Natural Populations , 1985 .
[38] S. Edwards,et al. A species tree for the Australo-Papuan Fairy-wrens and allies (Aves: Maluridae). , 2012, Systematic biology.
[39] S. Joly. JML: testing hybridization from species trees , 2012, Molecular ecology resources.
[40] Bin Ma,et al. From Gene Trees to Species Trees , 2000, SIAM J. Comput..
[41] W. Maddison,et al. Inferring phylogeny despite incomplete lineage sorting. , 2006, Systematic biology.
[42] C. Ané,et al. Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer. , 2011, Systematic biology.
[43] Patricia A. McLenachan,et al. A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting , 2009, The American Naturalist.
[44] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[45] M. Carling,et al. Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings , 2008, Genetics.
[46] Bryan C Carstens,et al. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. , 2008, Molecular phylogenetics and evolution.
[47] Ziheng Yang,et al. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. , 2003, Genetics.
[48] Bryan C Carstens,et al. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. , 2007, Systematic biology.
[49] Liang Liu,et al. BEST: Bayesian estimation of species trees under the coalescent model , 2008, Bioinform..
[50] Tianqi Zhu,et al. Evaluation of a bayesian coalescent method of species delimitation. , 2011, Systematic biology.
[51] Craig Moritz,et al. Patterns of persistence and isolation indicate resilience to climate change in montane rainforest lizards , 2010, Molecular ecology.
[52] Bruce Rannala,et al. The accuracy of species tree estimation under simulation: a comparison of methods. , 2011, Systematic biology.
[53] N. Takahata. A GENETIC PERSPECTIVE ON THE ORIGIN AND HISTORY OF HUMANS , 1995 .
[54] Bryan C. Carstens,et al. SpedeSTEM: a rapid and accurate method for species delimitation , 2011, Molecular ecology resources.
[55] R. Nichols,et al. Gene trees and species trees are not the same. , 2001, Trends in ecology & evolution.
[56] John E McCormack,et al. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. , 2009, Systematic biology.
[57] H. Munro,et al. Mammalian protein metabolism , 1964 .
[58] Bryan C. Carstens,et al. Delimiting species without monophyletic gene trees. , 2007, Systematic biology.
[59] R. Nielsen,et al. Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis , 2004, Genetics.
[60] M. Holder,et al. Difficulties in detecting hybridization. , 2001, Systematic biology.
[61] R. Nielsen,et al. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. , 2001, Genetics.
[62] A. Leaché. Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). , 2009, Systematic biology.
[63] James C. Wilgenbusch,et al. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics , 2008, Bioinform..
[64] Richard R. Hudson,et al. TESTING THE CONSTANT‐RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA , 1983, Evolution; international journal of organic evolution.
[65] Laura Kubatko,et al. Estimating species trees : practical and theoretical aspects , 2010 .
[66] L. Excoffier,et al. Computer programs for population genetics data analysis: a survival guide , 2006, Nature Reviews Genetics.
[67] B. Rannala,et al. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. , 2004, Systematic biology.