Bayesian Inference of Species Networks from Multilocus Sequence Data

doi:10.1093/molbev/msx307

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	Bayesian Inference of Species Networks from Multilocus Sequence Data
	Zhang, Chi 1,2,3; Ogilvie, Huw A.4,5; Drummond, Alexei J.5,6; Stadler, Tanja 1,2
刊名	MOLECULAR BIOLOGY AND EVOLUTION
	2018-02-01
卷号	35 期号:2 页码:504-517
关键词	Reticulate Evolution Hybridization Multispecies Coalescent Incomplete Lineage Sorting
DOI	10.1093/molbev/msx307
文献子类	Article
英文摘要	Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network, and we assume a multispecies network coalescent prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. To quantify the power of our method, we reanalyze two large data sets of genes from spruces and yeasts. For the three closely related spruces, we verify the previously suggested homoploid hybridization event in this clade; for the yeast data, we find extensive hybridization events. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides an extensible framework for Bayesian inference of reticulate evolution.
WOS关键词	LATERAL GENE-TRANSFER ; PHYLOGENETIC NETWORKS ; DIVERGENCE-TIME ; MOLECULAR CLOCK ; DNA-SEQUENCES ; LIKELIHOOD APPROACH ; POPULATION SIZES ; MIGRATION MODEL ; TREES ; COALESCENT
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
语种	英语
WOS记录号	WOS:000423713100018
资助机构	European Research Council under the Seventh Framework Programme of the European Commission (PhyPD)(335529) ; Australian Research Council(FL110100104)
内容类型	期刊论文
源URL	[http://124.16.247.212/handle/311034/8075]
专题	古脊椎动物与古人类研究所_图书馆1
作者单位	1.Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland 2.SIB, Lausanne, Switzerland 3.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing, Peoples R China 4.Australian Natl Univ, Res Sch Biol, Div Ecol & Evolut, Canberra, ACT, Australia 5.Univ Auckland, Ctr Computat Evolut, Auckland, New Zealand 6.Univ Auckland, Dept Comp Sci, Auckland, New Zealand
推荐引用方式 GB/T 7714	Zhang, Chi,Ogilvie, Huw A.,Drummond, Alexei J.,et al. Bayesian Inference of Species Networks from Multilocus Sequence Data[J]. MOLECULAR BIOLOGY AND EVOLUTION,2018,35(2):504-517.
APA	Zhang, Chi,Ogilvie, Huw A.,Drummond, Alexei J.,&Stadler, Tanja.(2018).Bayesian Inference of Species Networks from Multilocus Sequence Data.MOLECULAR BIOLOGY AND EVOLUTION,35(2),504-517.
MLA	Zhang, Chi,et al."Bayesian Inference of Species Networks from Multilocus Sequence Data".MOLECULAR BIOLOGY AND EVOLUTION 35.2(2018):504-517.