Bayesian Inference of Species Networks from Multilocus Sequence Data

doi:10.1093/molbev/msx307

IVPP-IR > 中科院古脊椎所（2000年以后）

	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
	2018-02-01
发表期刊	MOLECULAR BIOLOGY AND EVOLUTION
卷号	35 期号:2 页码:504-517
文章类型	Article
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.
关键词	Reticulate Evolution Hybridization Multispecies Coalescent Incomplete Lineage Sorting
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
DOI	10.1093/molbev/msx307
关键词[WOS]	LATERAL GENE-TRANSFER ; PHYLOGENETIC NETWORKS ; DIVERGENCE-TIME ; MOLECULAR CLOCK ; DNA-SEQUENCES ; LIKELIHOOD APPROACH ; POPULATION SIZES ; MIGRATION MODEL ; TREES ; COALESCENT
收录类别	SCI
语种	英语
项目资助者	European Research Council under the Seventh Framework Programme of the European Commission (PhyPD)(335529) ; Australian Research Council(FL110100104)
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS类目	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS记录号	WOS:000423713100018
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.205/handle/311034/8075
专题	中科院古脊椎所（2000年以后）
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.

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
Bayesian Inference o（674KB）	期刊论文	作者接受稿	开放获取	CC BY-NC-SA	浏览下载