A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model

doi:10.1111/mec.16433

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 应用数学研究所

	A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model
	Zhu, Tianqi 2,3; Flouri, Tomas 1; Yang, Ziheng 1
刊名	MOLECULAR ECOLOGY
	2022-04-04
页码	16
关键词	BPP introgression MSci multispecies coalescent recombination species delimitation species tree
ISSN号	0962-1083
DOI	10.1111/mec.16433
英文摘要	Phylogenomic analyses under the multispecies coalescent model assume no recombination within locus and free recombination among loci. Yet, in real data sets intralocus recombination causes different sites of the same locus to have different genealogical histories so that the model is misspecified. The impact of recombination on various coalescent-based phylogenomic analyses has not been systematically examined. Here, we conduct a computer simulation to examine the impact of recombination on several Bayesian analyses of multilocus sequence data, including species tree estimation, species delimitation (by Bayesian selection of delimitation models) and estimation of evolutionary parameters such as species divergence and introgression times, population sizes for modern and extinct species, and cross-species introgression probabilities. We found that recombination, at rates comparable to estimates from the human being, has little impact on coalescent-based species tree estimation, species delimitation and estimation of population parameters. At rates 10 times higher than the human rate, recombination may affect parameter estimation, causing positive biases in introgression times and ancestral population sizes, although species divergence times and cross-species introgression probabilities are estimated with little bias. Overall, the simulation suggests that phylogenomic inferences under the multispecies coalescent model are robust to realistic amounts of intralocus recombination.
资助项目	Biotechnology and Biological Sciences Research Council[BB/T003502/1] ; Biotechnology and Biological Sciences Research Council[BB/R01356X/1] ; China Natural Science Foundation[T2122017] ; China Natural Science Foundation[32070685] ; National Key R&D Program of China[2020YFA0712700] ; Youth Innovation Promotion Association of Chinese Academy of Sciences[201901]
WOS研究方向	Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
语种	英语
出版者	WILEY
WOS记录号	WOS:000777601900001
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/60206]
专题	应用数学研究所
通讯作者	Yang, Ziheng
作者单位	1.UCL, Dept Genet Evolut & Environm, London, England 2.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Random Complex Struct & Data Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Zhu, Tianqi,Flouri, Tomas,Yang, Ziheng. A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model[J]. MOLECULAR ECOLOGY,2022:16.
APA	Zhu, Tianqi,Flouri, Tomas,&Yang, Ziheng.(2022).A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.MOLECULAR ECOLOGY,16.
MLA	Zhu, Tianqi,et al."A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model".MOLECULAR ECOLOGY (2022):16.