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

doi:10.1111/mec.16433

CSpace > 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, Tianqi1,2 ; Flouri, Tomas 3; Yang, Ziheng 3
	2022-04-04
发表期刊	MOLECULAR ECOLOGY
ISSN	0962-1083
页码	16
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.
关键词	BPP introgression MSci multispecies coalescent recombination species delimitation species tree
DOI	10.1111/mec.16433
收录类别	SCI
语种	英语
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
WOS类目	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS记录号	WOS:000777601900001
出版者	WILEY
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/60207
专题	应用数学研究所
通讯作者	Yang, Ziheng
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Random Complex Struct & Data Sci, Beijing, Peoples R China 3.UCL, Dept Genet Evolut & Environm, London, England
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.