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

文献类型：期刊论文

作者Zhu, Tianqi2,3; Flouri, Tomas1; Yang, Ziheng1
刊名MOLECULAR ECOLOGY
出版日期2022-04-04
页码16
关键词BPP introgression MSci multispecies coalescent recombination species delimitation species tree
ISSN号0962-1083
DOI10.1111/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
WOS记录号WOS:000777601900001
出版者WILEY
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, Key Lab Random Complex Struct & Data Sci, Beijing, Peoples R China
3.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, 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.

入库方式： OAI收割

来源：数学与系统科学研究院

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