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A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model
Zhu, Tianqi1,2; Flouri, Tomas3; Yang, Ziheng3
2022-04-04
Source PublicationMOLECULAR ECOLOGY
ISSN0962-1083
Pages16
AbstractPhylogenomic 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.
KeywordBPP introgression MSci multispecies coalescent recombination species delimitation species tree
DOI10.1111/mec.16433
Indexed BySCI
Language英语
Funding ProjectBiotechnology 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 Research AreaBiochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS IDWOS:000777601900001
PublisherWILEY
Citation statistics
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/60207
Collection应用数学研究所
Corresponding AuthorYang, Ziheng
Affiliation1.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
Recommended Citation
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.
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