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

Zhu, Tianqi; Flouri, Tomáš; Yang, Ziheng; (2022) A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model. Molecular Ecology , 31 (10) pp. 2814-2839. 10.1111/mec.16433. Green open access

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Abstract

Phylogenomic analyses under the multispecies coalescent model assume no recombination within locus and free recombination among loci. Yet in real datasets 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 be 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, 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.

Type: Article
Title: A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1111/mec.16433
Publisher version: https://doi.org/10.1111/mec.16433
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: BPP, MSci, introgression, recombination, species delimitation, species tree, | multispecies coalescent
UCL classification: UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10146134
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