biostudies-literatureZhu TNational Key Research and Development Program of ChinaBiotechnology and Biological Sciences Research CouncilYouth Innovation Promotion Association of the Chinese Academy of Sciences2814-2829https://www.ebi.ac.uk/biostudies/studies/S-EPMC9321900biostudies-literatureUnknown31(10)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, andMolecular ecologyA simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.PMC9321900BB/T003502/1BB/R01356X/12020YFA0712700201901Yang ZFlouri TZhu TfalseA simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.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, and2022-01-01T00:00:00Z2022 May2025-04-19T11:19:18.381Z2025-04-19T11:19:18.381ZS-EPMC93219003531303310.1111/mec.16433