ArticlePLoS genetics2012
A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 121 citations in OpenAlex.
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- Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia.Scientific reports · 2023Article
- Ghost admixture in eastern gorillas.Nature ecology & evolution · 2023Article
- Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola.Scientific reports · 2022Article
- Comparative Population Genomics of Cryptic Speciation and Adaptive Divergence in Bicknell's and Gray-Cheeked Thrushes (Aves: Catharus bicknelli and Catharus minimus).Genome biology and evolution · 2022Article
- Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep.Communications biology · 2021Article
- Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks.Molecular ecology resources · 2021Article
- mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow.Genome biology and evolution · 2020Article
- Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data.PLoS genetics · 2020Article
- Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure.Genome biology and evolution · 2020Article
- Population Genomics in the Great Apes.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Recent advances in Bayesian inference of isolation-with-migration models.Genomics & informatics · 2019Article
- Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover.The Plant cell · 2019Article
- The comparative genomics and complex population history ofScience advances · 2019Article
- Phylogeny Estimation by Integration over Isolation with Migration Models.Molecular biology and evolution · 2018Article
- ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.Genome biology · 2018Article
- The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.PLoS genetics · 2018Article
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Authors and funding
11 authors at 5 institutions in 4 countries.
Funding
Abstract
We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.
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