A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.
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 recom...
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Genetics |
| Online Access: | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1003125&type=printable |
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| author | Thomas Mailund Anders E Halager Michael Westergaard Julien Y Dutheil Kasper Munch Lars N Andersen Gerton Lunter Kay Prüfer Aylwyn Scally Asger Hobolth Mikkel H Schierup |
| author_facet | Thomas Mailund Anders E Halager Michael Westergaard Julien Y Dutheil Kasper Munch Lars N Andersen Gerton Lunter Kay Prüfer Aylwyn Scally Asger Hobolth Mikkel H Schierup |
| author_sort | Thomas Mailund |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-22d1410b2ee74170b1496441aaac880c |
| institution | OA Journals |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-22d1410b2ee74170b1496441aaac880c2025-08-20T02:05:37ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042012-01-01812e100312510.1371/journal.pgen.1003125A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.Thomas MailundAnders E HalagerMichael WestergaardJulien Y DutheilKasper MunchLars N AndersenGerton LunterKay PrüferAylwyn ScallyAsger HobolthMikkel H SchierupWe 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.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1003125&type=printable |
| spellingShingle | Thomas Mailund Anders E Halager Michael Westergaard Julien Y Dutheil Kasper Munch Lars N Andersen Gerton Lunter Kay Prüfer Aylwyn Scally Asger Hobolth Mikkel H Schierup A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genetics |
| title | A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. |
| title_full | A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. |
| title_fullStr | A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. |
| title_full_unstemmed | A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. |
| title_short | A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. |
| title_sort | new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1003125&type=printable |
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