A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

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A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. / Mailund, Thomas; Halager, Anders E; Westergaard, Michael; Dutheil, Julien Y; Munch, Kasper; Andersen, Lars N; Lunter, Gerton; Prüfer, Kay; Scally, Aylwyn; Hobolth, Asger; Schierup, Mikkel H.

I: P L o S Genetics, Bind 8, Nr. 12, 2012, s. e1003125.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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Mailund, Thomas ; Halager, Anders E ; Westergaard, Michael ; Dutheil, Julien Y ; Munch, Kasper ; Andersen, Lars N ; Lunter, Gerton ; Prüfer, Kay ; Scally, Aylwyn ; Hobolth, Asger ; Schierup, Mikkel H. / A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. I: P L o S Genetics. 2012 ; Bind 8, Nr. 12. s. e1003125.

Bibtex

@article{ad241ce7b10d48b898c2ad1729160224,
title = "A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species",
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.",
author = "Thomas Mailund and Halager, {Anders E} and Michael Westergaard and Dutheil, {Julien Y} and Kasper Munch and Andersen, {Lars N} and Gerton Lunter and Kay Pr{\"u}fer and Aylwyn Scally and Asger Hobolth and Schierup, {Mikkel H}",
year = "2012",
doi = "10.1371/journal.pgen.1003125",
language = "English",
volume = "8",
pages = "e1003125",
journal = "P L o S Genetics",
issn = "1553-7390",
publisher = "public library of science",
number = "12",

}

RIS

TY - JOUR

T1 - A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

AU - Mailund, Thomas

AU - Halager, Anders E

AU - Westergaard, Michael

AU - Dutheil, Julien Y

AU - Munch, Kasper

AU - Andersen, Lars N

AU - Lunter, Gerton

AU - Prüfer, Kay

AU - Scally, Aylwyn

AU - Hobolth, Asger

AU - Schierup, Mikkel H

PY - 2012

Y1 - 2012

N2 - 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.

AB - 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.

U2 - 10.1371/journal.pgen.1003125

DO - 10.1371/journal.pgen.1003125

M3 - Journal article

C2 - 23284294

VL - 8

SP - e1003125

JO - P L o S Genetics

JF - P L o S Genetics

SN - 1553-7390

IS - 12

ER -