Tracking human population structure through time from whole genome sequences

PLoS Genetics
Ke WangStephan Schiffels

Abstract

The genetic diversity of humans, like many species, has been shaped by a complex pattern of population separations followed by isolation and subsequent admixture. This pattern, reaching at least as far back as the appearance of our species in the paleontological record, has left its traces in our genomes. Reconstructing a population's history from these traces is a challenging problem. Here we present a novel approach based on the Multiple Sequentially Markovian Coalescent (MSMC) to analyze the separation history between populations. Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression. We apply MSMC-IM to whole genome sequences from 15 worldwide populations, tracking the process of human genetic diversification. We detect traces of extremely deep ancestry between some African populations, with around 1% of ancestry dating to divergences older than a million years ago.

References

Mar 21, 2003·Current Biology : CB·Alec KnightJoanna L Mountain
Jun 13, 2003·Nature·Tim D WhiteF Clark Howell
Feb 18, 2005·Nature·Ian McDougallJohn G Fleagle
Jul 29, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Gilean A T McVean, Niall J Cardin
Mar 17, 2006·BMC Genetics·Paul Marjoram, Jeff D Wall
Aug 10, 2006·PLoS Genetics·Vincent Plagnol, Jeffrey D Wall
Jul 28, 2007·Molecular Biology and Evolution·Sarah A TishkoffJoanna L Mountain
Sep 1, 2012·Science·Matthias MeyerSvante Pääbo
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Oct 18, 2012·Nature Communications·Joseph K PickrellBrigitte Pakendorf
Dec 28, 2012·Nature Methods·Olivier DelaneauJonathan Marchini
Oct 8, 2013·American Journal of Human Genetics·Olivier DelaneauJonathan Marchini
Nov 22, 2013·Nature·Maanasa RaghavanEske Willerslev
Dec 20, 2013·Nature·Kay PrüferSvante Pääbo
Jan 31, 2014·Nature·Sriram SankararamanDavid Reich
Jun 24, 2014·Nature Genetics·Stephan Schiffels, Richard Durbin
Jan 20, 2016·Nature Communications·Stephan SchiffelsRichard Durbin
Apr 2, 2016·Current Biology : CB·Sriram SankararamanDavid Reich
May 6, 2016·PLoS Computational Biology·Jerome KelleherGilean McVean
Sep 23, 2016·Nature·Anna-Sapfo MalaspinasEske Willerslev
Oct 28, 2016·Nature Genetics·Po-Ru LohAlkes L Price
Feb 28, 2017·Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America·John A KammYun S Song
Sep 25, 2017·Cell·Pontus SkoglundDavid Reich
Apr 6, 2018·PLoS Genetics·Yongwook ChoiNicholas J Schork
May 5, 2018·Annual Review of Genomics and Human Genetics·Carina M Schlebusch, Mattias Jakobsson
Oct 6, 2020·Journal of the American Statistical Association·Jack KammYun S Song

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Citations

Jan 16, 2021·Molecular Ecology Resources·Christelle FraïsseCamille Roux
Feb 12, 2021·Nature·Anders BergströmPontus Skoglund
Feb 23, 2021·Nature·Chuan-Chao WangDavid Reich
Mar 27, 2021·Genetics·Per SjödinMattias Jakobsson
May 13, 2021·Molecular Ecology Resources·Thibaut Paul Patrick SellingerAurélien Tellier
Aug 12, 2020·Journal of Human Evolution·Osbjorn M PearsonChristian A Tryon
Jun 16, 2021·Molecular Biology and Evolution·Leo SpeidelSimon R Myers
Aug 6, 2021·Cell·Mohamed A AlmarriChris Tyler-Smith
May 25, 2021·Genome Biology and Evolution·K D AhlquistKelsey E Witt

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Datasets Mentioned

BETA
ERX1790596

Software Mentioned

shapeit
SHAPEIT2
EAGLE2
Beagle4
MSMC
SMC
diCal2
EAGLE
IM
Excel

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