Inferring demographic history from a spectrum of shared haplotype lengths

PLoS Genetics
Kelley Harris, Rasmus Nielsen


There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and diver...Continue Reading


May 17, 2014·PLoS Genetics·Matthew D RasmussenAdam Siepel
Aug 8, 2014·PLoS Genetics·Iain Mathieson, Gil McVean
Feb 5, 2014·Nature Reviews. Genetics·Krishna R Veeramah, Michael F Hammer
Jun 24, 2014·Nature Genetics·Stephan Schiffels, Richard Durbin
Aug 26, 2014·Theoretical Population Biology·Shai CarmiItsik Pe'er
Feb 4, 2014·Theoretical Population Biology·Asger Hobolth, Jens Ledet Jensen
Jun 2, 2014·Current Opinion in Immunology·Matteo Fumagalli, Manuela Sironi
Nov 8, 2015·Molecular Biology and Evolution·Alec J CoffmanRyan N Gutenkunst
Mar 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kelley Harris
Aug 25, 2015·American Journal of Human Genetics·Sharon R Browning, Brian L Browning
Nov 20, 2015·American Journal of Human Genetics·Pier Francesco PalamaraAlkes L Price
Nov 11, 2015·Nature Reviews. Genetics·Joshua G Schraiber, Joshua M Akey
Sep 24, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xumin NiShihua Zhang
Dec 17, 2014·Conservation Biology : the Journal of the Society for Conservation Biology·Jennifer C PiersonAndrew G Young
Sep 27, 2014·Molecular Ecology·Ian J Wang, Gideon S Bradburd
May 2, 2015·Evolution; International Journal of Organic Evolution·Christopher H MartinPeter C Wainwright
Dec 3, 2014·Current Opinion in Genetics & Development·Michael C CampbellSarah Tishkoff
May 13, 2015·Nature Reviews. Genetics·Fernando RacimoEmilia Huerta-Sánchez
Apr 23, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Shuo YangItsik Pe'er
Mar 20, 2016·Molecular Biology and Evolution·Irina PugachBrigitte Pakendorf
May 15, 2013·PLoS Biology·Peter Ralph, Graham Coop
Apr 16, 2015·PloS One·Anthony J GenevaDaniel Garrigan
Sep 1, 2015·PLoS Genetics·Daniel J BalickShamil R Sunyaev
Jun 22, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·James A CahillBeth Shapiro
Aug 27, 2014·Current Opinion in Genetics & Development·Vitor SousaLaurent Excoffier
Aug 12, 2016·The Journal of Heredity·Kristina M CammenAmy M Van Cise
Jan 13, 2015·Theoretical Population Biology·Alan R Rogers, Ryan J Bohlender
Jan 13, 2015·Genome Biology and Evolution·Ahmed Al-KhudhairAlexei Fedorov
Jan 20, 2017·Nature·Rasmus NielsenEske Willerslev
Apr 6, 2017·BMC Bioinformatics·Nathan K SchaeferRichard E Green
Jul 4, 2017·ELife·Daniel B Weissman, Oskar Hallatschek
Jan 5, 2018·Molecular Biology and Evolution·Irina PugachMark Stoneking
Dec 9, 2017·Science·Kelley Harris


Jul 1, 1997·Molecular Biology and Evolution·Z Yang, B Rannala
May 20, 1998·Proceedings of the National Academy of Sciences of the United States of America·A PolanskiR Chakraborty
Jun 15, 1999·Theoretical Population Biology·Carsten Wiuf, J Hein
Dec 22, 1999·Molecular Biology and Evolution·Jonathan K PritchardMarcus W Feldman
Apr 5, 2001·Proceedings of the National Academy of Sciences of the United States of America·P Beerli, J Felsenstein
Mar 8, 2002·Nature·Alan Templeton
Jun 8, 2002·Nature Genetics·Augustine KongKari Stefansson
May 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Scott H WilliamsonCarlos D Bustamante
Jul 29, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Gilean A T McVean, Niall J Cardin
Oct 28, 2005·Genome Research·Stephen F SchaffnerDavid Altshuler
Oct 29, 2005·Nature·International HapMap Consortium
Mar 17, 2006·BMC Genetics·Paul Marjoram, Jeff D Wall
Sep 9, 2006·Journal of Mathematical Biology·Carsten Wiuf
Oct 13, 2006·BMC Genetics·Emma BrunbergGabriella Lindgren
Nov 18, 2006·Science·James P NoonanEdward M Rubin
Oct 31, 2008·Genome Research·Alexander GusevItsik Pe'er
Feb 6, 2009·PLoS Biology·Alan HodgkinsonAdam Eyre-Walker
Feb 10, 2009·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Mar 25, 2009·Genome Research·Joseph K PickrellJonathan K Pritchard
May 9, 2009·PLoS Genetics·Graham McVickerPhil Green
Oct 2, 2009·Molecular Biology and Evolution·Jared L Strasburg, Loren H Rieseberg
May 8, 2010·Science·Richard E GreenSvante Pääbo
Oct 29, 2010·Nature·Gonçalo R AbecasisGil A McVean
Nov 9, 2010·Genetic Epidemiology·Yun LiGonçalo R Abecasis
Feb 12, 2011·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Mar 9, 2011·Statistical Applications in Genetics and Molecular Biology·Philippe Girard
May 3, 2011·PLoS Genetics·Priya MoorjaniDavid Reich
Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Simon GravelCarlos D Bustamante
Sep 20, 2011·Nature Genetics·Ilan GronauAdam Siepel
Sep 24, 2011·Science·Morten RasmussenEske Willerslev

Related Concepts

RCHY1 gene
CFC1 gene
Physiologic Pulse
Likelihood Functions
African Continental Ancestry Group
Chromosome Map
Genetics, Population
Structure of Left Hand

Related Feeds

Ancient DNA

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, but are notoriously difficult to analyze due to molecular damage and exogenous dna contamination. Discover the latest research on Ancient DNA here.