Inferring the history of population size change from genome-wide SNP data

Molecular Biology and Evolution
Christoph TheunertMark Stoneking

Abstract

Dense, genome-wide single-nucleotide polymorphism (SNP) data can be used to reconstruct the demographic history of human populations. However, demographic inferences from such data are complicated by recombination and ascertainment bias. We introduce two new statistics, allele frequency-identity by descent (AF-IBD) and allele frequency-identity by state (AF-IBS), that make use of linkage disequilibrium information and show defined relationships to the time of coalescence. These statistics, when conditioned on the derived allele frequency, are able to infer complex population size changes. Moreover, the AF-IBS statistic, which is based on genome-wide SNP data, is robust to varying ascertainment conditions. We constructed an efficient approximate Bayesian computation (ABC) pipeline based on AF-IBD and AF-IBS that can accurately estimate demographic parameters, even for fairly complex models. Finally, we applied this ABC approach to genome-wide SNP data and inferred the demographic histories of two human populations, Yoruba and French. Our results suggest a rather stable ancestral population size with a mild recent expansion for Yoruba, whereas the French seemingly experienced a long-lasting severe bottleneck followed by a drastic...Continue Reading

References

Mar 1, 1995·Chemotherapy·B M Kotecka, K H Rieckmann
Mar 10, 2001·Nature·E S LanderInternational Human Genome Sequencing Consortium
May 11, 2001·Nature·David ReichE S Lander
Sep 15, 2001·Genetical Research·Montgomery Slatkin
Nov 10, 2001·Annual Review of Genomics and Human Genetics·Montgomery Slatkin, B Rannala
Nov 24, 2001·Molecular Biology and Evolution·K Strimmer, O G Pybus
Jan 31, 2002·Trends in Genetics : TIG·Magnus Nordborg, Simon Tavaré
Mar 29, 2002·Nature Genetics·Scott D Briggs, Brian D Strahl
Jun 8, 2002·Nature Genetics·Augustine KongKari Stefansson
Oct 9, 2002·The American Journal of Pathology·James J YunAbbas Ardehali
Jan 18, 2005·Genetics·Laurent ExcoffierJean-Marie Cornuet
Feb 11, 2005·Molecular Biology and Evolution·Alexei J DrummondO G Pybus
Mar 1, 2005·Biochimica Et Biophysica Acta·Arshad MatherMonde Ntwasa
Oct 28, 2005·Genome Research·Stephen F SchaffnerDavid Altshuler
Oct 29, 2005·Nature·International HapMap Consortium
Dec 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Benjamin F VoightAnna Di Rienzo
Oct 24, 2006·Nature Genetics·Donald F ConradJonathan K Pritchard
Mar 14, 2007·Genome Research·Albert TenesaPeter M Visscher
Nov 6, 2007·Proceedings of the National Academy of Sciences of the United States of America·Nelson J R FagundesLaurent Excoffier
Feb 22, 2008·Genetics Research·Montgomery Slatkin
Apr 15, 2008·Molecular Biology and Evolution·Vladimir N MininMarc A Suchard
Oct 25, 2008·BMC Evolutionary Biology·Joseph Heled, Alexei J Drummond
Nov 26, 2008·Genome Research·Gary K ChenJeffrey D Wall
May 8, 2009·Molecular Biology and Evolution·Jeffrey D WallVincent Plagnol
Feb 12, 2011·American Journal of Human Genetics·Brian L Browning, Sharon R Browning

Citations

Jul 14, 2014·Molecular Biology and Evolution·Raphaël LebloisFrançois Rousset
Nov 22, 2015·Bioinformatics·Pierre PudloChristian P Robert
Jul 10, 2013·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Joseph Lachance, Sarah A Tishkoff
Aug 13, 2014·Molecular Ecology·John D RobinsonMichael J Hickerson
Jun 30, 2015·Evolution; International Journal of Organic Evolution·Kimberly J Gilbert, Michael C Whitlock
Apr 17, 2018·Molecular Biology and Evolution·Frédéric Austerlitz, Evelyne Heyer
Oct 16, 2018·Bioinformatics·Louis RaynalArnaud Estoup
Feb 21, 2019·Molecular Biology and Evolution·Flora JayFrédéric Austerlitz

Related Concepts

Bayesian Prediction
Genetic Equilibrium
Genetics, Population
Underpopulation
Linkage Disequilibrium
Genome
Evolution, Molecular
Single Nucleotide Polymorphism
Alleles
Cell Growth

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