Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

Scientific Reports
Xumin NiShuhua Xu

Abstract

The length of ancestral tracks decays with the passing of generations which can be used to infer population admixture histories. Previous studies have shown the power in recovering the histories of admixed populations via the length distributions of ancestral tracks even under simple models. We believe that the deduction of length distributions under a general model will greatly elevate the power. Here we first deduced the length distributions under a general model and proposed general principles in parameter estimation and model selection with the deduced length distributions. Next, we focused on studying the length distributions and its applications under three typical special cases. Extensive simulations showed that the length distributions of ancestral tracks were well predicted by our theoretical framework. We further developed a new method, AdmixInfer, based on the length distributions and good performance was observed when it was applied to infer population histories under the three typical models. Notably, our method was insensitive to demographic history, sample size and threshold to discard short tracks. Finally, good performance was also observed when applied to some real datasets of African Americans, Mexicans and S...Continue Reading

References

Feb 24, 2017·Scientific Reports·Ying ZhouShuhua Xu
Dec 10, 2016·Angewandte Chemie·Min JiangHua Fu
Jun 9, 2017·Molecular Biology and Evolution·Qidi FengShuhua Xu
Jun 23, 2018·Molecular Biology and Evolution·Thomas Dias-AlvesMichael G B Blum
Sep 13, 2018·European Journal of Human Genetics : EJHG·Xumin NiShuhua Xu
Sep 25, 2019·Evolutionary Applications·Maud DurantonPierre-Alexandre Gagnaire

Citations

Mar 22, 2008·American Journal of Human Genetics·Shuhua XuLi Jin
Sep 3, 2010·Nature·International HapMap 3 ConsortiumJean E McEwen
Mar 1, 2011·Genome Biology·Irina PugachMark Stoneking
Dec 6, 2011·Nature Methods·Olivier DelaneauJean-François Zagury
Apr 12, 2012·Genetics·Simon Gravel
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Dec 20, 2013·Nature·Kay PrüferSvante Pääbo
Jan 31, 2014·Nature·Sriram SankararamanDavid Reich
Feb 18, 2014·Science·Garrett HellenthalSimon Myers
Feb 20, 2014·Proceedings of the National Academy of Sciences of the United States of America·Joseph K PickrellDavid Reich
Apr 29, 2014·Genetics·Mason Liang, Rasmus Nielsen

Related Concepts

In Silico
Study
Genome
Projections and Predictions
Genetics, Population
Mexican
Theoretical Study
African American
South
Simulation

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