AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data

BMC Bioinformatics
Nathan K SchaeferRichard E Green

Abstract

Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Final...Continue Reading

References

Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·Andrew Rambaut, N C Grassly
Aug 30, 2001·Trends in Genetics : TIG·David Reich, Eric S Lander
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Sep 2, 2005·Nature·Chimpanzee Sequencing and Analysis Consortium
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
May 29, 2007·Journal of Theoretical Biology·A J McKane, D Waxman
May 20, 2009·Bioinformatics·Heng Li, Richard M Durbin
Jun 10, 2009·Bioinformatics·Heng Li1000 Genome Project Data Processing Subgroup
Aug 19, 2009·Nature Reviews. Genetics·Kent E Holsinger, Bruce S Weir
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
May 8, 2010·Science·Richard E GreenSvante Pääbo
Oct 29, 2010·Nature·Gonçalo R AbecasisGil A McVean
Feb 18, 2011·Molecular Biology and Evolution·Eric Y DurandMontgomery Slatkin
May 19, 2011·Nature Reviews. Genetics·Rasmus NielsenYun S Song
Jul 9, 2011·Current Biology : CB·Ceiridwen J EdwardsBeth Shapiro
Jul 25, 2012·Proceedings of the National Academy of Sciences of the United States of America·Webb MillerCharlotte Lindqvist
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Jun 12, 2013·PLoS Genetics·Kelley Harris, Rasmus Nielsen
Dec 20, 2013·Nature·Kay PrüferSvante Pääbo
Jan 31, 2014·Science·Benjamin Vernot, Joshua M Akey
Jan 31, 2014·Nature·Sriram SankararamanDavid Reich
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Feb 17, 2015·American Journal of Human Genetics·Benjamin Vernot, Joshua M Akey
Jun 23, 2015·Nature·Qiaomei FuSvante Pääbo
Jan 31, 2016·Molecular Ecology·Nathan K SchaeferRichard E Green

Citations

Sep 13, 2018·Genome Biology·Megan A Supple, Beth Shapiro

Methods Mentioned

BETA
genotyping
PCA
four hybrid

Related Concepts

Metazoa
Ursus
Hybridization, Intraspecies
Markov Chains
Computer Programs and Programming
Genome
Single Nucleotide Polymorphism
Genetic Speciation
Alzheimer's Disease
Ursidae Family

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