Inference of historical migration rates via haplotype sharing

Bioinformatics
Pier Francesco Palamara, Itsik Pe'er

Abstract

Pairs of individuals from a study cohort will often share long-range haplotypes identical-by-descent. Such haplotypes are transmitted from common ancestors that lived tens to hundreds of generations in the past, and they can now be efficiently detected in high-resolution genomic datasets, providing a novel source of information in several domains of genetic analysis. Recently, haplotype sharing distributions were studied in the context of demographic inference, and they were used to reconstruct recent demographic events in several populations. We here extend the framework to handle demographic models that contain multiple demes interacting through migration. We extensively test our formulation in several demographic scenarios, compare our approach with methods based on ancestry deconvolution and use this method to analyze Masai samples from the HapMap 3 dataset. DoRIS, a Java implementation of the proposed method, and its source code are freely available at http://www.cs.columbia.edu/~pier/doris.

References

Aug 26, 2014·Theoretical Population Biology·Shai CarmiItsik Pe'er
Nov 20, 2015·American Journal of Human Genetics·Pier Francesco PalamaraAlkes 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
Sep 15, 2015·Evolutionary Applications·Pierre-Alexandre GagnaireNicolas Bierne
Apr 23, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Shuo YangItsik Pe'er
Nov 12, 2015·European Journal of Human Genetics : EJHG·Giovanni FioritoGiuseppe Matullo
Jul 5, 2016·Nature Reviews. Genetics·Joanna L KelleyAndrew D Foote
Apr 5, 2017·PLoS Genetics·James XueShai Carmi
Jan 15, 2019·PLoS Genetics·Hussein Al-AsadiJohn Novembre
May 18, 2019·Molecular Ecology Resources·Erik Lundgren, Peter Ralph
May 19, 2020·Molecular Ecology Resources·Dave LutgenReto Burri
Jun 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Daniel N HarrisHeinner Guio
Apr 12, 2019·Scientific Reports·Ural YunusbaevBayazit Yunusbayev
Feb 11, 2014·The Journal of Heredity·Emily Jane McTavish, David M Hillis
Jan 22, 2017·Genetics·Harald RingbauerNicholas H Barton
Jun 19, 2019·Nature Communications·Amol C ShettyTracking Resistance to Artemisinin Collaboration (TRAC)
Sep 25, 2019·Evolutionary Applications·Maud DurantonPierre-Alexandre Gagnaire

Citations

Jul 29, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Gilean McVean, Niall Cardin
Apr 27, 2007·Bioinformatics·Liming LiangGonçalo R Abecasis
Oct 19, 2007·Nature·International HapMap ConsortiumJohn Stewart
Oct 31, 2008·Genome Research·Alexander GusevItsik Pe'er
Jul 2, 2010·Genetics·Anders AlbrechtsenRasmus Nielsen
Sep 30, 2010·Human Molecular Genetics·Brenna M HennCarlos D Bustamante
Feb 12, 2011·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Feb 18, 2011·Genome Research·Chad D HuffLynn B Jorde
Jul 27, 2011·Human Genetics·C VelezHarry Ostrer
Oct 11, 2011·Molecular Biology and Evolution·Alexander GusevItsik Pe'er
Nov 1, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Bonnie KirkpatrickEran Halperin
Jan 19, 2012·PLoS Genetics·Brenna M HennDavid Comas
Jan 24, 2012·Genetics·Sharon R Browning, Elizabeth A Thompson
Apr 12, 2012·Genetics·Simon Gravel
Jun 19, 2012·Annual Review of Genomics and Human Genetics·Daniel John Lawson, Daniel Falush
Jul 12, 2012·European Journal of Human Genetics : EJHG·Lide Han, Mark Abney
Aug 8, 2012·Proceedings of the National Academy of Sciences of the United States of America·Christopher L CampbellHarry Ostrer
Oct 30, 2012·American Journal of Human Genetics·Pier Francesco PalamaraItsik Pe'er
May 15, 2013·PLoS Biology·Peter Ralph, Graham Coop

Related Concepts

HapMap
Genome
Genetic Analysis
Genetic Screening Method
Doris
Human Migration
Genomics
Toxic Epidermal Necrolysis
Silo (Dataset)

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