Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data

Genetics
Matthew S AckermanMichael Lynch

Abstract

Population structure can be described by genotypic-correlation coefficients between groups of individuals, the most basic of which are the pairwise relatedness coefficients between any two individuals. There are nine pairwise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci. Although all nine coefficients can be estimated from pedigrees, six coefficients have been beyond empirical reach. We provide a numerical optimization procedure that estimates all seven reduced coefficients from population-genomic data. Simulations show that the procedure is nearly unbiased, even at 3× coverage, and errors in five of the seven coefficients are statistically uncorrelated. The remaining two coefficients have a negative correlation of errors, but their sum provides an unbiased assessment of the overall correlation of heterozygosity between two individuals. Application of these new methods to four populations of the freshwater crustacean Daphnia pulex reveal the occurrence of half siblings in our samples, as well as a number of identical individuals that are likely obligately asexual clone mates. Statistically significant negative estimates of these pairwise relat...Continue Reading

Citations

Jul 1, 1978·Annals of Human Genetics·B K SuarezT Reich
Jan 1, 1988·IMA Journal of Mathematics Applied in Medicine and Biology·Elizabeth A Thompson
Feb 1, 1983·Theoretical Population Biology·C C Cockerham, Bruce S Weir
Oct 1, 1995·Theoretical Population Biology·Y X Fu
Mar 21, 2000·American Journal of Human Genetics·M AbneyC Ober
Apr 25, 2006·Molecular Ecology·J Fernández, M A Toro
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Jun 22, 2010·Nature Genetics·Jian YangPeter M Visscher
Sep 30, 2010·Nature Reviews. Genetics·Joseph E PowellMichael E Goddard
Oct 12, 2010·Bioinformatics·Ani ManichaikulWei-Min Chen
Feb 5, 2011·Science·John K ColbourneJeffrey L Boore
Jul 25, 2013·Molecular Ecology·Sen XuMelania E Cristescu
Aug 21, 2013·Proceedings of the National Academy of Sciences of the United States of America·Abraham E TuckerMichael Lynch
Nov 19, 2014·Nature Reviews. Genetics·Doug Speed, David J Balding
Dec 5, 2014·PLoS Computational Biology·James F DentonMatthew W Hahn
Aug 1, 2015·Genetics·Takahiro Maruki, Michael Lynch
Sep 10, 2015·Molecular Biology and Evolution·Sen XuMichael Lynch
Jan 11, 2016·American Journal of Human Genetics·Matthew P ConomosTimothy A Thornton

Related Concepts

In Silico
Genome
Class crustacea
Genetics, Population
Daphnia pulex
Genetic Pedigree
Evaluation
Clone
Genomics
Sib Mating

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