Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data.
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 crustaceanDaphnia pulexreveal 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 relatedness coefficients, including inbreeding coefficients that were typically negative, underscore the difficulties that arise when interpreting genotypic correlations as estimations of the probability that alleles are identical by descent.
Department of Biology, Indiana University, Bloomington, Indiana 47405 matthew.s.ackerman@gmail.com.
Matthew S
0000-0002-4177-4681
MS
Ackerman
Department of Biology, Indiana University, Bloomington, Indiana 47405.
Parul
P
Johri
Department of Biology, Indiana University, Bloomington, Indiana 47405.
Ken
0000-0003-4289-6637
K
Spitze
Department of Biology, University of Texas Arlington, Texas 76019.
Sen
0000-0002-1304-9968
S
Xu
Department of Biology, Indiana University, Bloomington, Indiana 47405.|National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47405.
Thomas G
0000-0001-5487-553X
TG
Doak
Department of Biology, Indiana University, Bloomington, Indiana 47405.
Kimberly
K
Young
Department of Biology, Indiana University, Bloomington, Indiana 47405.
Michael
M
Lynch
D000483:Alleles; D000818:Animals; D003198:Computer Simulation; D003621:Daphnia / Q000235:genetics; D005828:Genetics, Population; D005838:Genotype; D006579:Heterozygote; D007178:Inbreeding; D008957:Models, Genetic
coancestry; identity by descent; population genomics; population structure; relatedness