A new likelihood estimator and its comparison with moment estimators of individual genome-wide diversity

Abstract

The inbreeding coefficient of an individual, F, is one of the central parameters in population genetics theory. It has found important applications in evolutionary biology, conservation and ecology, such as the study of inbreeding depression. In the absence of detailed and reliable pedigree records, researchers have developed quite a few estimators to estimate F or the genome-wide homozygosity from genetic marker data. The statistical properties and comparative performances of these metrics are rarely known, however, which impedes an informed choice of the most appropriate one in practical applications. In this investigation, I propose a new likelihood F estimator that makes efficient use of marker information and takes into account of allelic dropouts, null alleles and prior knowledge of inbreeding. I compare the likelihood estimator with three moment estimators of F and three metrics of genomic homozygosity (or heterozygosity) by analysing both simulated and empirical datasets. It is shown that the likelihood estimator invariably outperforms the other estimators and metrics across all datasets analysed. For a typical dataset in heterozygosity-fitness correlation studies involving 10-20 microsatellites and 50 individuals, the correlation between the likelihood estimator and F (the simulated true inbreeding coefficient) is about 8B35% higher than that between the moment estimators and F. A frequently applied metric, multilocus heterozygosity (MLH), and an F estimator based on the consideration of the proportion of alleles in homozygous conditions, F R , are shown to have particularly poor performances. The low correlation between MLH and fitness traits, which is widely observed in numerous empirical studies, might be partially caused by the adoption of this inefficient estimator of genomic inbreeding.

Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene

“…Average relatedness ( r ) within and among leks was estimated with 1000 bootstrap replicates (C o A ncestry ; [39]). A contemporary likelihood approach was employed for the comparison of individual dyads against a third reference [40], with relatedness values [41] gauged as follows: unrelated ( r  = 0); second cousin ( r  = 0.063); first cousin ( r  = 0.125); half-sib ( r  = 0.25); parent/offspring or full-sib ( r  = 0.5).…”

Low incidence of inbreeding in a long-lived primate population isolated for 75 years

“…Various marker-based estimators have been used to investigate the genome-wide diversity of populations (Pemberton 2008; Wang 2011). We calculated three commonly used estimators of inbreeding: standardized heterozygosity (SH), internal relatedness (IR), and homozygosity by loci (HL) (Slate et al 2004; Charpentier et al 2005b; Overall et al 2005; Ruiz-López et al 2009) to evaluate their performance in comparison to F .…”

Reconstructing paternal genotypes to infer patterns of sperm storage and sexual selection in the hawksbill turtle

“…HL is the proportion of loci at which an individual is homozygous, weighting the contributions of loci by expected homozygosity, and is one of several metrics that better correlate with genome‐wide heterozygosity than simple mean heterozygosity of typed loci (see also Amos et al . ; Wang ; but see Chapman et al . ).…”