Measuring individual inbreeding in the age of genomics: Marker-based measures are better than pedigrees

Inbreeding (mating between relatives) can dramatically reduce the fitness of offspring by causing parts of the genome to be identical by descent. Thus, measuring individual inbreeding is crucial for ecology, evolution and conservation biology. We used computer simulations to test whether the realized proportion of the genome that is identical by descent (IBD_G) is predicted better by the pedigree inbreeding coefficient (F_P) or by genomic (marker-based) measures of inbreeding. Genomic estimators of IBD_G included the increase in individual homozygosity relative to mean Hardy-Weinberg expected homozygosity (F_H), and two measures (F_ROH and F_E) that use mapped genetic markers to estimate IBD_G. IBD_G was more strongly correlated with F_H, F_E and F_ROH than with F_P across a broad range of simulated scenarios when thousands of SNPs were used. For example, IBD_G was more strongly correlated with F_ROH, F_H and F_E (estimated with ≥10 000 SNPs) than with F_P (estimated with 20 generations of complete pedigree) in populations with a recent reduction in the effective populations size (from N_e = 500 to N_e =75). F_ROH, F_H and F_E generally explained >90% of the variance in IBD_G (among individuals) when 35 K or more SNPs were used. F_P explained <80% of the variation in IBD_G on average in all simulated scenarios, even when pedigrees included 20 generations. Our results demonstrate that IBD_G can be more precisely estimated with large numbers of genetic markers than with pedigrees. We encourage researchers to adopt genomic marker-based measures of IBD_G as thousands of loci can now be genotyped in any species.