Linking Measures of Inbreeding and Genetic Load to Demographic Histories Across Three Species of Bears

Abstract

Historic and contemporary demography affect deleterious variation and inbreeding depression, meaning that measuring genetic diversity alone does not capture the nuances of genetic erosion. Contrasting genomic signatures generated by long-term evolutionary processes to those generated by contemporary changes may help differentiate between populations more or less likely to persist with low diversity or high genetic load. To better understand these interactions, we examined signatures of inbreeding and genetic load across three species of bears: American black (Ursus americanus), brown (U. arctos), and polar (U. maritimus). We sampled across each species' geographic range to represent intraspecific variation in demographic history and ecology. We found that ROH burden often varied more among populations within lineages of species than between species. Admixed populations generally had higher heterozygosity and lower ROH burden; this pattern reversed in small, isolated populations. Greater diversity, including harmful variation, was found in larger, admixed populations—especially those with higher historical effective population sizes (N_E). However, this did not necessarily correspond to more realized genetic load. While polar bears had low N_E and low realized load, brown and American black bears exhibited less realized load as N_E increased and greater realized load in populations with recent bottlenecks and/or indications of recent consanguineous matings. This vantage offers insight into genetic health and threats of genetic erosion within populations and species, which can meaningfully contribute to assessments of threat status. In American black bears, the composite of these metrics revealed a trend in the Louisiana population that may be diagnostic for management intervention based on contemporary demographic changes. In brown bears, the Apennine bear consistently fell outside of the range of values in other populations, reinforcing previous descriptions of isolation, inbreeding, and purging in this population. In polar bears, there were no regional trends that warranted concern with respect to genetic erosion.