Measuring American black bear genetic load in fixed structural variants and runs of homozygosity

Populations living in geographically isolated regions are expected to have reduced gene flow, increased genetic drift, and elevated levels of inbreeding, influencing both genetic load and possibly the distribution of structural variants. The American black bear (Ursus americanus) is widely found across Ontario, Canada, where populations inhabit diverse landscapes ranging from relatively intact contiguous forested landscapes to isolated regions such as the Saugeen Peninsula. Here, we investigated the population genomic history across five Ontario black bear populations using a combination of short-read (SR) and long-read (LR) sequencing data. We compared population genetic metrics including nucleotide diversity (π), Tajimas D, runs of homozygosity (ROH), and genome-wide structural variants (SVs) to assess population health and identify signatures of isolation. Our results showed that the isolated Saugeen Peninsula population is genetically distinct and exhibited reduced nucleotide diversity, greater ROH and SV abundance compared with mainland populations. The population also showed elevated genetic load in all genomic features, suggesting increased exposure of deleterious variation that are expressed in ROH and population specific SVs. We further discuss the integration of ROH, SVs and genetic load in conservation assessments.