Inbreeding and demographic history of caribou (Rangifer tarandus) in western Canada inferred from genome-wide SNP data

Assessing genetic diversity is essential for conserving endangered populations, yet comprehensive genomic evaluations remain limited for many declining species. Here, we investigated inbreeding levels and effective population sizes (Ne) of caribou (Rangifer tarandus) in western Canada, where populations have experienced pronounced declines over the past centuries due to anthropogenic pressures and climate change. We analyzed 33,346 Single Nucleotide Polymorphisms (SNPs) from 759 individuals representing 45 subpopulations within six metapopulations to: (1) assess inbreeding using runs of homozygosity (ROHs), (2) estimate contemporary and historical Ne, and (3) evaluate relationships between census size (Nc), inbreeding, and Ne. Small and endangered subpopulations, predominantly in southern regions, generally exhibited high inbreeding (FROH > 0.1), although some larger populations also showed elevated levels. Most subpopulations displayed a mixture of short and long ROHs, indicating both ancient shared ancestry and recent inbreeding. Twelve subpopulations had Ne <50, and 28 subpopulations and all metapopulations had Ne < 500, suggesting compromised short-term viability and long-term adaptive potential. Nc significantly predicted inbreeding (R{superscript 2} = 0.25), whereas contemporary Ne did not. Historical Ne reconstructions revealed a north-to-south gradient in bottleneck timing: northern populations declined in [~]1700-1780, central populations in [~]1780-1860, and southern populations in [~]1860-1940, likely driven by sequential impacts of climate shifts and anthropogenic disturbances. Our findings identify at-risk populations requiring urgent genetic intervention and demonstrate that integrating inbreeding and Ne estimates provides a robust framework for caribou recovery and the management of fragmented wildlife populations.