Mutation and Recombination Rates in Free-Ranging Polar Bears

Mutation rate () and recombination rate (r) are fundamental population-genetic parameters, yet demographic and conservation inference in polar bears (Ursus maritimus) has relied on values borrowed from humans and other mammals. Known values vary by an order of magnitude across mammals, and inaccuracies in these estimates propagate into downstream analyses, such as inferences of demographic history. To address this, we used high-coverage whole-genome resequencing of eight parent-offspring trios from the Western Hudson Bay subpopulation of polar bears. We identified 329 de novo mutations and estimated a pedigree-based germline mutation rate of 1.22 x 10?? per site per generation, which is within the mammalian range and close to values previously assumed for this species. Trio-based phasing yielded 522 crossovers across 16 meioses (32.6 per meiosis), and a pedigree-inferred recombination rate of 1.50 cM/Mb. From 44 unrelated individuals sampled from the same subpopulation, we inferred a demography-aware recombination map with a length-weighted genome-wide recombination rate of 3.03 cM/Mb (median 1.28 cM/Mb). We also identified 8,515 recombination hotspot regions covering 2.10% of the genome, accounting for 43.8% of total map length, a 20.9-fold concentration. Crossovers overlapped LD-defined hotspots 5.06-fold more often than expected by chance (p < 0.001). Nucleotide diversity was low and positively rank-correlated with recombination rate, consistent with linked selection. Genomic features explained only ~3% of recombination rate variation, with GC content and SINE abundance the only significant predictors. These species-specific parameters provide an empirical foundation for future demographic reconstruction and population projection in this vulnerable, ice-obligate species.