Glacial history and landscape features shape the hierarchical population genetic structure of woodland caribou ( Rangifer tarandus caribou ) in western Canada

Caribou, listed as a species at risk across Canada, have experienced a wide range of evolutionary and selective pressures at multiple scales, from large-scale range shifts and recolonisations driven by glacial cycles to more localized contemporary habitat degradation and fragmentation. Given these multi-scale evolutionary forces, genetic variation and diversity are expected to be hierarchically structured. Characterising hierarchical population structure is crucial to understanding a species’ evolutionary history and informing effective conservation and management strategies. In this study, we analysed genomic diversity and variation in woodland caribou ( Rangifer tarandus caribou ) across western Canada using genotypes from ∼33,000 Single Nucleotide Polymorphism (SNP) loci from 759 geo-referenced individuals spanning 45 pre-defined subpopulations. We employed genetic clustering methods and measures of genetic differentiation to characterize hierarchical population structure in the region and tested for latitudinal changes in heterozygosity resulting from post-glacial recolonisation and hybridisation. Our results confirm that woodland caribou genetic diversity and differentiation occur at multiple hierarchical levels, reflecting post-glacial recolonisation patterns and landscape heterogeneity. Notably, the major genetic clusters identified in our study do not align with current conservation units for the species in this region. We also observe elevated heterozygosity in the mid-latitudes of the sampled range, indicative of hybridisation following secondary contact during post-glacial recolonisation. These findings underscore the need to consider and include genetic diversity at all hierarchical levels in conservation planning, as wide-ranging species often experience diverse and complex evolutionary histories and pressures.