4 | DISCUSSION
Genome sequences of 30 caribou from across North America provided a comprehensive dataset in a non-model terrestrial mammal species-at-risk. We had unprecedented power to reconstruct phylogenomic and demographic history and measure levels of introgression between ecotypes, and to investigate the potential role this introgression has played in parallel evolution. Our results are concordant with previous mtDNA studies (Cronin et al., 2005; Flagstad & Røed 2003; Klütsch et al., 2012; Klütsch et al., 2016; Weckworth et al., 2012) which found two major mitochondrial DNA phylogenetic lineages, NAL and BEL, which likely correspond to divergence within refugia during glacial cycles (Flagstad & Røed 2003; Weckworth et al., 2012). We also found Peary caribou to be genetically distinct from the others in the BEL lineage (Figure 3a), supporting previous evidence of an additional High Arctic refugium (Klütsch et al., 2017). Demographic reconstruction over time showed differential population trajectories of the lineages starting approximately 100-120 kya, indicating divergence to have started well before the Last Glacial Maximum (Figure 2a-b).