Continent-wide phylogenomic framework reveals introgression as a driver of intra-specific diversity and enriched molecular pathways in caribou

Intra-specific diversification in the northern hemisphere is a recent phenomenon, particularly for vertebrates, due to climatic oscillations during the Quaternary. Caribou (Rangifer tarandus) are a recently diversified, keystone species in North America with a continental-wide distribution and a large amount of phenotypic variation. We assess patterns of intra-specific genetic variation and adaptive divergence, which are of critical interest to the fields of evolutionary biology and conservation. We characterized the relationship among caribou ecotypes and rapidly evolving genes among intra-specific lineages using phylogenomic analyses and a newly assembled chromosome-scale reference genome and 66 high-coverage genomes. Nine phylogenomic lineages showed different levels of introgression, with some lineages highly introgressed. Despite this, dN/dS ratios of all genes in the caribou genome (>30,000) identified 700-800 genes with significant signatures of positive selection in each lineage. These genes function in diverse pathways ranging from immune responses to circulatory systems, with the most enriched molecular pathways found in lineages with high levels of introgression. Glacial cycles and repeated introgression events between caribou lineages likely inflated both neutral and adaptive genetic variation: findings that are particularly timely given the importance of intra-specific diversity and adaptive variation in wild species for resilience to global change.