Environmental and Life Sciences Department, Trent University, Canada
Uncovering the evolutionary history of a species is important for management, for example the designation of conservation units. We also need to control for phylogenetic history when undertaking many analyses, for example in finding adaptive variation. However, processes such as introgression can mask the true evolutionary history making it difficult to infer. Caribou (Rangifer tarandus) in Canada are currently divided into 11 extant Designatable Units (DUs), all listed under the Federal Species At Risk Act. Genetic research is needed to refine these units as well as to enable the investigation of adaptive variation given environmental changes affecting caribou habitats. To achieve this, we assembled and annotated the first chromosome scale caribou reference genome with Dovetail Genomics, as well as 70 re-sequenced whole genomes from caribou across North America and Greenland, representing 9 of the 11 extant DUs. We reconstructed the phylogenomic history of each chromosome length scaffold, as well as sliding window analyses to determine how introgression has influenced reconstructions across the genome, and to uncover the evolutionary history of caribou ecotypes. We then use the annotated genes to test for genes under positive selection within the reconstructed lineages.
Our new genome assembly has an L90 of 30, with 99.5% of our genome assembly in 36 scaffolds, in line with other high quality chromosome scale assemblies in non-model organisms. Using this assembly, and our 70 re-sequenced genomes, we reconstructed whole chromosome phylogenies, which showed some overall consistent patterns between ecotypes. For example, caribou from the high Arctic consistently group together, as do the eastern migratory and boreal caribou from eastern Canada. However, we also revealed some topologies influenced by introgression, for example in the reconstruction of the evolutionary history of some northern mountain caribou. We find a number of genes under positive selection in caribou, including lineage specific genes, which indicates adaptive differences between our reconstructed intra-specific lineages. Our chromosome scale assembly is an invaluable resource for conservation genomic research. Coupled with the most in depth reconstruction of the evolutionary history of caribou representing nine of the DUs, our results will give vital knowledge for the refinement of these units as well as the baseline needed to study adaptive variation. Our approach to find the evolutionary history will potentially be useful in other species with high levels of introgression.