3.2 | Population and phylogenomic structure
Principal component analyses (PCAs) revealed four major clusters corresponding to the NAL and BEL as well as Peary and Greenland clusters (Figure 3a). For the former two groupings, North America and Beringia, the genome clustering did not conform to current subspecies or ecotype designations. Specifically, in the North American cluster, some caribou populations of the woodland subspecies grouped consistently, i.e. boreal caribou and eastern migratory caribou, but mountain caribou grouped with Beringian lineages. The Beringian cluster contained barrenground, Grant’s, northern mountain, southern mountain, and Northwest Territory boreal caribou (Figure 3a) consistent with their PSMC demographic history. These lineages provide evidence of the parallel evolution of similar ecotypes from distinct lineages and histories.
Finer resolution PCA of the NAL caribou showed all four boreal caribou were separated, particularly Ignace which may be due to genetic drift as it has a high inbreeding co-efficient (Table S1; Figure 3b). Eastern migratory caribou from Ontario/Manitoba clustered closest to Manitoba boreal caribou although all were well separated (Figure 3b). Eastern migratory caribou from Quebec/Labrador were closest to Cochrane boreal and not eastern migratory caribou from Ontario/Manitoba, and so indicates similar ecotypes may have evolved in parallel (Figure 3b; Table S1). Fine scale analysis of the BEL caribou, aside from Peary and Western Greenland, showed the Inner Mongolian reindeer and northern mountain caribou from Itcha-Ilgachuz separating, which again may be due to drift and inbreeding (Table S1; Figure 3c). Southern mountain caribou from Columbia North are also relatively well separated. The rest all formed a relatively tight cluster, with the Northwest Territories boreal caribou and the Grant’s caribou slightly separated (Figure 3c). We ran the 14 genomes that sat closely together in another PCA, and found the four barrenground caribou clustered together and the others to separate, especially the Northwest Territories boreal (Figure 3d).
Phylogenomic reconstruction using SNPs in RAxML (Figure 4) and conserved gene sequences from BUSCO (Figure 5), showed similar patterns. Both separated the NAL lineage from all others and within the NAL clade eastern migratory caribou from Ontario/Manitoba and those from Quebec/Labrador were not reconstructed as sister groups, again indicating parallel evolution of the eastern migratory ecotype. In the SNP phylogeny, which has been rooted based on the BUSCO phylogeny (Figure 5) and the Treemix analysis with the Sitka deer (Figure S8), within the NAL clade eastern migratory caribou from Quebec are reconstructed as sister to boreal caribou from Ontario, whereas eastern migratory caribou from Ontario were placed as sister to boreal caribou from Manitoba which matches the geography of the sampling locations (Figure 1; Figure 4). Within the BEL clade, the boreal caribou from the Northwest Territories are reconstructed as basal to all others. The rest were split into two clades, one of these with Northern mountain caribou from Itcha-Ilgachuz and the southern mountain Columbia North caribou. The other clade was further split into two, with the northern mountain caribou from the Northwest Territories, Atlin, and Frog in one, and the other with the barrenground caribou from the Northwest Territories and Manitoba, Grant’s caribou, the Inner Mongolia reindeer, and Peary and Western Greenland caribou forming a sister clade within the group (Figure 4).
The BUSCO phylogeny shows similar patterns to the SNP reconstruction although with shorter branch lengths between groups and lower support of nodes which is unsurprising given that is was reconstructed from conserved mammalian genes. Within the NAL clade, boreal caribou from Snow Lake are basal to all others, and then eastern migratory caribou from Quebec are sister to boreal caribou from Cochrane in one clade, with the eastern migratory caribou from Ontario with boreal caribou from Ignace and The Pas in another (Figure 5). As with the SNP phylogeny, the Northwest Territories boreal and all mountain caribou sat within the BEL clade as further evidence for parallel evolution of the woodland ecotype. In the BEL clade, boreal caribou from the Northwest Territories and the reindeer are basal. There are three major clades within this group, one containing barrenground caribou from the Northwest Territories and Manitoba and the Western Greenland and Peary caribou as a sister group within that clade, one containing the northern mountain caribou from Itcha-Ilgachuz and southern mountain caribou from Columbia North, and another containing the Grant’s caribou and the rest of the northern mountain populations (Figure 5).