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).