3.1 | Genome quality assessments and demographic
history
We sequenced 28 caribou genomes from across Canada and two caribou from
Greenland to high coverage (35.57 – 43.03X; Table S1) representing all
four subspecies and six Canadian Designatable Units (DUs; Figure 1 and
Table S1), and used an additional reindeer genome from a domesticated
animal in Inner Mongolia, sequenced by Li et al., (2019). Our caribou
genomes showed high quality and recovery of BUSCO genes in the assembly,
ranging from 92.7% to 93.1% of the more than 4,000 conserved genes
surveyed (Table S1), and missing data per individual was low at
0.3%-1.0% with the exception of the previously published reindeer
genome at 16.0% (Table S1).
A reconstruction of Rangifer demography over time using PSMC
indicated a major population size expansion starting approximately
100-200 kya with peak population sizes around the glacial interstitial
stage of a largely ice-free North America 120 kya (Figure 2a-b). This
timing corresponds to a divergence of lineages largely concordant with
the expansion and intra-specific diversification proposed by Banfield
(1961). These differential population trajectories correspond to
contemporary subspecies and ecotypes. The NAL and the Greenland caribou
have much lower population sizes than BEL caribou, including the boreal
caribou from the Northwest Territories, with Peary caribou being
intermediate to these groups (Figure 2a-b, Figure S6 for all plotted
together) consistent with an earlier divergence (Klütsch, Manseau,
Anderson, Sinkins, & Wilson, 2017). Population sizes for all caribou
lineages declined during the Wisconsin glaciation which lasted between
75-11 kya (Figure 2a-b), with the exception of the reindeer which has a
unique demographic trajectory likely as a result of domestication.
Contemporary inbreeding estimates varied greatly between different
individuals. For the North American caribou, they ranged from -0.009 to
0.311. They were highest for Greenland at 0.654, and the Inner Mongolia
reindeer also had an elevated co-efficient at 0.177, again reflecting
the origin of the latter as originating from a domesticated population
(Li et al., 2019; Table S1).