3.3 | Patterns of introgression
To assess the contribution of admixture and introgression among lineages in positioning caribou lineages, we applied Treemix and f3, f4, and f4-ratio statistics. The Treemix phylogeny with no migration events gave a similar topology to the RAxML tree (Figure 6a). When visualising seven migration events, which shows the least standard error and has the highest delta m score (Figure S7), we see migration from the ancestor of Peary and Western Greenland into both Northwest Territories and Manitoba barrenground, and a migration even from the ancestor of the NAL lineage into southern mountain caribou (Figure 6b). The other migration events all occur within the NAL group, including into Snow Lake from an ancestral group, from the ancestor of Cochrane and Ignace into Eastern migratory Ontario, from Cochrane into an ancestor of Snow Lake and The Pas and Eastern migratory Ontario, and from Eastern migratory Quebec into Cochrane. The tree shows large drift parameters for those individuals with high inbreeding co-efficients (Table S1; Figure 6b).
The f3 results gave significant signatures of the genomes of eastern migratory caribou in Ontario/Manitoba resulting from admixture between NAL boreal caribou from Igance (our reference NAL genomes, see Methods) and barrenground as well as from other genomes from the BEL. The f4-ratio statistic shows the Ontario/Manitoba eastern migratory caribou genomes to be of 7% barrenground origin. In contrast, there were no negative f3 scores for eastern migratory caribou in Quebec/Labrador, including from barrenground, with no proportion of their genome of barrenground origin. These results indicate that the eastern migratory caribou from the two disjunct ranges have different demographic histories (see Supporting Information for all statistics). Given the f3 results, we used the f4 statistic to test for introgression between the disjunct eastern migratory caribou populations and found evidence for introgression from Quebec into Ontario/Manitoba eastern migratory but not the other way around (Supporting Information).
The f4 results did not show introgression from Northwest Territories boreal, southern mountain Columbia North or any northern mountain population into NAL boreal caribou (full results for these tests in Supporting Information). The f4 results showed signatures of introgression from the NAL boreal caribou into southern mountain Columbia North, with the f4-ratio statistic indicating that 13.3% of their genomes shows NAL boreal origin. However, we find no strong evidence of introgression from NAL boreal into any of the northern mountain caribou (Supporting Information). The f4 results do indicate strong signatures of introgression from the NAL boreal caribou into Northwest Territories boreal caribou, with the f4-ratio test suggesting that 16.2% of their genomes originates from the NAL boreal caribou, indicating the possibility of parallel evolution of the same ecotype by adaptive introgression (Supporting Information).
We also used average genome-wide fD and fDM statistics to estimate the proportion of the genome resulting from introgression, comparable to the f4-ratio scores, and we found the same trends although generally lower with the fDM statistic, likely because it is a conservative estimate (full results in Supporting Information). This analysis also gives results in sliding windows across the genome, and for all comparisons, the regions of introgression appeared spread out throughout the genome encompassing both neutral and functional sites (Figures S9-S14).
To investigate the possibility of adaptive introgression in the parallel evolution of the Northwest Territories boreal caribou, we looked at the most highly introgressed regions from the NAL boreal caribou with an fDM score of at least 0.2. We compared the results with all mountain populations as these are unlikely to have undergone adaptive introgression in the process of parallel evolution given that they have varying levels of introgression depending on distance from the boreal populations, with those closest to the Northwest Territories boreal caribou having negligible levels. We found 49 highly introgressed regions (fDM 0.2 or above) originating from the NAL into Northwest Territories boreal caribou. Within these regions there was a total of 118 genes, with an average of 2.46 genes per introgressed region (Supporting Information for regions and gene lists). In the southern mountain Columbia North population, which is closest geographically to the boreal populations out of our sample locations and has very similar overall levels of introgression as Northwest Territories boreal caribou, we find 64 comparable regions, containing 244 genes and an average of 3.81 genes per region. The northern mountain populations all have fewer of these large, highly introgressed regions as expected from their overall very low levels of introgression from NAL, however the few genomic regions which have introgressed do also contain numerous gene sequences (Itcha-Ilgachuz 14 regions with 39 genes and an average of 2.79 genes per region; Frog has 6 regions with 18 genes and an average of three genes per region; Atlin has 8 regions with 26 genes and an average 3.25 genes per region; Redstone has 9 regions with 44 genes and an average 4.89 genes per region; see Supporting Information for regions and gene lists).