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).