4.1 | Parallel evolution and introgression in caribou
ecotypes
Our results confirm previous evidence that northern mountain and boreal
caribou from the Northwest Territories are within the BEL genomic
lineage, even though they are both currently within the woodland
subspecies, confirming that the woodland ecotype appears to have arisen
in parallel for both (Polfus et al., 2017). Our central mountain caribou
are also within the BEL genomic lineage, and this population has been
found to be highly admixed based on the two mtDNA lineages (McDevitt et
al., 2009). We found evidence for another, as yet undocumented, case of
parallel evolution within the eastern migratory ecotype. The eastern
migratory caribou from Ontario/Manitoba and those from Quebec/Labrador
are not sister groups (Figures 3b and 4) and have different demographic
and introgressive histories.
Recent studies are highlighting that introgression between lineages is
far more common than previously realised (Coates, Byrne, & Moritz,
2018; Hamilton & Miller, 2015), and the same appears to be true for
caribou with introgression likely playing a role in the evolution of the
ecotypes. We find more introgression between caribou from the different
lineages than anticipated, for example the barrenground caribou have
substantial introgression from the NAL. Introgression is also seen from
the NAL into the mountain caribou with an isolation by distance pattern,
with negligible levels of introgression into more northerly northern
mountain caribou. It thus seems unlikely that introgression drove the
parallel evolution of the woodland phenotype of the mountain caribou.
High levels of introgression coupled with the finding of many
introgressed genes makes a compelling case for parallel evolution
through adaptive introgression in the Northwest Territories boreal
caribou. However, when we compare the gene compliment of the most highly
introgressed regions in the Northwest Territories boreal caribou to
those found in the mountain caribou, we again find introgressed regions
spread across the genome including many genes, even though there are
fewer regions overall. There are a few explanations for this pattern,
including incomplete lineage sorting (ILS). ILS would be difficult to
exclude, especially given that they are closely related intra-specific
ecotypes (Lamichhaney et al., 2017). Whether these regions are a result
of ILS or introgression the high gene compliment suggests that they
could have persisted in the genome due to selection, even if they have
not been involved in the parallel evolution of phenotype, due to
filtration for maintenance of adaptive genome segments. Additionally,
when studying cases of adaptive introgression in inter-species
comparisons, areas of introgression are often restricted to single
genomic regions (Schweizer et al., 2018), however in intra-specific taxa
we may see larger introgressed regions persisting across the genome
because the fitness costs may be lessened. Fully teasing these patterns
apart in this case may be complicated because multiple processes are
likely acting in concert, including ILS and standing variation being
selected upon, coupled with differing levels of introgression as the
lineages have come into secondary contact. Additionally, given the PSMC
results it is possible that there have been multiple bouts of
introgression during glacial cycles over the last
~120,000 years as the lineages repeatedly came into
secondary contact. Demonstrating adaptive introgression is complicated
and requires the demonstration of the adaptive function of introgressed
regions, meaning most cases have thus far have been for well understood
traits or those controlled by a single locus (Taylor & Larson, 2019).
In contrast, investigating parallel evolution of ecotypes, which will
inevitably involve many functional regions, in a non-model species with
divergent intra-specific linages and complex demographic histories is a
difficult task.