The role of introgression and ecotypic parallelism in delineating
intra-specific conservation units
Abstract
Parallel evolution can occur through novel mutations, standing genetic
variation, or adaptive introgression. Uncovering parallelism and
introgressed populations can complicate management of threatened
species, particularly as admixed populations are not generally
considered under conservation legislations. We examined high coverage
whole-genome sequences of 30 caribou (Rangifer tarandus) from
across North America and Greenland, representing divergent
intra-specific lineages, to investigate parallelism and levels of
introgression contributing to the formation of ecotypes. Caribou are
split into four subspecies and 11 extant conservation units, known as
Designatable Units (DUs), in Canada. Using genomes from all four
subspecies and six DUs, we undertake demographic reconstruction and
confirm two previously inferred instances of parallel evolution in the
woodland subspecies and uncover an additional instance of parallelism of
the eastern migratory ecotype. Detailed investigations reveal
introgression in the woodland subspecies, with introgressed regions
found spread throughout the genomes encompassing both neutral and
functional sites. Our comprehensive investigations using whole genomes
highlight the difficulties in unequivocally demonstrating parallelism
through adaptive introgression in non-model species with complex
demographic histories, with standing variation and introgression both
potentially involved. Additionally, the impact of parallelism and
introgression on the designation of conservation units has not been
widely considered, and the caribou designations will need amending in
light of our results. Uncovering and decoupling parallelism and
differential patterns of introgression will become prevalent with the
availability of comprehensive genomic data from non-model species, and
we highlight the need to incorporate this into conservation unit
designations.