Population genetics of caribou in the Alaska-Yukon border region: implications for designation of conservation units and small herd persistence

Better knowledge of genetic relationships between the Fortymile caribou
herd and its neighbors is needed for conservation decision-making in
Canada. Here, we contribute the first fine-scale analysis of genetic
population structure in nine contiguous caribou herds at the geographic
boundaries between Barren-ground and Northern Mountain caribou, and at the
Alaska-Yukon border. Using pairwise differentiation metrics, STRUCTURE,
and discriminant analysis of principal components (DAPC) to analyze 15
microsatellite loci in 379 caribou, we found complex patterns of genetic
differentiation. The Fortymile was the only herd assigned to more than one
genetic cluster, indicative of its history as a larger herd whose range
expansions and gene flow to other herds were likely important to
maintaining diversity across a functioning genetic metapopulation. Some
small herds (Chisana, Klaza, and White Mountains) were genetically
distinct, while others (Hart River, Clear Creek, Mentasta) exhibited
little differentiation from herds they occasionally overlap, including
herds assigned to different conservation units (DUs). This genetic
connectivity does not result from demographic connectivity, as episodic
contact during rut, rather than herd switching, is the likely mechanism.
Unusually, one small herd (White Mountains) maintained genetic
differentiation despite rut overlap with Fortymile. Our data reveal that
some herds with different ecological and behavioral attributes are
demographically independent but nonetheless genetically connected. Thus,
we suggest that managing caribou for an appropriate level of genetic
connectivity, while also supporting herd persistence, will be essential to
conserve caribou genetic diversity in the region.