The Hawaiian monk seal, one of the world’s most endangered pinnipeds, has
faced decades of declines and been the focus of intensive conservation
efforts. A myriad of conservation threats has led to range-wide population
declines, but population trends among islands can vary widely in response
to heterogeneous threats. Populations in the Northwestern Hawaiian Islands
have been declining whereas Main Hawaiian Islands numbers are expanding.
Molecular data can provide information to disentangle population structure
and dynamics; however, previous studies have yielded insufficient
resolution in such a genetically depauperate species. Advances in genomic
technology and affordability offer a novel opportunity to revisit
questions about Hawaiian monk seal trends with high resolution markers
that provide better discrimination ability in low diversity species. Here,
we investigated region- and island-level population structuring and
connectivity. We used BestRAD sequencing on 169 seals from 14 islands that
span the archipelago to estimate genetic diversity, genetic
differentiation, population structure, and migration rates. We did not
find robust evidence for island-level population structure. For the first
time, our dataset provided resolution to differentiate regional
populations with low but significant genetic differentiation. Further,
DAPC analyses illustrated population structure with evidence for
connectivity, which mirrored our migration rate estimates. Future
conservation decisions will need to consider the balance of maintaining
connectivity between regions while not homogenizing and losing valuable
yet rare, regional unique variation.