Genomic analysis of population history for Hawaiian monk seals

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.