Microhaplotype Methods Enable Relationship Inference in a Bottlenecked Mammalian Species

Genetic methods provide the ability to assess key aspects of population biology. Recent advances in high‐throughput, low‐cost DNA sequencing are providing opportunities to study species with limited genetic diversity. In particular, microhaplotype genetic markers have exponentially increased our ability to elucidate kin relationships and social structure through accurate pedigree reconstruction. Northern elephant seals ( Mirounga angustirostris ) have extraordinarily low genetic variation—among the most depauperate of any mammal species—making it challenging to discern familial relationships with genetic methods. Here, we describe the discovery of a panel of 122 microhaplotype markers for the species, validated by genotyping population samples with a standard amplicon‐sequencing approach. Additionally, we correctly assigned known mother‐offspring pairs with high confidence in the inferred relationships, successfully overcoming historical obstacles to the use of genetic tools for relationship inference in pedigree studies of northern elephant seals. This work enables key conservation questions to be addressed for this species and provides an example of how to advance understanding of the ecology, behavior, and reproduction of other mammals with very low genetic diversity.