Toward a Genetic Management Framework: Population Genomics and Pedigree-Based Inference of Mating System Dynamics in the Endangered Hawaiian Monk Seal (Neomonachus schauinslandi)

Abstract

The Hawaiian monk seal (Neomonachus schauinslandi) is an endangered marine mammal endemic to the Hawaiian archipelago, with approximately 1,400 individuals remaining and exceptionally low genome-wide genetic diversity, largely due to a bottleneck associated with 19th-century hunting. Although intensive ecological management by the National Oceanic and Atmospheric Administration (NOAA) has supported recent population growth, no formal genetic monitoring program exists, and mating system dynamics, including the type of mating system along with potential inbreeding and sexual selection, remain unresolved. Because mating system dynamics can shape genetic diversity, effective population size (Ne), and therefore adaptive potential, they have important implications for species resilience in the face of natural and anthropogenic threats, including disease, habitat degradation, and climate change. I hypothesized that Hawaiian monk seals exhibit extremely low genetic diversity, weak island-level population structure, and an Ne trajectory consistent with the species’ demographic history. In terms of mating system dynamics, I hypothesized that the species exhibits mild polygyny consistent with closely related phocids, that recent active inbreeding is limited despite chronically small population size, and that offspring heterozygosity may exceed maternal heterozygosity if mate choice favors genetically diverse males. Using restriction site-associated DNA sequencing (RADseq) data from 112 individuals sampled across five Northwestern Hawaiian Islands (NWHI), I generated filtered SNP datasets optimized for pedigree-based and population genomic analyses. I used the R package SEQUOIA to reconstruct the first genomic pedigree for the species and validate parentage assignments against known mother-pup pairs; I then characterized relatedness, inbreeding, heterozygosity-based mate choice, population structure, and historical Ne. The pedigree correctly assigned 18 of 20 known mother-pup pairs, with the two unassigned pairs having low maternal genotyping rates, and identified two inferred sires, including one assigned to four offspring across multiple years and at least two confirmed dams. Island-level population structure was weak, genetic diversity was extremely low, and inbreeding coefficients approximated zero. Heterozygosity-based mate choice was not detected. These findings support mild polygyny or sequential monogamy rather than strict monogamy and establish a cost-effective genetic framework for integrating pedigree-based monitoring into Hawaiian monk seal conservation management.