Whole-genome resequencing reveals exceptions to panmixia in the exploited top fish predator Antarctic toothfish ( <i>Dissostichus mawsoni</i> )

Abstract Antarctic toothfish ( Dissostichus mawsoni ) are a critical top fish predator in the Southern Ocean for whom a changing climate and fishing pressure challenge our understanding of their population dynamics. Their complex, long-lived life history presents challenges to understanding their population dynamics that we endeavor to overcome through the use of both reduced-representation sequencing and whole-genome resequencing data from fish across different cohorts. Our unique sample set allowed us to compare genomic structure, diversity, and demographic changes between cohorts born before and after the year 2000, when changes to fisheries management practices in the Southern Ocean reduced incidences of illegal, unreported, and unregulated fishing. While our population structure analyses corroborate recent studies showing panmixia across circumpolar populations of D. mawsoni , comparisons between cohorts revealed key exceptions. A lack of admixture in fish born before 2000 contrasted with widespread admixture among post-2000 individuals, consistent with increased mixing and/or genotype influx. Concernedly, genome-wide diversity declined over time in the Ross Sea (management area 88), with the significant losses observed in heterozygosity between pre-2000 and post-2000 cohorts. Elevated levels of inbreeding in the Ross Sea, coupled with evidence for recent population contraction from positive Tajima’s D values, provided potential explanations for the observed reductions in genomic diversity. Our results reconcile circumpolar panmixia with localized erosion of diversity and elevated inbreeding in the Ross Sea sector, underscoring the value of temporal monitoring and the need to prioritize future research on the interplay between fisheries pressure and environmental change in driving population dynamics and genomic structure in tootfhish.