Whole genome analyses of the endangered Northern abalone (Haliotis kamtschatkana) reveal population differentiation and a genomic signature of a dramatic population decline

Despite widespread declines of many wildlife species, the effects of population decline on the genetic health and the recovery potential of affected species is still poorly understood, especially beyond a few charismatic species. The Northern abalone (or Pinto abalone; Haliotis kamtschatkana) is a marine gastropod mollusc of social, cultural and historical economic importance in the Pacific Northwest of North America that experienced a decline in population density due to commercial harvest and is currently listed as endangered in Canada under the Species at Risk Act. Previous genetic investigations based on microsatellites and reduced-representation approaches concluded that Northern abalone is panmictic throughout its range, from Alaska to California, and identified high levels of genetic variation with no indication of population decline. Using whole genome resequencing data from Northern abalone sampled across the northern part of the species range, we instead identified both: 1) significant differentiation between two genetic groups, albeit very concentrated in the genome; and 2) a strong signature of a dramatic population decline, without evidence of genetic inbreeding. Even though demographic reconstructions showed a timid signal of recent population expansion, the pervasive excess of rare alleles identified (including a high occurrence of singletons) may pose a genetic load risk, potentially hindering the species recovery. We also found evidence of historical, rather than current, connectivity throughout the area investigated. These results are important for management decisions and highlight the utility of whole genome data in conservation, especially in species with historically large effective population sizes like the Northern abalone.