Seascape Genomics of Red Abalone: Limited Range-Wide Population Structure and Evidence for Local Adaptation

Abstract

Characterising patterns of genetic diversity including evidence of local adaptation is relevant for predicting and managing species recovering from overexploitation in the face of climate change. Red abalone (Haliotis rufescens) is a species of conservation concern due to recent declines from overharvesting, disease and climate change, resulting in the closure of commercial and recreational fisheries. Using whole-genome resequencing data from 23 populations spanning their entire range (southern Oregon, USA, to Baja California, MEX) we investigated patterns of population connectivity and genotype-environment associations that would reveal local adaptation across the mosaic of coastal environments that define the California Current System (CCS). We discovered high genetic diversity that is shared within and among populations, suggesting high historical range-wide gene flow. We found little evidence for large selective sweeps between populations that occupy local habitats that vary by pH, strength of upwelling, chlorophyll, salinity and sea surface temperature. This is consistent with a broad range of species with similar life histories that show limited neutral or adaptive genetic variation across the same region and the same environments, suggesting that the mosaic of environmental variation across the CCS is insufficient to drive local adaptation in the face of high gene flow for some broad-cast spawning species. Given the high genetic connectivity across their range, state-mandated regulatory actions would be most effective if aligned across jurisdictional boundaries (i.e., Mexico, California and Oregon).

Keywords: Haliotis rufescens; California conservation genomics project (CCGP); conservation genomics; local adaptation; population structure; red abalone.