Little sharks in a genomic world: A high-resolution view of population structure in the California horn shark ( Heterodontus francisci )

The California horn shark (Heterodontus francisci) is a small demersal elasmobranch distributed along Pacific coastlines from California to Mexico, including several nearshore islands. Previous analyses of mitochondrial control region (mtCR) variation indicated that island populations are genetically distinct from mainland populations, while little to no structure was detected along contiguous coastlines over much larger distances, suggesting that deep-water channels may act as barriers to dispersal. However, this interpretation was inconsistent with the lack of detectable differentiation between the northern Channel Islands and Santa Catalina Island, separated by nearly 100 km of deep, cold water. To reexamine patterns of population connectivity, we used ddRADseq to genotype 3953 nuclear SNP loci from 175 specimens sampled across the range of H. francisci. Analyses identified at least five genetically distinct population units and recovered strong differentiation between the northern Channel Islands and Santa Catalina Island, supporting the hypothesis that deep-water channels are an important driver of population structure in H. francisci at spatial scales as small as 20 km (FST ≥ 0.020). Shallow but extensive population structure was associated with geographic distance along the mainland Pacific coast, spanning more than 1200 km of shoreline (FST ≤ 0.013). Overall, our results demonstrate substantial population subdivision across the range of H. francisci and reduced genetic diversity within island populations. These findings highlight the importance of considering population structure in the conservation and management of diminutive demersal sharks and support the development of stock-specific management strategies.