Seascape Genomics of the Smooth Hammerhead Shark Sphyrna zygaena Reveals Regional Adaptive Clinal Variation

ABSTRACT Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains understudied compared to other members of the family Sphyrnidae. Despite its vulnerable status, a comprehensive understanding of its genetic landscape remains lacking in many regions worldwide. The present study aimed to conduct a fine‐scale genomic assessment of Sphyrna zygaena within the highly dynamic marine environment of South Africa's coastline, using thousands of single nucleotide polymorphisms (SNPs) derived from restriction site‐associated DNA sequencing (3RAD). A combination of differentiation‐based outlier detection methods and genotype‐environment association (GEA) analysis was employed in Sphyrna zygaena. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Among these, notable correlations between adaptive variation and sea‐surface dissolved oxygen and salinity were evident. Conversely, analysis of 111,243 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches. These results provide evidence for the presence of differential selection pressures within a limited spatial range, despite high gene flow implied by the selectively neutral dataset. This study offers notable insights regarding the potential impacts of genomic variation in response to fluctuating environmental conditions in the circumglobally distributed Sphyrna zygaena. The present study conducted a fine‐scale genomic assessment of the globally threatened smooth hammerhead shark Sphyrna zygaena, within the regional context of South Africa. The analysis of 3RAD‐seq derived SNPs revealed a distinctive genetic cline from south to east, with adaptive variation showing correlations with environmental factors such as sea‐surface dissolved oxygen and salinity. Interestingly, while neutral SNP markers indicated high gene flow and lack of regional population differentiation, the presence of differential selection pressures suggests the potential impact of genomic variation in response to changing environmental conditions in S. zygaena.