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 were employed in Sphyrna zygaena. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Amongst 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.

Fin clip samples were obtained from KwaZulu-Natal Sharks Board’s bather protection program and the Reel Science Coalition, comprising of recreational anglers using rod and reel methods. To note, all samples were collected from juvenile S. zygaena (male PCL < 210 cm; female PCL < 250 cm; Table S1). Sampling occurred opportunistically between 2008 and 2021 along the south to east coast of South Africa (Table S1) across several coastal biogeographic zones (Potts et al., 2015). All sampling was conducted in full compliance with the necessary permits and ethical approval (Research Ethics, Animal Care and Use, #ACU-2021-21616) (Figure 1). Upon collection, all samples were stored in 95% ethanol for further processing. The collected samples were broadly categorized into nine sampling locations according to geographic region, namely: False Bay (FB; n = 2), Struisbaai (STR; n = 20), Witsand (WT; n = 2), Mossel Bay (MB; n = 22), Jeffrey’s Bay (JB; n = 8), Algoa Bay (AB; n = 5), southern KwaZulu-Natal (KZS; n = 21), central KwaZulu-Natal (KZC; n = 8), and northern KwaZulu-Natal (KZN; n = 7). Genomic DNA was isolated using a standard cetyltrimethylammonium bromide (CTAB) method (Sambrook and Russell, 2001), with the quality of DNA confirmed through gel electrophoresis (1% agarose), and the purity of samples assessed using a NanoDrop ND 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, USA). The quantification of the extracted total DNA was performed using a Qubit^TM dsDNA Quantification Assay Kit (Thermo Fisher Scientific, Waltham, USA).