Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains comparatively understudied compared to other members of the family Sphyrnidae, and despite its Vulnerable status, a comprehensive understanding of its genetic landscape remains lacking. 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 (OUTFlank and pcadapt) and Genotype-Environment Association (GEA) (Redundancy Analysis) analysis in Sphyrna zygaena were employed. 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, in addition to spatial factors were evident. Conversely, analysis of 110, 965 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches, including an assessment of isolation-by-distance (IBD) and isolation-by-environment (IBE), genetic clustering analyses (LEA, fastSTRUCTURE, and find.clusters), and a discriminant analysis of principal components (DAPC). 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 Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate areas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we characterized and compared eight complete mitochondrial genomes for five Gempylidae species [Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun] using Ion-Torrent sequencing. Using Bayesian Inference and Maximum-Likelihood tree search methods, we investigated the evolutionary relationships of seventeen Gempylidae species using mitogenome data. In addition, we estimate divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89 – 52.04 mya) million years ago; Gempylidae 1 [Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis], and Gempylidae 2 [Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus]. The present study demonstrates the superior performance of complete mitogenome data compared to individual genes in phylogenetic reconstruction. In addition to Cytochrome c oxidase subunit 1, NADH dehydrogenase subunit 2, and Cytochrome b, which are frequently employed in phylogenetic investigations, NADH dehydrogenase subunit 5 provided adequate resolving power. Analyses of selection pressure revealed purifying selection is predominant in Gempylidae mitogenomes. By including T. atun individuals from different regions we demonstrate the potential for the application of mitogenomes in species phylogeography.