DOI: 10.5061/dryad.931zcrjt8
title: Raw sequencing data (3RAD) for the smooth hammerhead shark Sphyrna zygaena

description: 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.
description: 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 <em>S. zygaena</em> (male PCL &lt;
 210 cm; female PCL &lt; 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<sup>TM</sup> dsDNA Quantification Assay Kit (Thermo
 Fisher Scientific, Waltham, USA).
description: # Regional population and seascape genomics of the smooth hammerhead shark
 *Sphyrna zygaena* reveals adaptive clinal variation despite high gene flow
 ##### Relevance Globally, hammerhead sharks have experienced severe
 declines owing to continued overexploitation and anthropogenic change.
 Specifically, the smooth hammerhead shark *Sphyrna zygaena*, as is
 evidenced from its listing as "Vulnerable" on the International
 Union of Conservation of Nature Red List, in addition to Appendix II of
 the Convention of International Trade in Endangered Species (CITES).
 Despite these concerns, *S. zygaena* remains comparatively understudied
 compared to other members of the family Sphyrnidae, with only one other
 regional population genetic analysis having been conducted in South
 Africa. Therefore, the present study sought to provide a fine-scale
 genomic assessment of the circumglobally distributed S. zygaena within the
 heterogeneous marine environment of the south to east coast of South
 Africa. Specifically, thousands of 3RAD-seq-derived single nucleotide
 polymorphisms (SNPs) were generated, aiming to elucidate the degree of
 subdivision of *S. zygaena* in this region and provide essential insights
 into the potential scale and relevant drivers of population subdivision. 
 ##### Data description A total of 95 *S. zygaena* samples were selected
 for genotyping following design 2 of the 3RAD-seq protocol (Bayona-Vásquez
 et al., 2019) and a detailed description of the library preparation
 protocol and laboratory procedures can be found in Klein et al. (2024).
 Samples were pooled with a 3RAD library from another project containing 96
 samples and underwent combined sequencing on a single flow cell.
 Sequencing was conducted using an Illumina NovaSeq 6000 platform
 ([https://emea.illumina.com/systems/sequencing-platforms/novaseq.html](https://emea.illumina.com/systems/sequencing-platforms/novaseq.html) at the Norwegian Sequencing Centre, Oslo, Norway. Here, all raw fastq files (forward and reverse sequencing files) are available.  **Files uploaded**: * SMO_3RAD-D2_Plate07_1_S1_L003_R1_001.fastq - SMO_3RAD-D2_Plate07_1_S1_L003_R2_001.fastq * SMO_3RAD-D2_Plate07_2_S2_L003_R1_001.fastq - SMO_3RAD-D2_Plate07_2_S2_L003_R2_001.fastq ##### Code/Software All code utilised for the processing of the abovementioned sequencing files, can be accessed from Github