Raw sequencing data (3RAD) for the smooth hammerhead shark Sphyrna zygaena

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..., 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 KwaZ..., , # Regional population and seascape genomics of the smooth hammerhead shark *Sphyrna zygaena* reveals adaptive clinal variation despite high gene flow

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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. Specif...

# 路氏双髻鲨（*Sphyrna zygaena）相关研究
全球范围内，双髻鲨科（Sphyrnidae）物种因持续过度捕捞及人为活动引发的环境改变，种群数量急剧下降。相较于双髻鲨科其他类群，路氏双髻鲨（*Sphyrna zygaena）的研究仍相对匮乏。尽管该物种已被列入国际自然保护联盟（International Union for Conservation of Nature, IUCN）红色名录列为易危（Vulnerable），且被纳入濒危野生动植物种国际贸易公约（Convention on International Trade in Endangered Species, CITES）附录II，但全球诸多区域仍缺乏对其遗传背景的全面认知。本研究旨在利用基于限制性酶切位点相关DNA测序（restriction site-associated DNA sequencing, 3RAD）获得的数千个单核苷酸多态性（single nucleotide polymorphisms, SNPs），对南非海岸线这一高度动态的海洋环境中的路氏双髻鲨开展精细尺度的基因组评估。本研究结合基于分化的异常位点检测方法与基因型-环境关联（genotype-environment association, GEA）分析手段，针对路氏双髻鲨展开研究。随后对推定适应性位点的后续分析揭示了一条清晰的南-东向遗传渐变群。其中，适应性变异与海面溶解氧之间存在显著关联……

本研究的鳍剪样本取自夸祖鲁-纳塔尔省鲨鱼委员会（KwaZulu-Natal Sharks Board）的泳者防护项目以及渔线科学联盟（Reel Science Coalition），后者由使用竿钓法的休闲垂钓者提供。需说明，所有样本均取自幼体路氏双髻鲨（雄性前尾长（precaudal length, PCL）<210cm，雌性PCL<250cm，详见表S1）。样本采集于2008年至2021年间，采用偶遇采样方式，覆盖南非南至东海岸的多个沿海生物地理分区（Potts等，2015），采样详情见表S1。所有采样工作均严格遵循相关许可及伦理审批要求（研究伦理、动物护理与使用许可，编号ACU-2021-21616），详见图1。样本采集后，所有样品均保存于95%乙醇中以待后续处理。采集的样本按地理区域大致划分为9个采样点，分别为：福尔斯湾（FB；n=2）、斯特鲁伊斯拜（STR；n=20）、维特桑德（WT；n=2）、莫塞尔湾（MB；n=22）、杰弗里湾（JB；n=8）、阿尔戈阿湾（AB；n=5）、南夸祖鲁……

# 路氏双髻鲨（*Sphyrna zygaena）的区域种群与海景基因组学研究揭示高基因流下的适应性渐变变异

## 研究意义
全球范围内，双髻鲨科物种因持续过度捕捞与人为活动导致的环境改变，种群数量急剧下降。具体而言，路氏双髻鲨已被列入国际自然保护联盟（IUCN）红色名录的易危等级，同时也被纳入濒危野生动植物种国际贸易公约（CITES）附录II。尽管存在这些保护关切，相较于双髻鲨科的其他物种，路氏双髻鲨的相关研究仍相对匮乏，目前南非境内仅开展过一项区域种群遗传分析。因此，本研究旨在对广泛分布于全球的路氏双髻鲨，在南非南至东海岸这一异质性海洋环境中开展精细尺度的基因组评估。具体……