Data from: Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers

The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being “near threatened”, current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide Single Nucleotide Polymorphisms (~7200 SNPs) and mitochondrial Control Region sequences (947bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise ΦST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (FST=0.023-0.035), mtDNA exhibited more divergence (ΦST=0.258-0.539) and high overall genetic diversity (h=0.794 ±0.014; π=0.004 ±0.000), consistent with the longstanding Eastern Pacific Barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.全基因组核质分子数据（cytonuclear molecular data）在不同时空尺度下划定管理单元与适应性单元的应用，对于过度捕捞的大型掠食性物种尤为关键——这类物种通常呈现小型局域种群的特征。尽管加拉帕戈斯真鲨（Carcharhinus galapagensis）被列为‘近危’物种，但目前对其栖息地利用与种群结构的认知仅局限于分布范围内的特定区域。本研究针对229个个体，利用全基因组单核苷酸多态性（Single Nucleotide Polymorphisms，简称SNPs，约7200个位点）与线粒体控制区序列（947bp），解析了太平洋全域的种群结构与连通性模式。中性SNPs至少界定出两个遗传分化显著的地理类群：东热带太平洋类群（涵盖墨西哥、加拉帕戈斯群岛东西两侧海域），以及中-西太平洋类群（包含豪勋爵岛、米德尔顿礁、诺福克岛、伊丽莎白礁、克马德克群岛、夏威夷群岛与南非海域种群）。异常位点SNPs则揭示了更为精细的种群结构：西太平洋、夏威夷、墨西哥与加拉帕戈斯种群各自为独立遗传单元。线粒体DNA（mtDNA）的成对ΦST分析同样得到一致结果，界定出三个区域种群：东太平洋、中太平洋与西太平洋种群。相较于中性SNPs（FST=0.023~0.035），线粒体DNA的遗传分化程度更高（ΦST=0.258~0.539），且整体遗传多样性水平较高（单倍型多样性h=0.794±0.014；核苷酸多样性π=0.004±0.000），这与东太平洋屏障这一长期公认的跨洋遗传阻隔格局相符，即东太平洋与中-西太平洋之间存在显著遗传分化。夏威夷种群与南非种群均归入西太平洋类群。东太平洋与西太平洋种群的有效种群规模处于中等至较高水平，分别为738与3421。本研究通过划定该物种在太平洋分布范围内的3~4个保护单元，解析了其生物学特性、种群连通性、遗传多样性与种群动态特征，可为该物种的优化保护工作提供科学依据。尽管落实此类保护管理策略仍面临挑战，但为实现流域与区域尺度下种群的长期存续与恢复力提升，这一举措必不可少。