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.

将全基因组核质分子数据（genome-wide cytonuclear molecular data）应用于不同时空尺度下的管理单元与适应性单元（management and adaptive units）鉴定，对于以小型局域种群为典型特征的过度捕捞大型掠食性生物而言尤为重要。尽管该物种被列为“近危（near threatened）”，目前对加拉帕戈斯真鲨（Carcharhinus galapagensis）的栖息地利用与种群结构的认知仍局限于其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（genome-wide Single Nucleotide Polymorphisms, 约7200个SNPs）与线粒体控制区序列（mitochondrial Control Region sequences, 947bp），评估了整个太平洋海域的种群结构与连通性。中性SNPs（neutral SNPs）至少界定出两个遗传分化的地理种群群：东热带太平洋种群群（涵盖墨西哥、加拉帕戈斯群岛东西两侧海域），以及中西太平洋种群群（涵盖豪勋爵岛、米德尔顿礁、诺福克岛、伊丽莎白礁、克马德克群岛、夏威夷海域与南非沿岸海域）。利用离群SNPs（outlier SNPs）则提示存在更精细的种群结构，可划分为西太平洋、夏威夷、墨西哥与加拉帕戈斯四个种群群。线粒体DNA（mitochondrial DNA, mtDNA）的成对ΦST统计量一致界定出三个区域种群群：东太平洋、中太平洋与西太平洋。与中性SNPs的FST统计量（FST=0.023~0.035）相比，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（Eastern Pacific Barrier）长期以来阻隔东太平洋与中西太平洋种群基因交流的结论相符。夏威夷种群与南非沿岸种群均聚类于西太平洋支系中。东、西太平洋种群的有效种群大小处于中等至较高水平（分别为738与3421）。本研究通过在该物种的太平洋分布范围内划定3~4个保护单元，对其生物学特性、种群连通性、遗传多样性与种群人口统计学特征的解析，可为该物种的优化保护工作提供科学依据。落实此类保护管理策略或具挑战性，但对于实现大洋盆地与区域尺度下的种群韧性维持而言至关重要。