Data from: Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos)

With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genomic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear SNPs and a mtDNA gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean we established that large oceanic distances represent barriers to gene flow, while genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia, differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in Western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.

Usage Notes
DArT_Loci_Information_(Momigliano_et_al_2017)Information on DArT loci genotyped in this study, including locus sequences for both alleles, read depth, genotype reproducibility and heterozygosity.Genotypes_of_All_Loci_Excluding_8_outliers_(Momigliano_et_al_2017)The file is in GenAlEx format, alleles coded as either "1" or "2". Individual and sampling location IDs are provided..Genotypes_Loci_from_Fst_Core_Distribution_(Momigliano_et_al_2017)Genotypes of all individuals for loci from the core distribution of Fst, i.e. excluding loci in the upper and lower 5% of the Fst distribution. This is the "neutral" dataset used in the manuscript for analyses of neutral genetic variation. The file is in GenAlEx format, alleles coded as either "1" or "2". Individual and sampling location IDs are provided.Genotypes_of_8_outlier_loci_(Momigliano_et_al_2017)Genotypes for all individuals for the eight outlier loci identified as potential targets of local selection. The file is in GenAlEx format, alleles coded as either "1" or "2". Individual and sampling location IDs are provided.

过度捕捞导致多个海洋生态系统中的海洋捕食者种群丰度大幅下降，解析基因组结构与局部适应（local adaptation）机制，可为海洋生物的可持续管理提供关键科学依据。尽管近年来分子生物学技术取得长足进步，但多数鲨鱼相关遗传研究仍仅采用少量中性标记来刻画其遗传结构。本研究依托5517个核单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点与1个线粒体DNA（mitochondrial DNA, mtDNA）基因，对灰礁鲨（*Carcharhinus amblyrhynchos*）的遗传结构模式进行解析，并检测其选择信号。研究样本采集自澳大利亚、印度尼西亚海域及印度洋大洋珊瑚礁群体，结果显示：大范围大洋距离构成了种群基因流的屏障，而大陆架海域的遗传分化则符合距离隔离模型。在澳大利亚与印度尼西亚海域，核SNP位点的遗传分化程度较弱，珊瑚礁充当踏脚石维持了长距离的种群连通性；而线粒体DNA的遗传分化更为显著，且在雌性个体中表现更强，提示灰礁鲨存在性别偏向的扩散行为。四项独立检测方法共鉴定出一批潜在受选择的基因组位点，表明澳大利亚东部灰礁鲨所经受的选择压力与西澳大利亚及印度尼西亚的种群存在显著差异。全位点平均遗传距离与异常位点（outlier loci）计算得到的遗传距离并无显著相关性，这一结果支持“两类数据集的遗传分化由不同演化过程驱动”的结论。这种异质性基因组分化模式暗示了局部适应的存在，对灰礁鲨的物种保护具有重要指导意义；此外，该研究还揭示，一类在中性位点上仅表现出微弱遗传分化的海洋物种，可能存在由局部选择驱动的隐秘遗传结构。

### 使用说明
1. **DArT_位点信息（Momigliano等人，2017）**：本研究中完成基因型分型的DArT（Diversity Arrays Technology）位点相关信息，包含两个等位基因的位点序列、测序读长深度、基因型重复性及杂合度数据。
2. **排除8个异常位点的所有位点基因型（Momigliano等人，2017）**：该文件采用GenAlEx格式存储，等位基因以"1"或"2"编码，文件中包含个体与采样地点的ID信息。
3. **基于Fst核心分布的位点基因型（Momigliano等人，2017）**：包含所有个体在Fst（遗传分化系数，Fixation Index）核心分布位点上的基因型，即剔除了Fst分布上下5%的极端位点。该数据集为本论文中中性遗传变异分析所用的“中性数据集”。文件采用GenAlEx格式存储，等位基因以"1"或"2"编码，文件中包含个体与采样地点的ID信息。
4. **8个异常位点的基因型（Momigliano等人，2017）**：包含所有个体在8个被鉴定为潜在局部选择靶标的异常位点上的基因型。文件采用GenAlEx格式存储，等位基因以"1"或"2"编码，文件中包含个体与采样地点的ID信息。