Data for manuscript "Minimal Introgression but Restricted Gene Flow: How Stocking and Dams Influence Wild Brook Trout (<i>Salvelinus fontinalis</i>) Genetics and Morphology"

<b>(A) Datasets</b>Here we share two datasets used in genomic and phenotypic analyses of Brook Trout populations in Rhode Island streams along with a sample information file:<b>(1) BT_All_popmap:</b> A file containing the list of all samples and their population of origin<b>(2) BT_ALL.vcf: </b>Contains genomic data of the full dataset (BT_All; 444 samples, 16,336 SNPs; in vcf format)<b>(3) CVAscores_AllSamples:</b> An excel file containing fish fork length and canonical variate scores of 251 samples used in the geometric-morphometric analysis.<b>(B) Abstract of the manuscript</b>1. Anthropogenic activities are increasingly influencing eco-evolutionary processes across spatial, temporal and biological scales. Freshwater ecosystems, harboring species which are important for subsistence, recreational and commercial fisheries, are particularly vulnerable. In North America, brook trout (<i>Salvelinus fontinalis</i>) populations have experienced widespread declines due to factors including habitat fragmentation and angling. To increase population densities and meet fishing demands, thousands of captive-bred individuals are released annually. Stocking, however, could lead to introgression of maladaptive genes into the wild population and in combination with the presence of dams, restricting gene flow, may reduce their evolutionary potential.2. Here, we sampled 495 fish from 14 inland and two coastal sites in the state of Rhode Island, USA and from two hatchery strains. We used quaddRAD to develop Single Nucleotide Polymorphism (SNP) markers and combined genetic and geometric-morphometric analyses to evaluate intraspecific variation, the consequences of stocking and test hypotheses, in a riverscape framework, on how dams influence gene flow.3. We found moderate genetic structure within streams with low levels of genetic diversity and effective population sizes but higher than the two hatchery strains. Importantly, we found no significant introgression from captive-bred individuals. However, we did detect isolation-by-distance and -by-resistance (due to dams) with evidence for upstream and downstream gene flow occurring mainly within catchments. Phenotypic differentiation also was apparent both between wild and hatchery brook trout, and even among streams, correlating with genetic distances.4. Our findings highlight the importance of fine-scale analyses in evaluating anthropogenic impacts and uncovering hidden intraspecific variation. Conservation efforts for wild brook trout populations, which harbor distinct genetic and phenotypic variation, will require careful attention, and our results will help inform management strategies across the species' range.Additional data and info can be found with the main manuscript.(A) 数据集 本研究共享两套用于罗德岛州溪流溪红点鲑（Brook Trout）种群基因组与表型分析的数据集，并附带一份样本信息文件： (1) BT_All_popmap：该文件包含所有样本及其来源种群的列表 (2) BT_ALL.vcf：包含完整数据集的基因组数据（对应BT_All数据集，共444个样本、16336个SNP位点，格式为VCF） (3) CVAscores_AllSamples：一份Excel文件，包含用于几何形态计量分析的251个样本的叉长与典范变量得分 (B) 论文摘要 1. 人为活动正日益影响不同空间、时间与生物尺度上的生态进化过程。淡水生态系统栖息着对生计、休闲与商业渔业具有重要价值的物种，因此尤为脆弱。在北美，溪红点鲑（Salvelinus fontinalis）种群因栖息地破碎化、垂钓等因素出现了大范围的种群衰退。为提升种群密度以满足渔业需求，每年都会放归数千尾人工繁育个体。然而，人工放流可能导致适应性不良的基因渐渗进入野生种群，加之水坝阻碍基因交流，可能进一步降低其进化潜力。 2. 本研究从美国罗德岛州的14个内陆位点与2个沿海位点，以及2个繁育系中采集了495尾溪红点鲑样本。研究采用quaddRAD技术开发单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，并结合遗传与几何形态计量分析，在河流景观框架下评估种内变异、人工放流的影响，同时验证关于水坝如何影响基因交流的相关假说。 3. 研究发现溪流内部存在中等程度的遗传结构，其遗传多样性与有效种群规模较低，但仍高于两个繁育系。值得注意的是，未检测到来自人工繁育个体的显著基因渐渗现象。不过，研究团队确实观测到了距离隔离与阻力隔离（由水坝导致）的现象，且有证据表明上下游的基因交流主要发生在流域内部。同时，野生与人工繁育溪红点鲑之间，甚至不同溪流之间均存在明显的表型分化，且与遗传距离存在相关性。 4. 本研究结果凸显了精细尺度分析在评估人为影响、揭示隐蔽种内变异方面的重要性。拥有独特遗传与表型变异的野生溪红点鲑种群，其保护工作需要得到细致关注，而本研究结果可为该物种分布范围内的管理策略制定提供参考。更多数据与信息可查阅主论文。