Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania's Appalachian region

Informed conservation of stream fishes requires detailed understanding of the effects of both natural processes and anthropogenic activities on genetic diversity. Brook Trout Salvelinus fontinalis, a salmonid native to eastern North America, typically resides in cold, high-quality stream ecosystems. The species has not only faced historical anthropogenic pressures, but also confronts current and future pressures. In a genetic analysis we used a reduced representation sequencing method (ddRADseq) to characterize 63 individuals from 23 streams where Brook Trout are native in the Appalachian region of Pennsylvania. A total of 2,590 loci passed filtering criteria, and 53% displayed significant association with a major stream drainage basin (Susquehanna or Allegheny; mean FST = 0.085). Mapping of the sequencing reads to the Atlantic Salmon Salmo salar genome revealed no clustering of high interdrainage FST values to specific genome regions. Evidence for genetic heterogeneity within each drainage basin was also detected. Stepwise regression of observed heterozygosity against geographic and environmental features revealed that drainage basin and effective area of watersheds were significant predictors of observed heterozygosity of Brook Trout within streams. Natural features such as waterfalls and major drainage basin, as well as the effects of dams and acid-mine drainage have fragmented habitat and shaped genetic diversity within Brook Trout populations in the Appalachian region of Pennsylvania, overall indicating the vulnerability of this species to increased industrialization.对溪流鱼类开展科学化保护，需深入厘清自然过程与人为活动对其遗传多样性的影响机制。溪红点鲑（Brook Trout，*Salvelinus fontinalis*）是原产于北美东部的鲑科鱼类，通常栖息于寒冷且水质优良的溪流生态系统中。该物种不仅历经历史人为活动带来的生存压力，当前及未来亦面临多重威胁。本研究采用简化基因组测序技术（ddRADseq），对宾夕法尼亚州阿巴拉契亚地区23条原生栖有溪红点鲑的溪流中的63尾个体进行遗传特征解析。最终共有2590个基因位点通过过滤标准，其中53%的位点与主要溪流流域（萨斯奎汉纳流域或阿勒格尼流域）存在显著关联，平均遗传分化系数（FST）为0.085。将测序读段比对至大西洋鲑（Atlantic Salmon，*Salmo salar*）参考基因组后发现，流域间高FST值的基因位点并未在特定基因组区域发生聚集。同时，本研究还在各流域内部检测到了遗传异质性的相关证据。以观测杂合度为因变量，对地理与环境特征开展逐步回归分析，结果显示流域类型与流域有效面积是影响溪流内溪红点鲑观测杂合度的显著预测因子。诸如瀑布、主要流域等自然特征，以及水坝与酸性矿山排水等人为活动，均已造成宾夕法尼亚州阿巴拉契亚地区溪红点鲑种群的栖息地破碎化，并塑造了其种群内的遗传多样性格局，整体表明该物种对工业化程度加剧具有较高的脆弱性。