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.科学开展溪流鱼类保护工作，需全面明晰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，多栖息于低温优质的溪流生态系统中。该物种不仅曾历经历史时期的人为活动胁迫，当前及未来仍面临多重生存压力。本研究采用简化代表性测序方法（reduced representation sequencing, ddRADseq），对采自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的63个个体进行遗传特征解析。最终共有2590个基因座（loci）通过过滤筛选，其中53%的基因座与两大主要溪流流域（萨斯奎汉纳流域与阿勒格尼流域）呈现显著关联，平均遗传分化指数FST=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，跨流域高FST值并未在特定基因组区域呈现聚集现象。本研究同时检测到各流域内部存在遗传异质性。以观测杂合度为因变量，地理与环境特征为自变量开展逐步回归分析，结果显示流域类型与流域有效面积是溪流内溪红点鲑观测杂合度的显著预测因子。瀑布、主要流域等自然特征，以及水坝与酸性矿山排水的影响，均已对宾夕法尼亚州阿巴拉契亚地区溪红点鲑种群的栖息地造成碎片化，并塑造了其种群内的遗传多样性；整体而言，这表明该物种对工业化程度加剧具有较高的脆弱性。