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.

基于充分认知的溪流鱼类保护工作，需要深入理解自然过程与人为活动对遗传多样性的双重影响。溪红点鲑（Brook Trout, *Salvelinus fontinalis*）是原生分布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。该物种不仅曾遭受历史时期的人为干扰压力，当前与未来亦面临诸多生存威胁。在本项遗传分析中，研究团队采用简化代表性测序技术（ddRADseq），对宾夕法尼亚州阿巴拉契亚地区23条原生栖息有溪红点鲑的溪流中的63个个体进行了遗传特征解析。最终共得到2590个通过过滤标准的基因位点，其中53%的位点与主要溪流流域（萨斯奎哈纳流域或阿勒格尼流域；平均遗传分化系数FST=0.085）存在显著关联。将测序读段比对至大西洋鲑（Atlantic Salmon, *Salmo salar*）基因组后，未发现跨流域高FST值在特定基因组区域存在聚集现象。研究同时在各流域内部检测到了遗传异质性证据。以观测杂合度为因变量、地理与环境特征为自变量的逐步回归分析显示，流域类型与流域有效面积是各溪流内溪红点鲑观测杂合度的显著预测因子。自然特征（如瀑布与主要流域）以及水坝和酸性矿山排水的影响，均已造成栖息地碎片化，并塑造了宾夕法尼亚州阿巴拉契亚地区溪红点鲑种群的遗传多样性格局，整体表明该物种对工业化程度加剧具有较高的脆弱性。