Data from: Spatial and temporal genetic structure of a river-resident Atlantic salmon (Salmo salar) after millennia of isolation

The river-resident Salmo salar (“småblank”) has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (FST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size Ne of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005–2008) compared with historical samples (1955–56 and 1978–79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta-population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important.

栖息于河流的大西洋鲑（Salmo salar，挪威语俗称“småblank”）在挪威南姆森河上游已与其他大西洋鲑种群隔离长达9500年，是欧洲唯一一种全程生命周期均在河流内完成的大西洋鲑种群。过去六十余年间的水电开发活动不仅设置了洄游障碍，还将该河流超50%的栖息地改造为静水环境。基于微卫星（microsatellites）与单核苷酸多态性（SNPs）的分析结果显示，småblank种群内的遗传变异仅为同河流内溯河洄游型大西洋鲑的约50%；二者间的遗传分化指数（FST）为0.24，这一水平与欧洲和北美两地溯河大西洋鲑之间的遗传分化程度相当。微卫星分析鉴定出småblank内部存在3个遗传亚种群，每个亚种群的有效种群大小（Ne）仅为数百个个体。与历史样本（1955—1956年、1978—1979年）相比，2005—2008年的当代样本未表现出杂合度与等位基因丰富度下降的迹象，但不同采样点之间的遗传分化程度随时间推移有所降低。单核苷酸多态性数据验证了småblank的亚种群分化现象，并揭示出亚种群间存在下游定向的不对称基因流。尽管存在此类基因流，下游区域的遗传变异并未高于上游区域。småblank的集合种群（meta-population）结构或许比单一泛交种群更能维持遗传变异，前提是亚种群间的基因流得以保持。småblank是大西洋鲑中一类独特的特有岛屿型种群，因其栖息范围受限且受到多种人为活动影响，当前处境岌岌可危。因此，维持种群规模、避免栖息地进一步碎片化具有重要意义。