Data from: Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages

Population structure of three ecotypes of Oncorhynchus nerka (sea-type Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River and Columbia River drainages was examined with microsatellite variation, with the main focus as to whether Kokanee population structure within the Fraser River drainage suggested either a monophyletic or polyphyletic origin of the ecotype within the drainage. Variation at 14 microsatellite loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee sampled from 121 populations in the two river drainages. An index of genetic differentiation, FST, over all populations and loci was 0.087, with individual locus values ranging from 0.031 to 0.172. Standardized to an ecotype sample size of 275 individuals, the least genetically diverse ecotype was sea-type Sockeye Salmon with 203 alleles, whereas Kokanee displayed the greatest number of alleles (260 alleles), with lake-type Sockeye Salmon intermediate (241 alleles). Kokanee populations from the Columbia River drainage (Okanagan Lake, Kootenay Lake), the South Thompson River (a major Fraser River tributary) drainage populations, and the mid-Fraser River populations all clustered together in a neighbor-joining analysis, indicative of a monophyletic origin of the Kokanee ecotype in these regions, likely reflecting the origin of salmon radiating from a refuge after the last glaciation period. However, upstream of the mid-Fraser River populations, there were closer relationships between the lake-type Sockeye Salmon ecotype and the Kokanee ecotype, indicative of the Kokanee ecotype evolving independently from the lake-type Sockeye Salmon ecotype in parallel radiation. Kokanee population structure within the entire Fraser River drainage suggested a polyphyletic origin of the ecotype within the drainage. Studies employing geographically restricted population sampling may not outline accurately the phylogenetic history of salmonid ecotypes.本研究针对弗雷泽河（Fraser River）与哥伦比亚河（Columbia River）流域内3种生态型红大马哈鱼（Oncorhynchus nerka，即红鲑Sockeye Salmon）——海生型红鲑（sea-type Sockeye Salmon）、湖栖型红鲑（lake-type Sockeye Salmon）以及科卡尼鲑（Kokanee）的种群遗传结构，基于微卫星（microsatellite）遗传变异展开分析，核心研究目标为探究弗雷泽河流域内科卡尼鲑的种群结构是否支持该生态型在流域内的单系或多系起源假说。研究采集了两大河流流域内121个种群的海生型红鲑、湖栖型红鲑与科卡尼鲑样本，对14个微卫星位点的遗传变异进行了检测。所有种群与位点的平均遗传分化指数FST为0.087，单个位点的FST值范围为0.031至0.172。以275个个体的样本量为标准化基准，遗传多样性最低的生态型为海生型红鲑，共检测到203个等位基因；科卡尼鲑的等位基因数量最多，达260个；湖栖型红鲑则处于中间水平，为241个等位基因。邻接（neighbor-joining）系统发育聚类分析结果显示，哥伦比亚河流域（奥卡诺根湖、库特奈湖）的科卡尼鲑种群、弗雷泽河主要支流南汤普森河流域的科卡尼鲑种群，以及弗雷泽河中游种群均聚为同一分支，表明上述区域内的科卡尼鲑生态型具有单系起源，这大概率反映了末次冰期结束后，鲑鱼从避难所向外辐射扩散的演化历程。但在弗雷泽河中游种群上游区域，湖栖型红鲑生态型与科卡尼鲑生态型之间存在更近的亲缘关系，这提示科卡尼鲑生态型可能独立于湖栖型红鲑生态型发生了平行演化辐射。对整个弗雷泽河流域的科卡尼鲑种群结构进行分析后发现，该生态型在流域内整体呈现多系起源的特征。仅采用地理受限的种群采样开展的研究，可能无法准确还原鲑科鱼类生态型的系统发育历史。