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.

本研究借助微卫星变异（microsatellite variation）分析手段，对弗雷泽河（Fraser River）与哥伦比亚河（Columbia River）流域内红鲑（Oncorhynchus nerka，俗称Sockeye Salmon）的三个生态型——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）的种群结构展开了系统解析，核心研究目标为探究弗雷泽河流域内的科卡尼鲑种群结构是否提示该生态型在该流域内具有单系（monophyletic）或多系（polyphyletic）起源。
研究团队对采自上述两个流域121个种群的海生型红鲑、湖栖型红鲑与科卡尼鲑，开展了14个微卫星位点的变异检测。所有种群与位点的遗传分化系数FST均值为0.087，单个位点的FST值分布范围为0.031至0.172。
以275个个体的生态型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（共检出203个等位基因），科卡尼鲑的等位基因数量最多（260个），湖栖型红鲑则处于中间水平（241个等位基因）。
邻接系统发育分析（neighbor-joining analysis）结果显示，源自哥伦比亚河流域（奥卡诺根湖、库特奈湖）、南汤普森河（弗雷泽河主要支流）流域种群以及弗雷泽河中游种群的科卡尼鲑种群聚为一支，表明上述区域的科卡尼鲑生态型为单系起源，这一结果大概率反映了末次冰期后从冰期避难所扩散的鲑鱼的起源模式。然而，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亲缘关系更为紧密，提示科卡尼鲑生态型是从湖栖型红鲑生态型独立演化而来的平行辐射事件。
整个弗雷泽河流域内的科卡尼鲑种群结构表明，该生态型在该流域内存在多系起源。仅采用地理限制的种群采样开展的研究，可能无法准确勾勒出鲑科（salmonid）鱼类生态型的系统发育历史。