Data from: The time of origin and genetic diversity of three isolated Kokanee populations in southwest Alaska

We examined the time of origin and genetic diversity of native kokanee, the nonanadromous ecotype of Sockeye Salmon Oncorhynchus nerka, from three isolated lakes in the Katmai National Park and Preserve in southwest Alaska. These kokanee evolved independently from Sockeye Salmon when migration barriers arose, blocking ocean access. We used information about the relative age of each barrier to hypothesize the relative time of origin for kokanee in each lake. In addition, we used data from 13 microsatellite loci to test our time of origin hypotheses and assess genetic diversity of kokanee from these three lakes and proximate Sockeye Salmon populations. Coalescent-based estimates of the time of origin for kokanee in Jo-Jo Lake (170 years before present [ybp]) and Devil’s Cove Lake (6,583 ybp) were consistent with the relative age of barriers isolating each lake. However, data from Dakavak Lake (1,379 ybp) suggested that the barrier was older than hypothesized. Indices of intrapopulation diversity were lower for kokanee than for Sockeye Salmon. Estimates for kokanee population divergence (RST; the FST analog for microsatellites) among the three lakes were consistent with time of origin estimates. Furthermore, the most recently isolated kokanee (Jo-Jo Lake population) were most closely related to neighboring Sockeye Salmon. Only the kokanee from Jo-Jo Lake exhibited a relatively low historical effective population size (Ne ≈ 107) and evidence of a genetic bottleneck. Taken together, the results of this study show that although rare, kokanee in Alaska are not ephemeral and can persist in isolation for hundreds of generations despite the colder temperatures and shorter growing season, that are thought to limit their sustainability in Alaska.

本研究针对阿拉斯加西南部卡特迈国家公园与自然保护区内三座隔离湖泊中的陆封型红大麻哈鱼（kokanee，即红大麻哈鱼（Sockeye Salmon，学名*Oncorhynchus nerka*）的非洄游生态型），探讨其起源时间与遗传多样性。当洄游障碍出现并阻断海洋洄游路径后，这些陆封型红大麻哈鱼便与洄游型红大麻哈鱼独立演化形成种群。我们依据各湖泊隔离屏障的相对形成时间，对三座湖泊内陆封型红大麻哈鱼的相对起源时间提出假说。此外，我们利用13个微卫星位点（microsatellite loci）的数据，对上述起源时间假说进行验证，并评估这三座湖泊中的陆封型红大麻哈鱼及邻近洄游型红大麻哈鱼种群的遗传多样性。基于溯祖理论的起源时间估计结果显示：乔乔湖（Jo-Jo Lake）的陆封型红大麻哈鱼起源于距今170年（ybp），魔鬼湾湖（Devil’s Cove Lake）的起源时间约为6583 ybp，该结果与各自湖泊隔离屏障的相对形成时间相符。但达卡瓦克湖（Dakavak Lake）的估计结果（距今1379 ybp）则表明，其隔离屏障的实际形成时间早于此前假说。陆封型红大麻哈鱼的种群内多样性指数低于洄游型红大麻哈鱼。三座湖泊间陆封型红大麻哈鱼的种群分化估计值（RST，即适用于微卫星数据的FST类似物）与起源时间估计结果一致。此外，隔离时间最晚的乔乔湖种群与邻近的洄游型红大麻哈鱼亲缘关系最近。仅乔乔湖的陆封型红大麻哈鱼表现出相对较低的历史有效种群大小（effective population size，Ne≈107）以及遗传瓶颈（genetic bottleneck）迹象。综合来看，本研究结果表明：尽管陆封型红大麻哈鱼在阿拉斯加较为罕见，但它们并非短暂存在的类群；即便面临阿拉斯加地区更低的水温与更短的生长季（这类环境通常被认为会限制其种群存续），它们仍可在隔离状态下存续数百代。