Data from: Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive vs. neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring run offspring that returned in spring (spring run), and fall run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally-listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11 and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.

中性遗传标记（neutral genetic marker）通常被用于界定物种内需要开展独立管理的独特种群单元。然而，人类活动引发的基因流改变可能会削弱该方法的分辨效能。本研究在人工增殖与生境改变引发高基因流的背景下，比较了适应性遗传标记（adaptive genetic marker）与中性遗传标记区分时间分化型奇努克鲑（Oncorhynchus tshawytscha）洄游群体的效能。我们以美国加州费瑟河中的奇努克鲑为研究对象，选取7个推定的洄游时间相关基因与10个微卫星位点（microsatellite locus），对其3个洄游群体进行界定：秋季洄游孵化亲鱼的子代（成体秋季返回淡水，即秋季洄游型）、春季洄游型子代（成体春季返回淡水，即春季洄游型），以及春季返回的秋季洄游型子代（FRS）。研究发现，基于3个生物钟基因（circadian clock gene，OtsClock1b、OmyFbxw11及Omy1009UW）的序列分化，秋季洄游型与美国联邦列为受威胁物种的春季洄游型群体间存在显著遗传分化，而中性遗传标记未检测到该分化。因此，本研究证实了遗传标记选择在解析复杂生活史类型中的重要性。本研究结果直接影响保护管理策略，并补充了此前太平洋鲑与大西洋鲑相关研究的证据，表明生物钟基因可调控洄游时间。