Thompson Tasha Q, O'Leary Shannon, O'Rourke Sean, Tarsa Charlene, Baerwald Melinda R, Goertler Pascale, Meek Mariah H
Michigan State University East Lansing Michigan USA.
Wild Salmon Center Portland Oregon USA.
Evol Appl. 2024 Jun 3;17(6):e13705. doi: 10.1111/eva.13705. eCollection 2024 Jun.
Intraspecific diversity plays a critical role in the resilience of Chinook salmon populations. California's Central Valley (CV) historically hosted one of the most diverse population complexes of Chinook salmon in the world. However, anthropogenic factors have dramatically decreased this diversity, with severe consequences for population resilience. Here we use next generation sequencing and an archive of thousands of tissue samples collected across two decades during the juvenile outmigration to evaluate phenotypic diversity between and within populations of CV Chinook salmon. To account for highly heterogeneous sample qualities in the archive dataset, we develop and test an approach for population and subpopulation assignments of CV Chinook salmon that allows inclusion of relatively low-quality samples while controlling error rates. We find significantly distinct outmigration timing and body size distributions for each population and subpopulation. Within the archive dataset, spring run individuals that assigned to the Mill and Deer Creeks subpopulation exhibited an earlier and broader outmigration distribution as well as larger body sizes than individuals that assigned to the Butte Creek subpopulation. Within the fall run population, individuals that assigned to the late-fall run subpopulation also exhibited an earlier and broader outmigration distribution and larger body sizes than other fall run fish in our dataset. These results highlight the importance of distinct subpopulations for maintaining remaining diversity in CV Chinook salmon, and demonstrates the power of genomics-based population assignments to aid the study and management of intraspecific diversity.
种内多样性在奇努克鲑鱼种群的恢复力中起着关键作用。加利福尼亚州的中央谷地（CV）历史上曾是世界上奇努克鲑鱼最多样化的种群复合体之一。然而，人为因素已大幅降低了这种多样性，对种群恢复力造成了严重后果。在这里，我们使用下一代测序技术以及在幼鱼洄游期间二十年间收集的数千个组织样本档案，来评估CV奇努克鲑鱼种群之间和种群内部的表型多样性。为了考虑档案数据集中高度异质的样本质量，我们开发并测试了一种用于CV奇努克鲑鱼种群和亚种群分配的方法，该方法允许纳入质量相对较低的样本，同时控制错误率。我们发现每个种群和亚种群的洄游时间和体型分布存在显著差异。在档案数据集中，被分配到米尔溪和鹿溪亚种群的春季洄游个体比被分配到巴特溪亚种群的个体表现出更早且更广泛的洄游分布以及更大的体型。在秋季洄游种群中，被分配到晚秋洄游亚种群的个体也比我们数据集中的其他秋季洄游鱼类表现出更早且更广泛的洄游分布以及更大的体型。这些结果凸显了不同亚种群对于维持CV奇努克鲑鱼剩余多样性的重要性，并证明了基于基因组学的种群分配在辅助种内多样性研究和管理方面的作用。
