Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA.
U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, Corvallis, OR, USA.
Mol Ecol. 2021 Oct;30(20):4970-4990. doi: 10.1111/mec.15811. Epub 2021 Feb 17.
Genetic diversity underpins species conservation and management goals, and ultimately determines a species' ability to adapt. Using freshwater environmental DNA (eDNA) samples, we examined mitochondrial genetic diversity using multigene metabarcode sequence data from four Oncorhynchus species across 16 sites in Oregon and northern California. Our multigene metabarcode panel included targets commonly used in population genetic NADH dehydrogenase 2 (ND2), phylogenetic cytochrome c oxidase subunit 1 (COI) and eDNA (12S ribosomal DNA) screening. The ND2 locus showed the greatest within-species haplotype diversity for all species, followed by COI and then 12S rDNA for all species except Oncorhynchus kisutch. Sequences recovered for O. clarkii clarkii were either identical to, or one mutation different from, previously characterized haplotypes (95.3% and 4.5% of reads, respectively). The greatest diversity in O. c. clarkii was among coastal watersheds, and subsets of this diversity were shared with fish in inland watersheds. However, coastal streams and the Umpqua River watershed appear to harbour unique haplotypes. Sequences from O. mykiss revealed a disjunction between the Willamette watershed and southern watersheds suggesting divergent histories. We also identified similarities between populations in the northern Deschutes and southern Klamath watersheds, consistent with previously hypothesized connections between the two via inland basins. Oncorhynchus kisutch was only identified in coastal streams and the Klamath River watershed, with most diversity concentrated in the coastal Coquille watershed. Oncorhynchus tshawytscha was only observed at one site, but contained multiple haplotypes at each locus. The characterization of genetic diversity at multiple loci expands the knowledge gained from eDNA sampling and provides crucial information for conservation actions and genetic management.
遗传多样性是物种保护和管理目标的基础，最终决定了一个物种适应环境的能力。本研究利用淡水环境 DNA（eDNA）样本，通过多基因代谢条码序列数据，从俄勒冈州和加利福尼亚州北部的 16 个地点的四个 Oncorhynchus 物种中，研究了线粒体遗传多样性。本研究的多基因代谢条码面板包括在群体遗传 NADH 脱氢酶 2（ND2）、系统发育细胞色素 c 氧化酶亚基 1（COI）和 eDNA（12S 核糖体 DNA）筛选中常用的目标。在所有物种中，ND2 基因座的种内单倍型多样性最大，其次是 COI，然后是 12S rDNA，除了 Oncorhynchus kisutch 外。O. clarkii clarkii 的序列要么与先前描述的单倍型完全相同，要么相差一个突变（分别为 95.3%和 4.5%的读取序列）。O. c. clarkii 的多样性最大的是在沿海流域，这些多样性的子集与内陆流域的鱼类共享。然而，沿海溪流和厄姆夸河流域似乎拥有独特的单倍型。从 O. mykiss 中获得的序列揭示了威拉米特流域和南部流域之间的不连续性，表明历史上的分歧。我们还发现，北德舒斯和南克拉马斯流域的种群之间存在相似性，这与之前通过内陆盆地假设的两者之间的联系是一致的。O. kisutch 仅在沿海溪流和克拉马斯河流域被识别，大部分多样性集中在沿海的科奎尔流域。O. tshawytscha 仅在一个地点观察到，但在每个基因座都包含多个单倍型。多个基因座遗传多样性的特征增加了从 eDNA 采样中获得的知识，并为保护行动和遗传管理提供了关键信息。
