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.

中文翻译：

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使用多基因 eDNA 元条形码估计太平洋鲑鱼和鳟鱼的遗传多样性

遗传多样性是物种保护和管理目标的基础，并最终决定了物种的适应能力。使用淡水环境 DNA (eDNA) 样本，我们使用来自俄勒冈州和加利福尼亚州北部 16 个地点的四种Oncorhynchus物种的多基因元条形码序列数据检查了线粒体遗传多样性。我们的多基因元条形码组包括常用于群体遗传 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) 筛选的靶标。ND2 基因座在所有物种中表现出最大的种内单倍型多样性，其次是 COI，然后是除Oncorhynchus kisutch之外的所有物种的 12S rDNA 。为O. clarkii clarkii恢复的序列与先前表征的单倍型相同或一个突变不同（分别为95.3％和4.5％的读数）。O. c.中最大的多样性。clarkii属于沿海流域，这种多样性的子集与内陆流域的鱼类共享。然而，沿海溪流和 Umpqua 河流域似乎拥有独特的单倍型。来自O. mykiss的序列揭示了威拉米特流域和南部流域之间的分离，表明了不同的历史。我们还确定了德舒特北部和克拉马斯南部流域人口之间的相似性，这与先前假设的两者之间通过内陆盆地的联系一致。鲇鱼仅在沿海溪流和克拉马斯河流域发现，大多数多样性集中在沿海科奎尔流域。Oncorhynchus tshawytscha仅在一个位点观察到，但在每个位点包含多个单倍型。多个位点的遗传多样性特征扩展了从 eDNA 采样中获得的知识，并为保护行动和遗传管理提供了重要信息。