Mamoozadeh Nadya R, Whiteley Andrew R, Letcher Benjamin H, Kazyak David C, Tarsa Charlene, Meek Mariah H
Department of Integrative Biology, Program in Ecology, Evolution, and Behavior, Michigan State University, Michigan, East Lansing, USA.
W.A. Franke College of Forestry and Conservation, Wildlife Biology Program, University of Montana, Missoula, Montana, USA.
Mol Ecol Resour. 2023 Aug 16. doi: 10.1111/1755-0998.13853.
Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large-scale mechanisms affecting local conservation status and implementing large-scale biodiversity monitoring programmes. However, cross-scale surveys of genetic diversity are often impractical within single studies, and combining datasets to increase spatiotemporal coverage is frequently impeded by using different sets of molecular markers. Recently developed molecular tools make surveys based on standardized single-nucleotide polymorphism (SNP) panels more feasible than ever, but require existing genomic information. Here, we conduct the first survey of genome-wide SNPs across the native range of brook trout (Salvelinus fontinalis), a cold-adapted species that has been the focus of considerable conservation and management effort across eastern North America. Our dataset can be leveraged to easily design SNP panels that allow datasets to be combined for large-scale analyses. We performed restriction site-associated DNA sequencing for wild brook trout from 82 locations spanning much of the native range and domestic brook trout from 24 hatchery strains used in stocking efforts. We identified over 24,000 SNPs distributed throughout the brook trout genome. We explored the ability of these SNPs to resolve relationships across spatial scales, including population structure and hatchery admixture. Our dataset captures a wide spectrum of genetic diversity in native brook trout, offering a valuable resource for developing SNP panels. We highlight potential applications of this resource with the goal of increasing the integration of genomic information into decision-making for brook trout and other species of conservation or management concern.
了解遗传多样性如何在具有保护或管理意义的物种的时空尺度上分布，对于识别影响当地保护状况的大规模机制以及实施大规模生物多样性监测计划至关重要。然而，在单个研究中进行跨尺度的遗传多样性调查往往不切实际，而且由于使用不同的分子标记集，合并数据集以增加时空覆盖范围常常受到阻碍。最近开发的分子工具使基于标准化单核苷酸多态性（SNP）面板的调查比以往任何时候都更可行，但需要现有的基因组信息。在这里，我们对溪鳟（Salvelinus fontinalis）的原生范围内的全基因组SNP进行了首次调查，溪鳟是一种适应寒冷的物种，在北美东部一直是大量保护和管理工作的重点。我们的数据集可用于轻松设计SNP面板，以便将数据集合并用于大规模分析。我们对来自原生范围大部分地区的82个地点的野生溪鳟以及用于放流工作的24个孵化场品系的养殖溪鳟进行了限制性位点相关DNA测序。我们在溪鳟基因组中鉴定出超过24,000个SNP。我们探索了这些SNP在跨空间尺度解析关系的能力，包括种群结构和孵化场混合情况分析。我们的数据集捕捉了原生溪鳟广泛的遗传多样性，为开发SNP面板提供了宝贵资源。我们强调了这一资源的潜在应用，目标是将基因组信息更多地整合到溪鳟以及其他具有保护或管理意义的物种的决策中。
