Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population‐level allele frequencies and estimates of the number of genetic contributors in an eDNA sample. Using a panel of microsatellite loci developed for the round goby (Neogobius melanostomus), we tested the similarity between eDNA‐based and individual tissue‐based estimates of allele frequencies from experimental mesocosms and in a field‐based trial. Subsequently, we used a likelihood‐based DNA mixture framework to estimate the number of unique genetic contributors in eDNA samples and in simulated mixtures of alleles. In both mesocosm and field samples, allele frequencies from eDNA were highly correlated with allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples. DNA mixture analyses were able to estimate the number of genetic contributors from mesocosm eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low‐frequency alleles. With this study we document the application of eDNA and multiple amplicon‐based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in eDNA samples. With proper validation, this approach has the potential to advance noninvasive survey methods to characterize populations and detect population‐level genetic diversity.

中文翻译：

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核eDNA估计实验中观和实地样本中的种群等位基因频率和丰度

环境DNA（eDNA）方法学的进步导致了在水生环境中检测物种和群落的能力的提高，但是大多数研究都通过针对线粒体基因组中的可变位点来强调物种一级的生物多样性。在这里，我们证明了eDNA方法还具有检测核基因组内种内多样性的能力，从而可以评估群体水平的等位基因频率并估计eDNA样品中遗传贡献者的数量。使用为圆形虾虎鱼（Neogobius melanostomus）开发的一组微卫星基因座），我们在实验和中场试验中测试了基于eDNA的等位基因频率与基于单个组织的等位基因频率估计之间的相似性。随后，我们使用了基于似然的DNA混合框架来估计eDNA样本和等位基因模拟混合物中独特的遗传贡献子的数量。在中观和野外样品中，来自eDNA的等位基因频率与来自基因型圆形虾虎鱼组织样品的等位基因频率高度相关，这表明可以从水样中可靠地扩增出核标记。DNA混合物分析能够估计中观eDNA样本的遗传贡献者数量以及多达58个个体的模拟DNA混合物，其正向或负向偏差的程度取决于低频等位基因的过滤方案。通过这项研究，我们记录了eDNA和多种基于扩增子的方法在获得种内核遗传信息并估计eDNA样品中某物种的绝对丰度中的应用。通过适当的验证，这种方法有可能推动非侵入性调查方法来表征种群并检测种群水平的遗传多样性。