Sigsgaard Eva Egelyng, Jensen Mads Reinholdt, Winkelmann Inger Eleanor, Møller Peter Rask, Hansen Michael Møller, Thomsen Philip Francis
Department of Bioscience Aarhus University Aarhus C Denmark.
Natural History Museum of Denmark University of Copenhagen Copenhagen Ø Denmark.
Evol Appl. 2019 Nov 18;13(2):245-262. doi: 10.1111/eva.12882. eCollection 2020 Feb.
Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.
从水样中提取的环境DNA（eDNA）最近显示出作为水生大型生物群体遗传信息宝贵来源的潜力。与传统的基于组织的方法相比，这种方法具有几个潜在优势，包括eDNA采样是非侵入性的，而且通常成本效益更高。目前，eDNA方法仅限于线粒体DNA（mtDNA）的单标记研究，eDNA单倍型组成与真实单倍型组成之间的关系仍需彻底验证。这将需要测试生物信息学和统计软件，以校正错误序列以及相对序列丰度中的偏差和随机变异。然而，基于eDNA的群体遗传方法在基础研究和应用研究方面都具有深远的潜力。在本文中，我们简要概述了迄今为止基于eDNA的群体遗传学所取得的成就，并概述了该领域未来发展的前景，包括核DNA（nuDNA）变异和表观遗传信息的估计。我们讨论了与eDNA样本相对的个体组织样本所面临的挑战，并评估eDNA是否可能提供组织样本无法获得的其他类型信息。最后，我们提供了一些建议，以确定在不同的研究环境中eDNA方法是否是一个有用且合适的选择。我们的讨论主要限于当代水生系统，但这些优势、挑战和观点在很大程度上可以推广到具有不同时空重点的eDNA研究中。
