Environmental DNA metabarcoding in the Cape Fold aquatic ecoregion: Opportunities and challenges for eDNA uptake in an endemism hotspot

IF 2.8 2区生物学 Q2 ECOLOGY Freshwater Biology Pub Date : 2024-09-18 DOI:10.1111/fwb.14331

Alexander Van Nynatten, Rowshyra A. Castañeda, Albert Chakona, Nathan R. Lovejoy, Olaf L. F. Weyl, Nicholas E. Mandrak

引用次数: 0

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褶皱角水生生态区的环境 DNA 代谢编码：在一个地方性热点地区吸收 eDNA 的机遇与挑战

环境 DNA（eDNA）元编码有可能极大地改善淡水系统生物多样性的调查。然而，这种方法在全球特有物种热点地区仍很少使用，部分原因是 eDNA 代谢标码的成功有两大障碍：（1）公共参考序列数据库中的区域分类代表性不足；（2）与传统调查相比，物种发生率和丰度估计不一致。我们在南非开普福德水生生态区的两条河流的上游采集了 eDNA 样本并进行了目测调查。我们为鱼类的区域多样性建立了参考序列数据库，以改进特有物种的分类。我们还比较了每个采样点的 eDNA 代谢编码序列结果和目测调查（浮潜和水下摄像机）得出的鱼类发生率数据和相对丰度估计值的一致性。在没有补充当地特有物种参考序列数据库的情况下，仅有 1%的 eDNA 元条码读数可归类为鱼类物种。在补充了区域参考序列后，共检测到 9 个物种，99% 的读数被分类。使用 eDNA 和目测方法检测到的物种之间存在很强的正相关关系（Φ = 0.75）。然而，eDNA 代谢标码比目测方法检测到更多的物种。此外，在所调查的大多数小水池中，目测调查所观察到的相对读数频率与丰度存在显著相关性（R2 = 0.85-0.88, p <0.001）。不完整的公共参考序列数据库阻碍了 eDNA 代谢标码在高流行区的应用。本地参考序列库可以克服这些挑战。如果实施得当，eDNA 代谢标码将大有可为，其结果将与更常用且劳动密集型的目测调查一致或更好。目前迫切需要像 eDNA 代谢标定这样高效的调查方法来改善全球的水生生物监测工作。了解 eDNA 代谢标定测序结果与传统调查方法之间的关系是在高地方性生态区域实施该方法的关键一步。

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来源期刊

Freshwater Biology 生物-海洋与淡水生物学

CiteScore

5.90

自引率

3.70%

发文量

162

审稿时长

2 months

期刊介绍： Freshwater Biology publishes papers on all aspects of the ecology of inland waters, including rivers and lakes, ground waters, flood plains and other freshwater wetlands. We include studies of micro-organisms, algae, macrophytes, invertebrates, fish and other vertebrates, as well as those concerning whole systems and related physical and chemical aspects of the environment, provided that they have clear biological relevance. Studies may focus at any level in the ecological hierarchy from physiological ecology and animal behaviour, through population dynamics and evolutionary genetics, to community interactions, biogeography and ecosystem functioning. They may also be at any scale: from microhabitat to landscape, and continental to global. Preference is given to research, whether meta-analytical, experimental, theoretical or descriptive, highlighting causal (ecological) mechanisms from which clearly stated hypotheses are derived. Manuscripts with an experimental or conceptual flavour are particularly welcome, as are those or which integrate laboratory and field work, and studies from less well researched areas of the world. Priority is given to submissions that are likely to interest a wide range of readers. We encourage submission of papers well grounded in ecological theory that deal with issues related to the conservation and management of inland waters. Papers interpreting fundamental research in a way that makes clear its applied, strategic or socio-economic relevance are also welcome. Review articles (FRESHWATER BIOLOGY REVIEWS) and discussion papers (OPINION) are also invited: these enable authors to publish high-quality material outside the constraints of standard research papers.