Navigating the Murky Waters: Variation in Low Abundance Sequence Filtration in Fish eDNA Metabarcoding

Q1 Agricultural and Biological Sciences
Mariana Blanco, Brooke Walker, Mark Duchene, Rachel Morris, Lauren Weeks, Evelyn Denomme-Brown, Robert Hanner
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引用次数: 0

Abstract

Environmental DNA (eDNA) metabarcoding is a valuable tool for assessing fish communities and informing environmental management strategies. Well-defined and informed methodologies are necessary to increase the repeatability and accuracy of eDNA results. This review evaluates 87 fish eDNA metabarcoding studies with a focus on low abundance sequence filtration methods used. This study aims to reveal the variety of methodological approaches used in eDNA metabarcoding and to provide recommendations based on these findings. A rubric of 32 criteria was developed to standardize the evaluation process, focusing not only on low abundance sequence filtration methods, but also on the incorporation of replicates, controls, primer validations, data availability, and other best practice criteria. We found diverse approaches to low abundance sequence filtering which showed little justification for threshold selection. While most studies incorporated some form of negative control or replicate, their implementation and reporting were inconsistent. There was also limited use of positive controls and primer validation throughout the studies. We recommend the adoption of various practices: (1) increasing the use of controls and replicates, (2) providing rationale behind low abundance filtering criteria or omitting it entirely, (3) completing analyses to validate primers, (4) improving the completion and appropriate communication of methods and results, and (5) making raw sequence data publicly available. Refined methodologies in eDNA metabarcoding research are imperative to ensure the reproducibility and accuracy of fish community assessment and environmental management practices. This is especially important as this tool continues to integrate into conservation and management efforts.

Abstract Image

在浑浊的水域航行:鱼类eDNA元条形码中低丰度序列过滤的变化
环境DNA (eDNA)元条形码是评估鱼类群落和制定环境管理策略的重要工具。明确的和知情的方法是必要的,以提高可重复性和准确性的eDNA结果。本文综述了87项鱼类eDNA元条形码研究,重点介绍了采用的低丰度序列过滤方法。本研究旨在揭示用于eDNA元条形码的各种方法方法,并根据这些发现提出建议。制定了32项标准,以标准化评估过程,不仅关注低丰度序列过滤方法,还关注重复、对照、引物验证、数据可用性和其他最佳实践标准的结合。我们发现了不同的低丰度序列滤波方法,这些方法表明阈值选择的合理性很小。虽然大多数研究采用了某种形式的阴性对照或重复,但它们的实施和报告是不一致的。在整个研究中,阳性对照和引物验证的使用也很有限。我们建议采用各种做法:(1)增加对照和重复的使用,(2)提供低丰度过滤标准背后的理由或完全忽略它,(3)完成分析以验证引物,(4)改进方法和结果的完整性和适当的沟通,以及(5)公开原始序列数据。为了确保鱼类群落评估和环境管理实践的可重复性和准确性,精细化的eDNA元条形码研究方法势在必行。随着这一工具继续融入保护和管理工作,这一点尤为重要。
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来源期刊
Environmental DNA
Environmental DNA Agricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics
CiteScore
11.00
自引率
0.00%
发文量
99
审稿时长
16 weeks
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