Evidence‐based strategies to navigate complexity in dietary DNA metabarcoding: A reply
Evidence‐based strategies to navigate complexity in dietary DNA metabarcoding: A reply
复制标题
应对饮食 DNA 元条形码复杂性的基于证据的策略：答复
DOI：
10.1111/mec.16712
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发表时间：
2022
影响因子：
4.9
通讯作者：
Kartzinel, Tyler R.
中科院分区：
文献类型：
--
作者：
Littleford‐Colquhoun, Bethan L.;Sackett, Violet I.;Tulloss, Camille V.;Kartzinel, Tyler R.
消除饮食DNA元编码研究中出现的错误的低丰度序列显然是有益的，但清除所有低丰度序列可能会消除真实序列并使生态分析复杂化。我们先前的文献审查指出，DNA序列相对读取丰度(RRA)阈值可以帮助减少假阳性分类群的出现，但历史上对这一效用的强调加剧了对相关风险的不确定性，从而夸大了假阴性率(Littleford-Colquhoun等人，2022年)。为了解决这个问题，我们结合了一项模拟研究和一组经验数据，以说明这个问题，并为模拟研究和敏感性分析提供蓝图，以帮助调查人员避免过度纠正，从而增强对生态推断的信心。需要认识到丰度过滤的成本和好处，因为准确地描述饮食分布对于了解动物的饮食、营养和营养网络至关重要。我们论文的一篇评论强调了提高认识的必要性，强调了误导性的概念，即“物种之间的假阳性相互作用可能在网络生态中呈现根本不正确的网络结构，而假阴性将提供正确但不完整的网络版本”(Tercel&Cuff，(2022))。断言结果的可靠性将被假阳性侵蚀，但对真阳性的遗漏具有弹性，这是危险的，与证据背道而驰。不幸的是，丰度过滤方法引入假阴性的比率高于消除假阳性的比率，从而破坏了对原本可靠的测序数据的分析。过度纠正可能会从本质上改变并最终破坏生态解释。
It is clearly beneficial to eliminate low‐abundance sequences that arise in error during dietary DNA metabarcoding studies, but to purge all low‐abundance sequences is to risk eliminating real sequences and complicating ecological analyses. Our prior literature review noted that DNA sequence relative read abundance (RRA) thresholds can help ameliorate false‐positive taxon occurrences, but that historical emphasis on this utility has fostered uncertainty about the associated risk of inflating the false‐negative rate (Littleford‐Colquhoun et al., 2022). To address this, we combined a simulation study and an empirical data set to both illustrate the issue and provide blueprints for simulation studies and sensitivity analyses that can help investigators avoid overcorrecting and thereby bolster confidence in ecological inferences. Awareness of both the costs and the benefits of abundance‐filtering is needed because accurately characterizing dietary distributions can be critically important for understanding animal diets, nutrition and trophic networks. Highlighting the need to raise awareness, a critique of our paper emphasized the misleading notion that “false positive interactions between species can present fundamentally incorrect network structures in network ecology, whereas false negatives will provide a correct but incomplete version of the network” (Tercel & Cuff, 2022). Asserting that the reliability of results will be eroded by false positives but resilient to the omission of true positives is risky and runs counter to evidence. Unfortunately, abundance‐filtering methods can introduce false negatives at higher rates than they eliminate false positives and thereby undermine the analysis of otherwise reliable sequencing data. Overcorrecting can qualitatively alter and ultimately undermine ecological interpretations.
影响因子：
4.6
作者：
Kelly, Ryan P.;Shelton, Andrew Olaf;Gallego, Ramon
通讯作者：
Gallego, Ramon
饮食元条形码中数据管理的复杂认识论挑战：对 Littleford-Colquhoun 等人的“预防原则和饮食 DNA 元条形码：常用丰度阈值改变生态解释”的评论（2022）
影响因子：
4.9
作者：
M. P. Tercel;J. Cuff
通讯作者：
J. Cuff