Multispecies site occupancy modelling and study design for spatially replicated environmental DNA metabarcoding
Multispecies site occupancy modelling and study design for spatially replicated environmental DNA metabarcoding
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DOI：
10.1111/2041-210x.13732
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发表时间：
2021-10-16
影响因子：
6.6
通讯作者：
Kadoya, Taku
中科院分区：
文献类型：
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作者：
Fukaya, Keiichi;Kondo, Natsuko Ito;Kadoya, Taku
环境 DNA (eDNA) 元条形码已广泛应用于以非侵入性且经济高效的方式衡量生物多样性。然而，由于多种因素可能导致固有的多阶段工作流程中出现假阴性，因此使用 eDNA 元条形码进行物种检测并不完善。 eDNA 元条形码多阶段工作流程中的不完美检测也提出了研究设计的问题，即如何在不同阶段之间分配可用资源以优化调查效率。在这里，我们提出了用于 eDNA 元条形码研究的多物种位点占用模型的变体，其中在感兴趣区域内的多个位点收集样本。与处理二进制检测数据的传统位点占用模型不同，该模型描述了序列读取的变化，即高通量测序仪的输出。它明确解释了 eDNA 元条形码和种间异质性的分层工作流程，并允许在工作流程的不同阶段分析物种可检测性的变异来源。我们还引入了贝叶斯决策分析框架，以确定在有限预算下优化物种检测有效性的研究设计。该模型在日本霞浦湖流域的淡水鱼类群落中的应用突显了物种可检测性的显着不均匀性，表明特定物种检测存在偏差的潜在风险。位点占用概率较低的物种往往难以检测，因为它们的捕获概率较低且序列读取较少。预测序列读数的预期丰度在物种之间变化高达 23.5 倍。对研究设计的分析表明，确保环境样本的多次现场复制是实现更高物种检测有效性的首选，前提是每次复制确保数以万计的序列读取。所提出的框架使eDNA元条形码的应用更具容错性，使生态学家能够更有效地监测生态群落。
Environmental DNA (eDNA) metabarcoding has become widely applied to gauge biodiversity in a non-invasive and cost-efficient manner. The detection of species using eDNA metabarcoding is, however, imperfect owing to various factors that can cause false negatives in the inherent multistage workflow. Imperfect detection in the multistage workflow of eDNA metabarcoding also raises an issue of study design, namely, how available resources should be allocated among the different stages to optimize survey efficiency. Here, we propose a variant of the multispecies site occupancy model for eDNA metabarcoding studies where samples are collected at multiple sites within a region of interest. Unlike traditional site occupancy models that deal with binary detection data, this model describes the variation in sequence reads, the output of the high-throughput sequencers. It explicitly accounts for the hierarchical workflow of eDNA metabarcoding and interspecific heterogeneity and allows the analysis of the sources of variation in the detectability of species throughout the different stages of the workflow. We also introduced a Bayesian decision analysis framework to identify the study design that optimizes the effectiveness of species detection with a limited budget. An application of the model to freshwater fish communities in the Lake Kasumigaura watershed, in Japan, highlighted a remarkable inhomogeneity in the detectability of species, indicating a potential risk of the biased detection of specific species. Species with lower site occupancy probabilities tended to be difficult to detect as they had lower capture probabilities and fewer sequence reads. The expected abundance of sequence reads was predicted to vary by up to 23.5 times among species. An analysis of the study design suggested that ensuring multiple within-site replications of the environmental samples is preferred to achieve higher species detection effectiveness, provided that tens of thousands of sequence reads were secured per replicate. The proposed framework makes the application of eDNA metabarcoding more error-tolerant, allowing ecologists to monitor ecological communities more efficiently.