Combining sampling gear to optimally inventory species highlights the efficiency of eDNA metabarcoding

Biodiversity surveys may require the use of multiple types of sampling gear to maximize the efficiency of species detections, yet few studies have investigated how to optimally distribute effort among gear. In this study, we conducted eDNA metabarcoding and capture-based sampling surveys (electrofishing, fyke netting, gillnetting, and seining) to sample fish species richness in a large northern temperate lake. We evaluated the success of the sampling methods individually and in combination to determine the allocation of effort and cost across sampling gear that provides the optimal approach for lake-wide species inventories. We found that eDNA metabarcoding detected more species than any other sampling method, including 11 species that were not detected with any capture-based approach. Optimal gear combination analyses revealed that detected species richness is maximized when most of the effort or budget is allocated to eDNA metabarcoding, with smaller allocations to seining and fyke ne..., See manuscript for a complete description of methods., All scripts used for bioinformatics, taxonomic assignments, and statistical analyses are available on GitHub: https://github.com/karaandres/Oneida_metabarcoding生物多样性调查通常需采用多种采样设备以最大化物种检出效率，但目前鲜有研究探讨如何在各类采样设备间最优分配调查投入。本研究针对一处大型北温带湖泊开展鱼类物种丰富度调查，采用环境DNA metabarcoding（eDNA metabarcoding）与捕获式采样法（包括电捕鱼法、折叠诱捕网法、刺网法及围网法）。本研究分别评估了各采样方法及其组合的效果，旨在明确各类采样设备的投入与成本分配方案，为全湖范围的物种调查提供最优策略。研究结果显示，环境DNA metabarcoding的物种检出量高于其余所有采样方法，其中包含11种未被任何捕获式采样法检出的鱼类。最优采样设备组合分析结果表明，当将大部分调查投入或预算分配至环境DNA metabarcoding，并将少量投入分配至围网法与折叠诱捕网法……完整方法描述详见手稿。本研究中用于生物信息学分析、物种分类注释及统计分析的全部代码均已上传至GitHub：https://github.com/karaandres/Oneida_metabarcoding