Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-offs in Resource-Limited Settings

Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics, and computational demands limit its broader use, particularly in resource-limited settings. We systematically evaluated multiple workflow components, including four DNA extraction methods, two primer sets, three Nanopore basecalling models, and two demultiplexing pipelines. Across 144 workflow combinations tested in an aquarium with 15 fish species, we mapped trade-offs between cost, sensitivity, and processing speed using a hierarchical Bayesian model to assess where time and resource savings are possible without compromising detection.

环境DNA（Environmental DNA, eDNA）分析可通过从微量遗传物质中检测生物体实现生物多样性监测，但高昂的试剂成本、冷链物流需求与计算资源负担限制了其更广泛的应用，尤其在资源匮乏地区。本研究系统评估了多组实验流程组件，涵盖4种DNA提取方法、2套引物组、3种Nanopore碱基识别模型以及2种解复用测序流程。研究团队在包含15种鱼类的水族箱环境中，对共计144种流程组合开展了测试，通过分层贝叶斯模型（hierarchical Bayesian model）量化了成本、检测灵敏度与处理速度之间的权衡关系，以评估在不降低检测性能的前提下，可实现时间与资源节约的优化路径。