Biodiversity conservation and management requires surveillance that captures the full spectrum of taxa. Here, we showcase the potential for a portfolio of visual, extractive, and molecular methods for detecting previously hidden components of tropical fish biodiversity in an economically and culturally valuable marine site that spans a tropical-temperate ecotone—the Ningaloo Coast World Heritage Area. With scale and practicality in mind, we demonstrate how environmental DNA (eDNA) methods deployed in a stratified sampling design can yield a more comprehensive monitoring program for species presence than current alternatives (e.g., extractive sampling via anesthetic). eDNA from filtered water samples detected up to six times as many cryptobenthic fish species per site than samples collected with anesthetic, indicating it is a potentially powerful tool for assessing biodiversity of tropical fishes. However, there were also species that were only found when using anesthetic and the contribution of cryptobenthic species to overall diversity of the fish assemblage was unexpectedly low, suggesting not all cryptobenthic fish species have been detected with eDNA. There were also distinct differences in cryptobenthic assemblages both among sites and sample depths (2–3 m) when using eDNA from filtered water, suggesting this technique may be able to identify fine scale spatial differences in cryptobenthic fish assemblage. eDNA collected from water detects the most cryptobenthic species and is therefore an efficient tool for rapidly assessing biodiversity, but extractive techniques may still be required for biological and monitoring studies, and when combined with eDNA sampling provides the most comprehensive assessment of cryptobenthic fishes.

中文翻译：

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隐秘的生物多样性：珊瑚礁鱼类调查的组合方法

生物多样性保护和管理需要监测来捕获所有类群。在这里，我们展示了一系列视觉、提取和分子方法的潜力，用于检测跨越热带温带生态交错带的具有经济和文化价值的海洋地点（宁加洛海岸世界遗产区）中以前隐藏的热带鱼类生物多样性成分。考虑到规模和实用性，我们展示了分层采样设计中部署的环境 DNA (eDNA) 方法如何能够比当前的替代方法（例如通过麻醉剂提取采样）产生更全面的物种存在监测计划。每个地点的过滤水样中的 eDNA 检测到的隐底栖鱼类种类数量是用麻醉剂收集的样品的六倍，这表明它是评估热带鱼类生物多样性的潜在强大工具。然而，也有一些物种仅在使用麻醉剂时才被发现，并且隐底栖物种对鱼类组合整体多样性的贡献出乎意料地低，这表明并非所有隐底栖鱼类物种都已被 eDNA 检测到。当使用过滤水中的 eDNA 时，不同地点和样本深度（2-3 m）的隐底栖鱼类组合也存在明显差异，表明该技术可能能够识别隐底栖鱼类组合的精细尺度空间差异。从水中收集的 eDNA 可检测最多的隐底栖物种，因此是快速评估生物多样性的有效工具，但生物和监测研究可能仍需要提取技术，并且与 eDNA 采样相结合可提供对隐底栖鱼类最全面的评估。