Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual-based surveys. However, eDNA-based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling-theory methods to estimate species richness in under-sampled and hyper-diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the ‘Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower-bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies.

中文翻译：

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从超多样性区域的环境 DNA 估计扩展和隐藏的物种多样性

物种清单是我们评估生物多样性模式和人类影响的基石。然而，基于视觉观察的历史清单往往不完整，影响了随后对生态机制、灭绝风险和管理成功的分析。环境 DNA (eDNA) 元条形码是一种新兴工具，可以提供比经典的基于视觉的调查更广泛的生物多样性评估。然而，基于 eDNA 的清单仍然受到抽样工作和参考数据库不完整的限制。在这项研究中，我们提出了一个新的框架，将 eDNA 调查和抽样理论方法相结合，以估计样本不足和超多样化地区的物种丰富度，在这些地区，一些物种仍然没有出现在清单中或未被目视调查发现。我们将这个框架应用于珊瑚三角中心的沿海鱼类多样性，这是全球最丰富的海洋生物多样性热点。结合来自 279 个水下视觉普查、92 个 eDNA 样本和一个广泛的自定义遗传参考数据库的数据，我们表明 eDNA 元条形码记录了 196 个假定的水下视觉普查未检测到的物种，其中 37 个物种不在区域清单中。我们提供了 'Raja Ampat Bird's Head Peninsula' 生态区海洋鱼类的更新清单，其中包含 2534 种，包括 1761 种已确认和 773 种极可能存在的物种。基于稀有物种发生率的 Chao 下界多样性估计表明，该地区可能拥有额外的 123 种鱼类，包括远洋、隐底生物和脆弱物种。