Data from: The importance of standardization for biodiversity comparisons: a case study using Autonomous Reef Monitoring Structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French Polynesia

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data. Illustrating the ability of ARMS-based metabarcoding to capture a wide spectrum of biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine metazoan phyla, were detected from 3 ARMS (2.607 m2 area) collected on coral reefs in Mo'orea, French Polynesia. Significant differences were found between processing and preservation methods, demonstrating the need to standardize methods for biodiversity comparisons. We recommend the use of a standardized protocol (NOAA method) combined with DMSO preservation of tissues for sessile macroorganisms because it gave a more accurate representation of the underlying communities, is cost effective and removes chemical restrictions associated with sample transportation. We found that sequences identified at ? 97% similarity increased more than 7-fold (5.1% to 38.6%) using a geographically local barcode inventory, highlighting the importance of local species inventories. Phylogenetic approaches that assign higher taxonomic ranks accrued phylum identification errors (9.7%) due to sparse taxonomic coverage of the understudied cryptic coral reef community in public databases. However, a ? 85% sequence identity cut-off provided more accurate results (0.7% errors) and enabled phylum level identifications of 86.3% of the sequence reads. With over 1600 ARMS deployed, standardizing methods and improving databases are imperative to provide unprecedented global baseline assessments of understudied cryptic marine species in a rapidly changing world.

随着宏条形码技术（metabarcoding）的发展、高通量测序（high-throughput sequencing）成本的下降，以及诸如自主礁体监测装置（autonomous reef monitoring structures，ARMS）这类系统化采样设备的进步，研究人员已能够从隐秘海洋群落中获取海量的多样性数据。然而，若在区域乃至全球尺度下用于研究此类群落的方法未实现标准化，这种检测能力的提升也会带来分析层面的挑战。本研究针对基于细胞色素c氧化酶I（cytochrome c oxidase I）宏条形码数据的多样性评估工作，对比并评估了四种ARMS野外处理方法、保存介质以及当前主流生物信息学流程所潜藏的偏差。为验证基于ARMS的宏条形码技术可捕获广泛的生物多样性，研究团队从法属波利尼西亚莫雷阿岛珊瑚礁采集的3组ARMS样本（总面积2.607平方米）中，共检测到3372个操作分类单元（Operational Taxonomic Units，OTUs）以及28个门类，其中涵盖33个海洋后生动物门类中的17个。不同处理与保存方法间存在显著差异，这表明开展生物多样性对比研究时，方法标准化的必要性。针对固着大型生物，我们推荐采用标准化方案（美国国家海洋和大气管理局方案，National Oceanic and Atmospheric Administration，NOAA）结合二甲基亚砜（dimethyl sulfoxide，DMSO）进行组织保存：该方法可更精准地反映目标群落的真实情况，兼具成本效益，且可消除样本运输过程中的化学限制条件。我们发现，借助地理区域专属的条形码名录，相似度≥97%的序列数量增长了7倍以上（从5.1%升至38.6%），这凸显了区域物种名录的重要性。由于公共数据库中对研究较少的隐秘珊瑚礁群落的分类学覆盖度不足，采用高级分类单元赋值的系统发育分析方法会产生9.7%的门类鉴定误差。不过，采用序列相似度≥85%的截值阈值可获得更精准的结果（误差仅0.7%），并能对86.3%的序列读取结果进行门类水平的鉴定。目前全球已部署超过1600组ARMS样本，在当前全球环境快速变化的背景下，亟需统一研究方法并完善数据库，以实现对研究较少的隐秘海洋物种前所未有的全球基线评估。