Data and code for 'Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in marine ecological community assessment recovery'

This is the data and code used in the paper: <i>Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities</i>. (PeerJ, 2024 12:e17091)dbMEM.R - R code for spatial autocorrelation analysisrank_abundance.R - R code for rank abundance curvesSAC.R - R code for species accumulation curvesCCA_BRUV_eDNA.R - R code for community structure analysisvert_rep_analysis.R - R code for species accumulation curves and CCA for replicate analysisAll other datasets are those used in these R scripts.<br><br><b>Abstract</b><br><br>Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe.

本数据集对应论文《带饵远程水下视频（Baited Remote Underwater Video, BRUV）与环境DNA（environmental DNA, eDNA）监测海洋生态群落的成本-效能分析》（PeerJ, 2024, 12:e17091）中所使用的数据与代码。<br><br>dbMEM.R：用于空间自相关分析的R代码<br>rank_abundance.R：用于绘制等级多度曲线的R代码<br>SAC.R：用于绘制物种累积曲线的R代码<br>CCA_BRUV_eDNA.R：用于群落结构分析的R代码<br>vert_rep_analysis.R：用于重复分析的物种累积曲线与典范对应分析（Canonical Correspondence Analysis, CCA）的R代码<br><br>其余数据集均为上述R脚本所使用的数据。<br><br><b>摘要</b><br><br>监测生态系统中物种的多样性与分布，是评估修复策略成效的核心前提。生物监测方法可全面评估物种多样性并降低数据采集偏差，在生物多样性研究中具有重要意义。此外，确保此类方法具备成本效益且所需投入最小化，亦是高效开展环境监测的关键。本研究针对两种非破坏性采样技术——带饵远程水下视频（BRUV）与环境DNA（eDNA）元条形码测序技术——在海洋脊椎动物物种调查中的物种检出效能、成本与人力投入进行对比。本次对比研究在苏塞克斯海岸开展，该区域已实施《近岸拖网捕捞禁令》，该禁令旨在恢复1980年代存在的茂密海带床及其伴生生物多样性。<br><br>研究结果显示，整体而言BRUV调查的成本低于eDNA监测，但eDNA的物种检出量几乎是BRUV的三倍。两种方法的人力投入水平基本相当，但若eDNA分析委托外部机构完成，则牵头研究人员的投入会更少。此外，增加eDNA的重复采样次数可获得更具信息量的群落结构分析结果。研究还发现，联合使用两种监测方法可更全面地展现生物多样性：BRUV数据可补充eDNA监测未检出的物种，并提供额外的环境与生活史相关指标。<br><br>本研究的结果将作为苏塞克斯湾海洋脊椎动物群落的基线数据，助力未来的生物多样性监测研究项目，以了解在拖网捕捞压力解除后生态系统恢复过程中的群落结构变化。尽管本研究仅针对区域尺度开展，但其研究结果对全球范围内的海洋生物多样性与保护监测项目均具有参考价值。