A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure

Seawater contains a wealth of genetic information, representing the biodiversity of numerous species residing within a particular marine habitat. Environmental DNA (eDNA) metabarcoding offers a cost effective, non-destructive method for large scale monitoring of environments, as diverse taxonomic groups are detected using metabarcoding assays. A large-scale eDNA monitoring program of marine vertebrates was conducted across three sampling seasons (Spring 2018, Autumn 2019 and Spring 2019) in coastal waters of Brazil. The program was designed to investigate eDNA as a testing method for long term monitoring of marine vertebrates following the Fundão tailings dam failure in November 2015. While no baseline samples were available prior to the dam failure there is still value in profiling the taxa that use the impacted area and the trajectory of recovery. A total of 40 sites were sampled around the mouths of eight river systems, covering approximately 500km of coastline. Metabarcoding assays ..., Seawater samples were collected at 40 sites along the coastline of Brazil. DNA was extracted using the DNeasy blood and tissue kit (Qiagen). Two PCR assays used in this study were the 16S rRNA primer set Fish_Sygnathid_Short (Nester et al., 2020) and the COI Elasmobranch multiplex (West et al., 2020).  Multiplex identifier-tagged amplicons were blended into libraries and sequenced on an Illumina MiSeq instrument. 
Environmental factors including turbidity (Tu; NTU), temperature (Tm; °C), dissolved oxygen (DO; mg/L), chlorophyll-a fluorescence (Ch; μg/L, salinity (S; PSU), conductivity (Co; mS/cm) and photosynthetically active radiation (PAR; μMol/m²/s) were measured near the surface using an oceanographic grade XR Data Logger (RBR XRX-620). , , # A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure

[https://doi.org/10.5061/dryad.sqv9s4n3t](https://doi.org/10.5061/dryad.sqv9s4n3t)

## Description of the data and file structure

The spreadsheet **Sample ID information.xlxs** contains the information for each sample as labelled in the fasta files. 
The spreadsheet physical **WQ data 2018-2019 20230905.xls** contains data on environmental factors. An explanation of data variables are in the tab, data description.

Bioinformatic analysis was performed in accordance with Mousavi-Derazmahalleh et al., (2021). eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity. Molecular Ecology Resources. doi: 10.1111/1755-0998.13356. The eDNAFlow is available from GitHub ([https://github.com/mahsa-mousavi/eDNAFlow)](https://github.com/mahsa-mousavi/eDNAFlow)).

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海水蕴含着丰富的遗传信息，承载着特定海洋生境内众多物种的生物多样性。环境DNA（eDNA）元条形码（metabarcoding）技术可通过元条形码检测试剂盒实现对多样分类类群的识别，是一种经济高效且无破坏性的大规模环境监测手段。本研究针对巴西近岸海域，在三个采样季（2018年春季、2019年秋季与2019年春季）开展了大规模海洋脊椎动物eDNA监测项目，旨在评估eDNA作为2015年11月Fundão尾矿坝溃坝后海洋脊椎动物长期监测手段的可行性。尽管溃坝前未采集到基线样本，但厘清受影响区域的物类组成及其恢复轨迹仍具有重要研究价值。本次研究共在8个河口水域周边设置40个采样点，覆盖约500公里的海岸线。元条形码检测实验……研究人员于巴西沿岸40个采样点采集海水样本，采用DNeasy血液与组织试剂盒（Qiagen）提取DNA。
本研究使用的两套PCR检测体系分别为16S rRNA引物组Fish_Sygnathid_Short（Nester等，2020）与COI板鳃类多重PCR体系（West等，2020）。将带有多重标识符标签的扩增子混合构建测序文库，随后在Illumina MiSeq测序仪上完成测序。
研究人员采用海洋级XR数据记录仪（RBR XRX-620）在近表层测量了多项环境因子，包括浊度（Tu；NTU）、水温（Tm；℃）、溶解氧（DO；mg/L）、叶绿素a荧光强度（Ch；μg/L）、盐度（S；PSU）、电导率（Co；mS/cm）以及光合有效辐射（PAR；μMol/m²/s）。

# 2015年Fundão尾矿坝溃坝后巴西海域海洋脊椎动物eDNA生物多样性时空大规模调查
https://doi.org/10.5061/dryad.sqv9s4n3t

## 数据与文件结构说明
电子表格《Sample ID information.xlsx》包含fasta文件中标记的每个样本的相关信息。
电子表格《WQ data 2018-2019 20230905.xls》包含环境因子相关数据，数据变量的说明详见其"data description"工作表。
生物信息学分析参照Mousavi-Derazmahalleh等（2021）的研究方法完成。eDNAFlow是一款基于Nextflow与Singularity开发的自动化、可复现且可扩展的环境DNA序列分析工作流，相关成果发表于《Molecular Ecology Resources》，DOI: 10.1111/1755-0998.13356。该eDNAFlow工作流可从GitHub（https://github.com/mahsa-mousavi/eDNAFlow）获取。
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