Optimization of wetland environmental DNA metabarcoding protocols for Great Lakes region herpetofauna

Many species of reptiles and amphibians (herpetofauna) rely on wetlands that are being degraded and lost at a high rate. Characterization of herpetofauna diversity in different wetland types may help guide conservation strategies. However, traditional survey methods often involve sampling within small temporal windows and gear deployed may be taxonomically biased, thus, they may fail to accurately characterize species presence/absence and diversity. In contrast, environmental (e)DNA metabarcoding has been shown to effectively survey entire aquatic communities and can provide a useful complement to traditional surveys. The objective of this study was to design and optimize eDNA sampling and laboratory protocols for wetland herpetofauna. Protocols evaluated included different water sampling approaches (point versus transect sampling), seasonality of sampling, and choice of metabarcoding marker (mitochondrial 12S versus 16S rDNA). Samples collected from 10 sites across southern Michigan de..., , , # Data from: Optimization of wetland environmental DNA metabarcoding protocols for Great Lakes region herpetofauna

[https://doi.org/10.5061/dryad.8w9ghx3wv](https://doi.org/10.5061/dryad.8w9ghx3wv)

This repository contains analysis scripts and input data files associated with the eDNA metabarcoding of herpetofauna communities in Michigan wetlands and subsequent analyses for “Optimization of wetland environmental DNA metabarcoding protocols for Great Lakes region herpetofauna”. 

## Description of the data and file structure

Alignment and taxonomy files for 279 species (12S) and 305 species (16S) are in the `alignment_taxonomy.zip` file. 

* `Vertebrate_12S_align_072821_NoPrimers.fas` and `Vertebrate_16S_align_111722_NoPrimers.fas` contain sequence alignments for species with accession numbers (if available) and scientific names. If produced by our lab, there is no accession number, but a four-letter code (first two letters of genus and specific epithet) and the sample number. 
* `Ver...

诸多爬行类与两栖类物种（herpetofauna，即两栖爬行类动物）依赖湿地生存，但当前湿地正以极高速率发生退化与丧失。对不同湿地类型中的两栖爬行类多样性进行表征，可为保护策略制定提供科学指引。然而传统调查方法往往仅能在有限的时间窗口内实施采样，且所采用的采样装置可能存在分类学偏向性，因此难以精准刻画物种的检出/未检出情况及群落多样性水平。与之相对，环境DNA（eDNA，environmental DNA）元条形码测序技术已被证实可有效对整个水生群落进行调查，能够作为传统调查方法的有效补充。本研究的目标是为湿地两栖爬行类动物设计并优化eDNA采样与实验室实验方案。本次评估的实验方案涵盖不同的水体采样方式（点位采样与样带采样）、采样季节选择，以及元条形码测序标记的选取（线粒体12S与16S核糖体DNA（rDNA））。研究团队从密歇根州南部的10个采样点位采集了样本，# 数据来源：《五大湖区域两栖爬行类动物湿地环境DNA元条形码测序方案优化》

[https://doi.org/10.5061/dryad.8w9ghx3wv](https://doi.org/10.5061/dryad.8w9ghx3wv)

本数据集仓库包含与密歇根州湿地两栖爬行类群落eDNA元条形码测序相关的分析脚本与输入数据文件，以及服务于《五大湖区域两栖爬行类动物湿地环境DNA元条形码测序方案优化》一文的后续分析数据。

## 数据与文件结构说明

包含279个物种（12S标记）与305个物种（16S标记）的序列比对与分类学文件存于`alignment_taxonomy.zip`压缩包中。

* `Vertebrate_12S_align_072821_NoPrimers.fas`与`Vertebrate_16S_align_111722_NoPrimers.fas`文件包含带有登录号（若有）与学名的物种序列比对结果。若序列由本实验室生成，则无登录号，取而代之的是四字母编码（属名前两个字母加种加词前两个字母）与样本编号。

* `Ver...