Data from: Recovering plant-associated arthropod communities by eDNA metabarcoding historical herbarium specimens

1\. Data description

In general, the data is generated by an eDNA metabarcoding workflow. We extracted eDNA from herbaria (up to 60-year-old), from freeze-dried homogenates of a German state monitoring project on forest health (uo to 20-year-old) and tested different storing methods of plants for their influence on the arthropod community. The herbaria were further tested with a non-destructive method of "washing" with water. We used two PCR primers, 1) "NoPlant", short NP, NoP, Nop, or NoPl (doi: 10.1098/rsbl.2022.0091), and 2) "ZBJ" (doi: 10.1111/j.1755-0998.2010.02920.x.). Note that only for the homogenized and washed off herbaria samples both primers were used, otherwise only NoPlant. PCR triplicates were only done for homogenized herbaria and for the german state monitoring project. For further questions on the methods, please see the Methods part of the paper (doi: tba) or contact the lead author.

2\. Tables provided:

\- Herbaria_metadata: Metadata of the samples. The metadata contains seperate columns: "Seq_ID", which refers to the fastq file name of the samples from "Herbaria_homogen_NP" and "Herbaria_homogen_ZBJ" fastq files; "Sample_ID", which refers to the individual sample; "Replicate", which refers to the replicate of the sample - there are no replicates for the washing samples (ending in Seq_ID with "_WO", or in "Sampling_method" column are "wash_off_herbaria"); "common name" of the herbarium plant species sampled; "Species", which is the scientific name; "Herbarium", which is the country and year also used in the main figures of the paper; "Processing", which shows how they were processed in the lab; "Primer", which is the primer used to amplify in PCR; "Sampling_method_library", which shows again which sampling method was used for the samples overall, also being the same for extraction and PCR controls the samples belong to.

\- German_state_forest_monitoring_project: Metadata of the samples. The metadata contains seperate columns: "Seq_ID" refers to the fastq file of the "German_state_forest_monitoring" fastq files; "Sample_ID" refers to the sample ID; "Replicate" refers to the replicate of each sample; "Plant_species" refers to the plant species that was taken as a homogenate; "Site" refers to the site the samples were taken from: "Year" refers to the year the samples were taken.

\- Storage_method_comparison: Metadata of the samples. The metadata contains seperate columns: "Sample_ID", which refers to the sample ID but is the same as the Seq_ID from the fastq files; "common name" of the herbarium plant species sampled; "Species", which is the scientific name; "Method", shows the method that was used for storing and wheather it is a PCR or extraction control, which were used for all samples

3\. Fastq-files:

\- Herbaria_homogen_NP

\- Herbaria_homogen_ZBJ

\- German_state_forest_monitoring

\- Storage_method_comparison

1. 数据集说明

总体而言，本数据集通过环境DNA（eDNA）宏条形码（metabarcoding）流程生成。研究从保存年限最长60年的标本馆（herbaria）样本，以及德国国家级森林健康监测项目的冻干匀浆样本（最长保存20年）中提取了eDNA，并测试了不同植物储存方法对节肢动物（arthropod）群落的影响。此外，针对标本馆样本采用水淋洗的无损方法开展了检测。

本研究使用两类聚合酶链式反应（PCR）引物：① 引物"NoPlant"，简称NP、NoP、Nop或NoPl（DOI: 10.1098/rsbl.2022.0091）；② 引物"ZBJ"（DOI: 10.1111/j.1755-0998.2010.02920.x）。

需注意，仅针对匀质化且经淋洗的标本馆样本同时使用了两类引物，其余样本仅使用NoPlant引物。仅针对匀质化标本馆样本及德国国家级森林健康监测项目样本设置了三次重复PCR扩增实验。若需了解实验方法的更多细节，请查阅论文的方法部分（DOI: tba）或联系第一作者。

2. 提供的表格

• 标本馆样本元数据（Herbaria_metadata）：样本元数据，包含以下独立列：
`"Seq_ID"`：对应来自`Herbaria_homogen_NP`与`Herbaria_homogen_ZBJ`的FASTQ格式测序文件的样本文件名；
`"Sample_ID"`：单个样本的唯一标识；
`"Replicate"`：样本的重复组别——淋洗样本（`Seq_ID`以`_WO`结尾，或`Sampling_method`列标注为`wash_off_herbaria`）无重复设置；
`"common name"`：所采集标本馆植物物种的通用名称；
`"Species"`：物种的拉丁学名；
`"Herbarium"`：标本馆藏地与采集年份，该信息亦用于论文主图；
`"Processing"`：样本在实验室中的处理流程；
`"Primer"`：PCR扩增时使用的引物；
`"Sampling_method_library"`：再次说明样本整体采用的采样方法，该信息与样本所属的提取对照、PCR对照一致。

• 德国国家级森林健康监测项目元数据（German_state_forest_monitoring_project）：样本元数据，包含以下独立列：
`"Seq_ID"`：对应`German_state_forest_monitoring`的FASTQ格式测序文件的样本；
`"Sample_ID"`：样本唯一标识；
`"Replicate"`：每个样本的重复组别；
`"Plant_species"`：作为匀浆样本的植物物种；
`"Site"`：样本采集地点；
`"Year"`：样本采集年份。

• 储存方法对比元数据（Storage_method_comparison）：样本元数据，包含以下独立列：
`"Sample_ID"`：样本唯一标识，与对应FASTQ格式测序文件的`Seq_ID`完全一致；
`"common name"`：所采集标本馆植物物种的通用名称；
`"Species"`：物种的拉丁学名；
`"Method"`：样本储存所用的方法，以及该样本是否为PCR对照或提取对照，所有样本均设置了此类对照。

3. FASTQ格式测序文件
- Herbaria_homogen_NP
- Herbaria_homogen_ZBJ
- German_state_forest_monitoring
- Storage_method_comparison