Data from: Recovering plant-associated arthropod communities by eDNA metabarcoding historical herbarium specimens
Description
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
Files
Steps to reproduce
Please see the methods section of the paper Recovering plant-associated arthropod communities by eDNA metabarcoding historical herbarium specimens, Current Biology, in press (doi: tba).