eDNAmap: instruction
24 Apr. 2025
Overview

eDNAmap is software that analyzes species/ASV tables obtained from environmental DNA metabarcoding analysis to compare species distribution and biota. The database consists of species/ASV lists obtained from regions centered around the western North Pacific Ocean.
Users can,

1. investigate the distribution of species you're interested in.
2. upload a species/ASV list with individual counts/sequence numbers and compare species composition between sampling locations.
3. plot sampling locations on a map.


Tutorial
As an example, we will upload and analyze the OUT_Miya22.xlsx file (Miya et al. 2022) obtained from the coastal waters of the Boso Peninsula.
The user uploads the OUT_Miya22.xlsx file, which consists of the Reads sheet and Location sheet (see below), from the "Species/ASV table > Upload excel file" option and then presses the SUBMIT button.

Search species:
(1) Search for the species name selected from the dropdown menu.
(2) Search for the keyword entered in the text box.
(3) Search by uploading a list of species names or ASV-IDs.
If an upload file is present (3), the search words from steps (1) and (2) will not be used.
Station name on map: Specify whether to plot the station names on the map.
ASV comparison criteria: Restrict the use of ASVs with few detection points when comparing species/ASV compositions among points for nMDS and cluster analysis.
Distance method for composition comparison: Specify whether to use the Jaccard or Bray-Curtis method as the distance measure when performing comparative analysis of species/ASV compositions among stations. For the Bray-Curtis method, the numbers in the ASV file must be written as percentages.
PDF file: You can choose whether to output the analysis results as PDF files.
Species/ASV table: Select already installed species/ASV tables for analysis. You can also compare them with the species/ASV table uploaded by the user.
 
Input file: Enter the read and location information into the .xlsx file.
 
Outputs: Click the link next to "Status > Finished" to download.

Users can independently perform PERMANOVA and environmental correlation analyses using various .R scripts downloaded as outputs.
 
Citation

Inoue et al. eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity with Special Reference to Teleost Fish. submitted.
Dependencies
Table handling: pandas
Map tools: Generic Mapping Tools
Haetmap: pheatmap in R, Version 4.3.2.
nMDS, PERMANOVA, hclust: vegan in R