README.md

Contact

Pierre Veron

📧 pierre [dot] veron [dot] 2017 [at] polytechnique [dot] org

Project

This project is the source and code associated with the publication:

Pierre Veron, Romane Rozanski, Virginie Marques, Stéphane Joost, Marie Emilie Deschez, Verena M Trenkel, Pascal Lorance, Alice Valentini, Andrea Polanco F., Loïc Pellissier, David Eme, Camille Albouy, Environmental DNA complements scientific trawling in surveys of marine fish biodiversity, ICES Journal of Marine Science, 2023. DOI: 10.1093/icesjms/fsad139

In this project, we compare two sampling methods for fishes (eDNA and scientific trawling) under the scope of multi-component indices of diversity. The data are taken from the EVHOE 2019 measurement campaign in the Bay of Biscay (Northern Atlantic). We compared eDNA metabarcoding and trawling for assessing:

• taxonomic diversity
• functional diversity
• phylogenetic diversity
• abundance.

This repository allows to reproduce the analyses and the figures in this publication, and the same data. The whole analysis is perfored in R version 4.1.2.

How to use it

The script main.R calls the used R packages, loads the data, runs the analyses and draws the figures. This script calls all the other scripts in the right order.

Project architecture

├───data
│   └───icons
│       └───char
├───diversity_indices
├───figures
├───output
│   ├───trees
│   ├───trees_merged
│   ├───trees_null
│   └───trees_null_merged
├───R
│   ├───functions
│   │   ├───fonctions_source_f
│   │   └───fonctions_source_p
│   ├───graphics
│   └───process_data
└───renv

• main.R the main script that calls the other scripts
• renv.lock information on the environments and versions
• eDNA_trawling.Rproj metadata for the project (for RStudio)
• renv/:directory loaded by renv for restoring the environment (see above)
• data/ the data associated with the project:
  • eDNA_2019_reads.csv the number of reads from the metabarcoding analysis, per station and taxa,
  • eDNA_metadata.csv information about the conditions of sampling for eDNA (position, depth...)
  • GISdata.rds background of the maps used in the figures
  • incidence_matrix.csv presence or absence of each taxon in each station and each sampling method
  • incidence_matrix_eDNA.csv incidence matrix only for eDNA
  • incidence_matrix_trawl.csv incidence matrix only for trawling
  • name_stations.csv name of the stations
  • reftax.csv the classification of each taxa detected by the methods
  • reftax_species.csv list of all Atlantic species belonging to the genus detected by the methods and their classification
  • traits.csv functional traits used to generate the functional space
  • traits_cat.csv list of the types of traits
  • trawl_2019_abundance.csv the number of individuals caught by the trawl per taxa and site
  • trawl_metadata.csv position of each trawling sample
  • trees.rds phylogenetic trees used for the phylogenetic indices of diversity.
• diversity_indices/ the formatted output of the scripts:
  • alpha.csv, alpha_merged.csv, alpha_ses.csv, alpha_merged_ses.csv: alpha indices of diversity on each of the sampling methods and on the merged communities (trawling+eDNA) and their SES values
  • phylo_signal_alpha and phylo_signal_gamma.csv: result from the analysis of phylogenetic signal of clustering on the trees.
• figures/ contains the figures generated by the scripts and used in the manuscript
• output/ contains the raw output from the script (in RDS format). If the file contained in this directory are cleaned, the program will re-run the analyses (it might take a long time). Please note that this directory should contain at least the folders trees, trees_merged, trees_null and trees_null_merged. Once the analyses are run, their results are stored here and accessed by the script R/process_data/diversity_indices.R to avoid computing several times the same indices.
• R/ contains the scripts used to load the data, run the analyses, store the results and draw the figures.