Data and code for: "Combining environmental DNA and remote sensing variables to model fish biodiversity in tropical river ecosystems"
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Combining environmental DNA and remote sensing variables to model fish biodiversity in tropical river ecosystems General Information This repository contains the code used for the analysis presented in the paper: "Combining environmental DNA and remote sensing variables to model fish biodiversity in tropical river ecosystems." Authors: Robin Bauknecht, Loïc Pellissier, Sébastien Brosse, Vincent Prié, Manuel Lopes-Lima, Pedro Beja, Monika K. Goralczyk, Andrea Polanco Fernandez, Jorge A. Moreno-Tilano, Rafik Neme, Mailyn A. Gonzalez, Shuo Zong Correspondence: Robin Bauknecht – rbauknecht@ethz.ch Shuo Zong – shuo.zong@usys.ethz.ch Link to paper: https://doi.org/10.1016/j.ecoinf.2025.103251 Repository Structure This repository is organized as an R Project. Open the `.Rproj` file in RStudio for streamlined access to the analysis workflow. data/ folder: - swarm_output_clean/: Cleaned output from the SWARM clustering algorithm - rs_variables/: Remote sensing variables for each sampling site - site_sample_mapping/: Links samples to sampling sites (typically two replicates per site) scripts/ folder: - global_model.Rmd: Global biodiversity modeling - local_model_maroni.Rmd: Modeling for the Maroni River - local_model_oyapock.Rmd: Modeling for the Oyapock River - plots.R: Code for generating plots - helper_functions.R: Reusable helper functions - calculating_per_sample_metrics.R: Script for calculating per-sample biodiversity metrics Raw eDNA Sequencing Data In addition to the cleaned SWARM output included in this repository, raw sequencing data is available from the following sources: - Magdalena River: https://www.doi.org/10.16904/envidat.666 - Casamance: https://www.doi.org/10.16904/envidat.672 - Kinabatangan https://www.doi.org/10.16904/envidat.734 - African Rivers https://www.doi.org/10.16904/envidat.682 - Guiana Rivers Some raw reads are available via: https://datadryad.org/stash/dataset/doi:10.5061/dryad.pvmcvdnmr This study additionally includes new sites. Correlation tags for these are provided in data/additional_tags_guiana.csv and can be used together with the raw read files in the above repository to process these additional samples. --- Please reach out to the corresponding authors for any questions or collaboration inquiries. Funding This work was supported by a China Scholarship Council grant awarded to S. Z. This project has also received support from the project NORTE-01-0145-FEDER-000046 under the Norte Portugal Regional Operational Programme (NORTE2020), through the European Regional Development Fund (ERDF) and the Portugal 2020 Partnership Agreement. Additionally, M. L.-L. was funded by FCT - Fundação para a Ciência e Tecnologia [contract 2020.03608.CEECIND].
