Data and code for: "Combining environmental DNA and remote sensing variables to model fish biodiversity in tropical river ecosystems"
Domaine:
environment and energygeospatialType de record:
softwaredataset
Créateur:
BauPelBro
Éditeur:
Hôte:
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.e…
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:
- Casamance:
- Kinabatangan
- African Rivers
- Guiana Rivers
Some raw reads are available via:
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.
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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].