Agricultural land use and ensuing eutrophication shape parasitic trematode communities in rural African lakes

Description

Dataset (csv and nexus files) used for the analyses presented in the study: "Agricultural land use and ensuing eutrophication shape parasitic trematode communities in rural African lakes". Context and findings: Land use is a major driver of biodiversity loss, but impacts differ greatly among taxonomic and functional groups. Parasites are ubiquitous and taxonomically diverse, yet how anthropogenic environmental change affects their communities is scarcely documented. The small, confined catchments of crater lakes in western Uganda provide a unique opportunity to assess the effects of land use on the communities of parasitic trematodes. Together these catchments cover a very large gradient of anthropogenic impact intensity both on land (naturally vegetated catchment to complete agricultural conversion) and in the water (unimpacted to highly eutrophied) whereas variation in natural environmental conditions is limited. Surveying 34 of these lakes, we applied state-of-the-art molecular biomonitoring to genotype all infections by parasitic trematodes in 2385 Bulinus tropicus snails, their regionally most common intermediate host organism. The 45 trematode taxa identified infect a diverse range of final vertebrate hosts and can cause significant public and veterinary health burdens. Using constrained ordinations and generalised additive models, we found that B. tropicus is most abundant in catchments that are partially covered with crop fields, whereas trematode abundance increases with B. tropicus abundance and peaks at intermediate aquatic productivity. Trematode diversity also increases with aquatic productivity but levels off in the most eutrophied lakes. These overall positive relationships likely occur because more productive lakes can sustain a higher abundance and variety of intermediate and final hosts, hence promoting transmission. Files: - R_script_trematode_diversity.R : R script to perform the explorative and inferential analyses of the study and create plots and figures. - ML_concat_tree_renamed3b.nexus: Phylogenetic tree topology of the trematode taxa encountered in the study, used to compute phylogenetic diversity - all_RD_processed_snails.csv: List of the snail specimens identifiers and lake code where the sample was obtained - df_Bulinus_analysis4.csv: Dataset of the environmental variables associated with each lake studied (referenced using lake name, code and coordinates) -diag_size: Size of each snail and RD-PCR diagnostic for trematode infection - host_ID.csv: Identification of each trematode taxon and their final hosts - seqtab_clean_valid_spe.csv: Outputs of high-throughput sequencing pipeline, used to infer trematode infection identity - table_snail.csv: Specimen ID and species identification of the snail hosts collected - wannes_data.csv: Additional environmental data for the study lakes

Steps to reproduce

Download the files, import in R, open the R script, set the correct working environment, install required packages, run the script.

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