Energy input, habitat heterogeneity, and host specificity drive avian haemosporidian diversity at continental scales

The correct identification of biotic and abiotic drivers affecting parasite diversity and assemblage composition at different spatial scales is crucial for understanding how pathogen distribution responds to anthropogenic disturbance and climate change. Here, we used a database of avian haemosporidian parasites to identify such drivers and their effect on the taxonomic and phylogenetic diversity of genera Plasmodium, Haemoproteus, and Leucocytozoon from three zoogeographic regions. We explored how parasite diversity is related to energy input (i.e., temperature, precipitation, and potential evapotranspiration [PET]), to habitat heterogeneity (i.e., climatic seasonality, vegetation density, ecosystem heterogeneity, human disturbance, and host richness), and to a novel assemblage-level metric related to parasite niche overlap (degree of generalism). We found that the relative importance of the predictors differed between the three studied parasite genera and across diversity metrics. Amon..., We acquired records from MalAvi, a global database with at least 2400 haemosporidian lineages of mtDNA sequences of a cytochrome b (cyt-b) gene fragment (479 bp) that has been used as a barcode. We considered each haplotype as a unique parasite lineage and in the case of duplicated sequences with different names, we randomly assigned duplicated sequences to the same lineage name. We then downloaded the Host and Sites Table (accessed on March 2023), we validated geographic coordinates at country level, final table had 10302 records based on 286 references published between 2006 and 2023.     , , # Energy input, habitat heterogeneity, and host specificity drive avian haemosporidian diversity at continental scales

[https://doi.org/10.5061/dryad.hx3ffbgkg](https://doi.org/10.5061/dryad.hx3ffbgkg)
This repository contains the scripts necessary to reproduce the analysis presented in the homonymous paper published in Proceedings B.

## Description of the data and file structure

This dataset is composed of 5 R scripts (*.R), one script contains functions and the other four contain the workflow to reproduce the analysis, the relationships between data and scripts are described below.

* Note: The first two scripts load the files from a folder called \"data\", and the resulting files are saved in a folder called \"out\". In addition, all scripts load functions from a subfolder called \"functions\" within a folder called \"scripts\". Make sure to modify these paths in the scripts or create these folders with the corresponding files (input) on your workspace.

### Details for `1diversity met...