DOI: 10.5061/dryad.c2fqz616h
title: Biotic homogenisation in bird communities leads to large-scale changes in species associations

description: This is the dataset used for the manuscript Biotic homogenisation in bird
 communities leads to large-scale changes in species associations Aim: The
 impact of global change on biodiversity is commonly assessed in terms of
 changes in species distributions, community richness and community
 composition. Whether and how much associations between species, i.e. the
 degree of correlation in their spatial co-occurrence, are also changing is
 much less documented and mostly limited to local studies of ecological
 networks. In this study, we quantify changes in large-scale patterns of
 species associations in bird communities in relation to changes in species
 composition. Location: France. Time period: 2001-2017. Major taxa studied:
 Common breeding birds. Methods: We use network approaches to build three
 community-aggregated indices reflecting complementary aspects of species
 association networks. We characterise the spatio-temporal dynamics of
 these indices using a large-scale and high-resolution dataset of bird
 co-abundances of 109 species monitored for 17 years (2001-2017) from 1,969
 sites across France. We finally test whether spatial and temporal changes
 in species association networks are related to species homogenisation
 estimated as the spatio-temporal dynamics of β-diversity and the
 proportion of habitat generalists. The consistency of these relationships
 is tested across three main habitats, namely woodland, grassland and human
 settlements. Results: We document a directional change in
 association-based indices in response to modifications in β-diversity and
 in the proportion of generalists in space and time. Weaker associations
 and sparser networks were related to lower β-diversity and a higher
 proportion of generalists, suggesting an overlooked aspect of biotic
 homogenisation affecting species associations. We report that this overall
 pattern is not constant across habitats, with opposite relationships
 between biotic homogenisation and change in species association networks
 in urban versus forest communities suggesting distinct homogenisation
 processes. Main Conclusions: Although species association contain only
 partial signatures of species interactions, our study highlights that
 biotic homogenisation translates to finer changes in community structure
 by affecting the number, strength and type of species associations.
description: Dataset exctracted from the French
 Breeding Bird Survey with bird information (data_publi.csv) and site
 localisation (square_centroid.csv). Intermediate data (data_publi.RData)
 correspond to main steps of the analysis as their obtention might take a
 while from initial data. Rmarkdown report
 (Script_association_betadiversity.Rmd) with R script explaining how data
 analyses were conducted.
description: Download the Rmarkdown file (.Rmd, also visible in .html) and the
 data files (.csv and/or .RData). You can then either explore the initial
 data (.csv) and re-run the entire analysis but it might be time consuming,
 or re-run some analyses using intermediate results (.RData).