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.

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.

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).