DOI: 10.5061/dryad.pc866t1mg
title: Climate overrides the effects of land use on the functional composition and diversity of mediterranean reptile assemblages.

description: Aim: To test the hypothesis that spatial variations in climate and land
 use explain the distribution and diversity of reptiles’ ecological traits
 in a biodiversity hotspot of the Mediterranean basin. Location: French
 Mediterranean region Taxon: Reptiles (25 species) Methods: We defined 288
 species assemblages from 27858 opportunistic occurrence records within 10
 x 10 km square grid cells. Using a RLQ analysis, we investigated the
 distribution of nine ecological traits describing reptiles’ reproductive,
 dietary and behavioural strategies along environmental gradients formed by
 10 climatic, topographic and land-use descriptors. After homogenizing
 survey effort through rarefaction, we used generalized additive models to
 assess variations in species richness and several measures of functional
 diversity and composition along these gradients.   Results:
 Although ecological traits were not structured by environmental gradients
 at a species level, species richness and all measures of functional
 diversity varied non-linearly with climate, elevation and secondarily land
 use. Species richness and body size peaked at intermediate altitudes,
 indicating a climatic transition zone between Mediterranean and
 medio-european herpetofaunas. Conversely, functional diversity increased
 from Mediterranean plains, dominated by urbanization and agriculture, to
 higher elevations. These changes were associated with shifts towards less
 productive, more diurnal and more forest-related species. Main
 conclusions: Species-scale patterns are insufficient to assess regional
 variations in ecological traits in space. Our results support the
 hypothesis that climatic limitations in species’ distributions, rather
 than environmental filtering, explain the taxonomic and ecological
 diversity of reptiles at a regional scale. Although secondary to climate,
 land abandonment has a strong structuring effect which may contribute to
 homogenize the composition of reptile assemblages.
description: <b>Readme file : data
 for Barnagaud et al, Diversity & Distributions, 2020.
 </b> These
 datafiles and R scripts relate to : Barnagaud, JY, Geniez, P, Chelyan, M
 & Crochet, PA. 2020. Climate overrides the effects of land use on
 the functional composition and diversity of mediterranean reptile
 assemblages. Diversity & Distributions.  All the necessary information
 with respect to the data is provided in the article. It is unwise to use
 these data without reading the article before, and we strongly encourage
 any user to get in touch with us ahead.  Corresponding author : please
 contact Jean-Yves Barnagaud : jean-yves.barnagaud@ephe.psl.eu or jean-yves.barnagaud@cefe.cnrs.fr  
description: <b>List of
 files</b> <b>Folder “data” contains
 all the necessary data to run the analyses. </b> <i>Barnagaud_et_al_DivDib_2020_ecological_traits.txt</i> : ecological trait matrix. See Appendix S2 of the article for the description of traits and acronyms. <i>Francewgs84.shp</i> : a ESRI shapefile with the contours of France for mapping purpose (not used in the analyses). Downloaded freely from https://www.data.gouv.fr/fr/datasets/contours-des-regions-francaises-sur-openstreetmap/ <i>grid10x10_337cells.shp</i> : a ESRI shapefile with the grid used to define reptile assemblages. <i>grid_centroids.txt : </i>the centroids of the grid cells used to define reptile assemblages (also present in other datafiles) <i>initial_site_species_matrix.txt</i> : this matrix contains the raw site*species matrix. Rows are grid cells (matches with the two previous files) and columns are species (matches with the ecological trait matrix). Data are expressed in numbers of records per grid cell and species. Note that the original geolocated individual records are not provided due to the privacy policy of the database. <i>occurrence_matrices_observed_rarefied.RData : </i>this datafile is generated by the script “rarefaction.R” <i>rarefied_observed_diversity_indices.RData : </i>this datafile is generated by the script “rarefaction.R” <i>reptile_data.RData :</i> tables of the RLQ analysis used in the script “RLQ_analysis.R”. table.L corresponds to the sites*species matrix created by the script “rarefaction.R”. table.Q is the trait matrix reformatted for use with the ade4 library. table.R is the environmental trait matrix. <i>species_index.txt: </i>index of species’ names and acronyms   <b>Folder “scripts” contains all the necessary R codes to run the analyses. </b> <i>rarefaction.R </i>: all the necessary computations to create the rarefied species assemblages and compute diversity indices and community-averaged traits. <i>RLQ_analysis.R</i> performs the coinertia analysis and RLQ analysis, and generates Figures 1 and 2 of the article. Note that these figures have been reworked in Powerpoint for readability (compilation of the multiple panels and addition of variables acronyms. <i>statistical_analysis.R</i> : performs the generalized additive models to analyse the correlations of diversity indices with environmental gradients and generates figures 3,4 and 5.   <b>Species, variables and traits acronyms are defined in the article.</b>