DOI: 10.5061/dryad.2z34tmpxf
title: Data from: Effects of vegetation density on the diversity of lizards in an area of the Brazilian Cerrado

description: The Cerrado is a highly threatened biome that harbors a great portion of
 Brazilian biodiversity, including many endemic species. Such richness may
 reflect its environmental heterogeneity, which includes different
 vegetation types (from grasslands to forests). Several endemic species in
 the Cerrado are strongly associated with open vegetation types. Recent
 studies have shown that woody encroachment can negatively impact several
 components of biodiversity. In the present study, we provide information
 on variation in lizard diversity across different vegetation types in a
 protected area located in the southern portion of the Cerrado and
 evaluated the effect of vegetation density on lizard taxonomic,
 functional, and phylogenetic diversity. We predicted that the three
 aspects of lizard diversity would be negatively affected by vegetation
 density and that Beta diversity would vary significantly across the
 vegetation gradient. We confirmed nearly all of our predictions, except
 for functional diversity, which, contrary to our expectations, was
 positively influenced by vegetation density. We also found that Beta
 diversity indices based on both species composition/abundance and
 phylogenetic features of communities experience a significant turnover
 across the vegetation density gradient. This study greatly strengthens
 previous studies that suggest a negative impact of vegetation density
 (and, consequently, woody encroachment) on lizard diversity. Therefore,
 managers of protected areas in the Cerrado should consider the use of
 strategies to avoid woody encroachment, like fire management with
 prescribed fires.
description: # Effects of vegetation density on the diversity of lizards in an area of
 the Brazilian Cerrado
 [https://doi.org/10.5061/dryad.2z34tmpxf](https://doi.org/10.5061/dryad.2z34tmpxf) ## Description of the data and file structure ### Files and variables **Supplementary Figures_FINAL.pdf** Supplementary material that includes figures and tables are not included in the main manuscript.  Figure S1. Phylogenetic tree of lizard species sampled with pitfall traps at the Santa Bárbara Ecological Station. Only species with more than five individuals sampled are included. Colors represent each family. Blue: Gymnophtalmidae; Gold: Teiidae; Orange: Anolidae; Purple: Scincidae. Figure S2. Shepard plot (or stress plot) to observe the goodness of fit of the data into the NMDS analysis.Figure S3. Half-normal plots with Simulation Envelopes of the best fitted generalized linear models showing the predicted effect of A − NDVI (300 m buffer) on lizard richness; B− NDVI (300 m buffer) on lizard abundance. Figure S4. Forest plot illustrating 95% CI of models of taxonomic, phylogenetic and functional diversity, and LCBD in different scales. Error bar colors represent model’s slope, positive (blue) or negative (red). **Supplementary Tables_FINAL.xlsx** Supplementary tables of the study Table S1. Data extracted from Oskyrko et al. (2024) Table S2. Binnary functional data and maximum body mass of lizards species of Santa Bárbara Ecological Station. Data extracted from Oskyrko et al. (2024). Red numbers indicate data obtained in the field. Table S3. Results for estimates of lizards diversity (Shannon index) at Santa Bárbara Ecological station in each vegetation type based on coverage-based rarefaction curves. Table S4. General scale model selection table for species richness, abundance, phylogenetic, functional, and beta diversity of lizards sampled with pitfall traps at Santa Bárbara Ecological Station. Rd: Residual deviance, Df: Degrees of freedom, SW: P-value of Shapiro-Wilk test. Numbers in red represent statistically significant results (P &lt; 0.05) or 95% confidence intervals that not included zero. Table S5. Results of (partial) Mantel tests between taxonomic (both incidence-based and abundance-weighted), functional and phylogenetic pairwise β diversity (βsor and βbray) and its spatial turnover (βsim and βbal) and nestedness (βsne and βgra) components of lizard metacommunities of Santa Bárbara Ecological Station. Numbers in red indicate significant results (P&lt;0.05). **data_GLM.csv** CSV file (Comma-Separated Values) contains all variables used in GLM analyses. Each column represents a different variable: * **Sampling_unit** – A set of two 40 m-long pitfall trap lines where lizards were captured. * **Veg_type** – The vegetation type class sampled. * **Rich_liz** – Total species richness in each sampling unit. * **Abu_liz** – Total lizard abundance in each sampling unit. * **NRI_liz** – Net Relatedness Index in each sampling unit. * **NTI_liz** – Nearest Taxon Index in each sampling unit. * **SESFDis_liz** – Standardized Effect Size of **Functional Dispersion** in each sampling unit. * **SESFric_liz** – Standardized Effect Size of **Functional Richness** in each sampling unit. * **SESFeve_liz** – Standardized Effect Size of **Functional Evenness** in each sampling unit. * **NDVI_100, NDVI_150, NDVI_200** – **Normalized Difference Vegetation Indices** at different spatial scales in each sampling unit. * **Lat, Lon** – Latitude and longitude of each sampling unit. **lizards_abundance_per_site.csv** CSV file (Comma-Separated Values) contains data on lizard abundance per site (species with n &gt; 5). ## Code/software ### Data Formats #### **Metadata and Binary Files:** * **Excel Files:** * **.xlsx/.xls**: Utilized for organizing and presenting data summaries. * **.csv**: data utilized to perform the analyses. * **Text Files:** * **.pdf**: May include supplementary figures. ## Access information Table S2, binnary functional data and maximum body mass of lizards species of Santa Bárbara Ecological Station, was extracted from Oskyrko et al. (2024). * Oskyrko, O., Mi, C., Meiri, S. & Du, W. (2024). ReptTraits: a comprehensive dataset of ecological traits in reptiles. Scientific Data, 243. * [https://www.nature.com/articles/s41597-024-03079-5](https://www.nature.com/articles/s41597-024-03079-5)