DOI: 10.5061/dryad.3tx95x6sb
title: Data from: Context-dependent body size evolution in lacertid lizards: Differential role of structural habitat and climate across radiations

description: Body size plays a pivotal role in organismal performance, physiology, and
 ecology, making its evolution a key focus in biology. This study
 investigates the effects of structural habitat (climbing vs.
 ground-dwelling) and climatic variables on body size evolution within the
 diverse Lacertidae lizard family and across phylogenetic scales. Our
 results reveal how structural habitat drives diversification rather than
 convergence toward specific morphological optima, with evolutionary rates
 varying substantially among phylogenetic groups. Gallotinae exhibits the
 highest evolutionary rates, likely due to island-driven dynamics, while
 Eremiadini and Lacertini display contrasting patterns linked to habitat
 use and evolutionary history. On the other hand, climatic variables
 influence body size variation by group. In Eremiadini, significant
 associations with temperature and precipitation seasonality align with the
 seasonality, heat conservation, and starvation resistance hypotheses.
 Lacertini body size negatively correlates with precipitation seasonality,
 supporting the seasonality hypothesis, while Gallotinae remains unaffected
 by climate, reflecting the unique pressures of insular evolution. The
 study highlights the importance of phylogenetic scale in understanding
 macroevolutionary patterns, revealing how broad-scale analyses may obscure
 context-specific eco-evolutionary dynamics. By focusing on coherent
 taxonomic groups, this research provides critical insights into how
 structural and climatic factors shape morphological diversity within
 Lacertidae.
description: # Context-dependent body size evolution in lacertid lizards: Differential
 role of structural habitat and climate across radiations
 [https://doi.org/10.5061/dryad.3tx95x6sb](https://doi.org/10.5061/dryad.3tx95x6sb) ## Description of the data and file structure Context-dependent body size evolution in lacertid lizards: differential role of structural habitat and climate across radiations. **Authors** Pablo Vicent-Castelló1,2,3,4, Urtzi Enriquez-Urzelai5, Fernando Martínez-Freíria1,2, Joan Garcia-Porta6, Antigoni Kaliontzopoulou3 1\. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal 2\. BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal 3\. Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals de la Universitat de Barcelona (BEECA), Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona 4\. Departamento de Biologia, Faculdade de Ciências da Universidade do Porto 5\. Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 60300 Brno, Czech Republic 6\. Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain **ORCID corresponding author: [https://orcid.org/0000-0002-4858-4055](https://orcid.org/0000-0002-4858-4055)** **Email corresponding author: [pablovicent0000@gmail.com](mailto:pablovicent0000@gmail.com)** This README is intended to explain what is in each script and what its function is. A list of scripts is provided with a brief description, focusing on what elements you need to run the script and what the outputs are. All the analyses have been run using R code and Rstudio platform. **1. Files** 1.1 00aa_SVL_log_all.csv * csv. file containing the mean logarithmic snout-vent length per species. Information is a combination of data obtained from field campaings and literature.  * SP: species names * SVL: snout-vent length 1.2 00aa_SVL_raw_all.csv * csv. file containing the mean raw snout-vent length per species.  * SP: species names * SVL: snout-vent length 1.3 Habitat_Use_data_2cat.csv * Csv. file containing the structural habitat use information per species that comprises two different categories: ground dwelling and climbing. * SP: species names * hab: habitat use (ground-dwelling, climbing) 1.4 Lacertidae_tree_2_2.tre * Dated Lacertidae phylogenetic tree with. Tree obtained from García-Porta et al., 2019. DOI: [https://doi.org/10.1038/s41467-019-11943-x](https://doi.org/10.1038/s41467-019-11943-x) 1.5 02a_simmaps_1000_ARD_246_datedtree_2cat.bin * .bin file that contains the ancestral state reconstruction of the structural habitat for the entire Lacertidae phylogeny. This file is obtained from Vicent-Castelló et al 2025. DOI: [https://doi.org/10.1093/jeb/voaf003](https://doi.org/10.1093/jeb/voaf003) 1.6 03_models_ENV_morpho_datedtree_newSVL_nhm_1.bin * .bin file that contains the results from the fitting of environmental BM and OU models. Output from: "2.7 03_Analyses_EvoModels__OUwie_habitat_use_3.R" 1.7 03_ouwieMODs_morpho_INS_6cat_2.bin * .bin file that contains the results from the fitting of BM1, OU1, BMS, OUM models using the structural habitat and phylogenetic group reconstruction. Output from: "2.6 02a_Analyses_Simmap_EvoModels_habitat_use_modification_simmaps.R"  1.7 03_ouwieMODs_morpho_Clade_2.bin * .bin file that contains the result from the fitting of BMS and OUM models using the clade-specific classification. Output from: "2.7 03_Analyses_EvoModels__OUwie_clade_2.R" 1.8 03_ouwieMODs_SVL_2cat_datedtree_newSVL_nhm_1.bin * .bin file that contains the results from the fitting of BM1, OU1, BMS, OUM models using the structural habitat reconstruction. Output from: "2.7 03_Analyses_EvoModels__OUwie_habitat_use_3.R" 1.9 03_Temp_from_Cramer.txt * txt. file that contains the temperature values from Cramer et al 2011. DOI: [https://doi.org/10.1029/2011JC007255](https://doi.org/10.1029/2011JC007255) 1.10 03_whitenoisemodel_log.bin * .bin containing the white noise fitting model. Output from: "2.7 03_Analyses_EvoModels__OUwie_habitat_use_3.R" 1.11 tribe.csv * csv. file containing the structural habitat plus phylogenetic group categorization.  * SP: species names * tribe: tribe category (Eremiadini, Lacertini, Gallotinae) 1.12 red.zip * zip. file containing all the distribution ranges of the species, obtained from different sources such as IUCN.  1.13 WC.zip * zip. file containing the topographic rasters of all climatic variables, obtained from different sources. More info in the main text (Material and method section). 1.14 env_data_.csv; env_data_withseasonality.csv; ndvi_annual.csv * Environmental data per species obtained from the script "02_Data_prep_preparing_env95_v3_FMF.R" * precAvg: Mean of average annual precipitation (mm) across the species’ distribution. Related to the water conservation hypothesis. * precMmax: Maximum of average annual precipitation. Water conservation hypothesis. * precMmin: Minimum of average annual precipitation. Water conservation hypothesis. * srad.avg: Mean of average annual solar radiation. Represents available environmental energy. * sradMmax: Maximum of average annual solar radiation (kWh/m²/year). * sradMin: Minimum of average annual solar radiation. * tavg.avg: Mean of average annual temperature (degree C). Related to the heat balance and heat conservation hypotheses. * tavgMmax: Maximum of average annual temperature. Heat balance and conservation. * tavgMmin: Minimum of average annual temperature. Heat balance and conservation. * tmaxMmax: Maximum of the maximum annual temperature. Reflects upper thermal limits. * tmaxMmin: Minimum of the maximum annual temperature. * tminMmax: Maximum of the minimum annual temperature. * tminMmin: Minimum of the minimum annual temperature.  * vapr.avg: Mean vapor pressure (humidity proxy). Influences evaporative potential and water loss. * vaprMmax: Maximum vapor pressure. * vaprMmin: Minimum vapor pressure. * wind.avg: Mean wind speed. May affect evaporative cooling and microhabitat conditions. * windMmax: Maximum wind speed. * windMmin: Minimum wind speed. * elev.avg: Mean elevation across the species’ distribution. Affects climate, oxygen availability, and habitat. * elevMmax: Maximum elevation. * elevMmin: Minimum elevation. * arid.avg: Mean aridity index. Related to seasonality and starvation resistance hypotheses. * aridmax: Maximum aridity. * aridmin: Minimum aridity. * ndvi.avg: Mean Normalized Difference Vegetation Index (NDVI) across the species’ distribution. Reflects primary productivity, indicating the average level of green vegetation. * ndvimax: Maximum NDVI value. Indicates the most vegetated and productive areas occupied by the species. * ndvimin: Minimum NDVI value. Represents the least vegetated or most arid zones within the species' range. * sp: Species name --- **2. Scripts** 2.1 00ab_Figure_Histograma_densities_SVL.R * Density plot visualization. 2.2 00b_Figure_Tree_SVL_Habitat_use.R * Phylogenetic tree visualization and Figure 1. construction.  2.3 01a_Analyses_PhylogeneticSignal_SVL.R * Performing Bloomberg's K analyses to assess the phylogenetic signal. 2.4 01c_Analyses_PGLS_HabUse.R * Phylogenetic ANOVAs to assess body size-structural habitat associations.  2.5 01d_Analyses_PGLS_HabUse_groups.R * Phylogenetic ANOVAs to assess body size-structural habitat associations by phylogenetic groups. 2.6 02a_Analyses_Simmap_EvoModels_habitat_use_modification_simmaps.R * Manual modification of the simmaps "02a_simmaps_1000_ARD_246_datedtree_2cat.bin" in order to account not only for the structural habitat but also for the phylogenetic group in the ancestral state reconstruction. * Downstream model fitting analyses utilizing the modified ancestral state reconstruction.  * Output: "03_ouwieMODs_morpho_INS_6cat_2.bin" 2.7 03_Analyses_EvoModels__OUwie_clade_2.R * Model fitting analysis utilizing ancestral state reconstruction only accounting for clade categorization * Output: "03_ouwieMODs_morpho_Clade_2.bin" 2.7 03_Analyses_EvoModels__OUwie_habitat_use_3.R * Model fitting analyses utilizing ancestral state reconstruction only accounting for structural habitat * Model fitting analyses employing as a determinant factor paleotemperature from Cramer et al 2011. DOI: [https://doi.org/10.1029/2011JC007255](https://doi.org/10.1029/2011JC007255) * Outputs: "03_whitenoisemodel_log.bin"; "03_ouwieMODs_SVL_2cat_datedtree_newSVL_nhm_1.bin"; "03_models_ENV_morpho_datedtree_newSVL_nhm_1.bin" * Information such as: AIC, likelihood, deltaAIC, best model selected is in those files. 2.7 04a.PhyloEM_model_shift detection_major1.R * Shift detection - without a priori clasification 2.9 03b.Explore_EvolMod_Hab.R * Comparison between the outputs ("03_ouwieMODs_morpho_INS_6cat_2.bin"; "03_whitenoisemodel_log.bin"; "03_ouwieMODs_SVL_2cat_datedtree_newSVL_nhm_1.bin"; "03_models_ENV_morpho_datedtree_newSVL_nhm_1.bin", "03_ouwieMODs_morpho_Clade_2.bin") from all the model fittings (modified simmaps, normal simmaps and paleotemperature and white noise), to obtain the best fit for body size evolution. To compare the models we used the modified Akaike Information Criterion (AICc), selecting the model with the lowest value. If more than one model were equally supported (ΔAICc &lt; 4), we chose the simplest one as the best supported model.  2.9 02_Data_prep_preparing_env95_v3_FMF.R * Obtaining the environmental data from climatic and topographic variables and the distribution ranges of the species at 10 mins of resolution (0.17 degrees). Here are being used the files "lac_dists.shp" in red.zip and all the climatic variables on WC.zip.  * Output: "env_data_.csv", "env_data_withseasonality.csv", "ndvi_annual.csv" 2.10 03_Analyses_PhyloLM_def_new.R * Modified phylogenetic regressions that allow to include BM or OU model of evolution. The regressions are between logSVL and climatic variables por especies.