DOI: 10.5061/dryad.280gb5mxk
title: Walking or hanging: the role of habitat use for body shape evolution in lacertid lizards

description: Differences in habitat use impose ecological constraints which in turn
 lead to functional and morphological differences through adaptation. In
 fact, a convergent evolutionary pattern is evident when species exhibit
 similar responses to similar environments. In this study we examine how
 habitat use influences the evolution of body shape in lizards from the
 family Lacertidae. We divided our species set into two categories:
 ground-dwellers and climbers, which encompasses the verticality and
 horizontality aspects of the habitat. We performed phylogenetic
 comparative analyses employing 186 species and seven linear morphological
 traits. Our results show contrasting patterns between head and limb shape,
 which are considered distinct functional blocks. We observed differences
 in forelimb proportions, but not in hindlimb length, contrary to what was
 documented in other lizard groups, demonstrating a novel axis in the
 limb-locomotion-habitat relationship in this family. In addition, a clear
 effect of habitat use on head shape was detected. We observed that
 climbing species present on average flatter heads than ground-dwelling
 species, as well as different evolutionary trajectories. These findings
 suggest the complex interplay between habitat use and morphological
 evolution in lizards, highlighting how distinct selective pressures drive
 divergent adaptations in different functional traits. 
description: # Walking or hanging: the role of habitat use for body shape evolution in
 lacertid lizards
 [https://doi.org/10.5061/dryad.547d7wmjf](https://doi.org/10.5061/dryad.547d7wmjf) ## Description of the data and file structure Title: Walking or hanging: the role of habitat use for body shape evolution in lacertid lizards Authors: Pablo Vicent-Castelló1,2,3, Anthony Herrel4,5,6,7, D. James Harris1,2, 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. Département Adaptations du Vivant, Bâtiment, UMR 7179 MECADEV C.N.R. S/M.N.H.N., d'Anatomie Comparée, Paris, France 5. Department of Biology, Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium 6. Department of Biology, University of Antwerp, Wilrijk 2610, Belgium 7. Naturhistorisches Museum Bern, Bern 3005, Switzerland corresponding author: [pablovicent0000@gmail.com](mailto:pablovicent0000@gmail.com) Abstract: Differences in habitat use impose ecological constraints which in turn leads to functional and morphological differences through adaptation. In fact, a convergent evolutionary pattern is evident when species exhibit similar responses to similar environments. In this study we examine how the habitat use influences the evolution of body shape in lizards from the family Lacertidae. We divided our species set in two categories: ground-dwellers and climbers, which encompasses the verticality and horizontality aspects of the habitat. We performed various phylogenetic comparative analyses employing 186 species and seven linear morphological traits. Our results show contrasting patterns between functional block traits (head vs limbs). We observed differences in fore limb proportions, but not in hind limb length, contrary to what was documented in other lizard groups demonstrating a novel axis in the limb-locomotion-habitat relationship in this family. In addition, a clear effect of the habitat use on head shape was detected. We observed that climbing species present on average flatter heads than ground-dwelling species, as well as different evolutionary trajectories. --- 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 Habitat_Use_data_2cat.csv** Csv. file containing the structural habitat use information per species that comprises two different castegories: ground dwelling and climbing.  **1.2 Lacertidae_tree_2_2.tre** Dated Lacertidae 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) **1.3. 00ab_all_morph_GLS_resid_complete_datedtree_186.bin** Dataset with the log, mean, size corrected morphological trait data. This dataset contains: head length, head width, head height, mouth length, hindlimb length, forelimb length and trunk.  **1.3.1. 00ab_all_morph_NHM_AK_AH_186.csv** Raw morphological data for all individuals analyzed in this study. It contains the information of ead length, head width, head height, mouth length, hindlimb length, forelimb length and trunk in millimeters.  **1.4 "simmaps_2cat_1000_ARD_datedtree.bin"** Output from the script "02_Simmap_habitat_use_2cat_ARD.R". It contains the ancestral state reconstruction of the structural habitat for the entire phylogeny.  ### **2. Scripts** **2.1 00b_PhylogeneticSignal_allmorph.R** Performing Pagel's lambda analyses to assess the phylogenetic signal. **2.2 00f_PCAs_DensityPlot_.R** PCA and Density plot visualization. **2.3 07_Morphological_disparity.R** Morphological disparity analyses. **2.4 01_PGLS_allmorph_sizecorrectedGLS_BOXPLOT.R** Phylogenetic ANOVAs and MANOVAs, with a boxplot visualization. **2.5 02_Simmap_habitat_use_2cat_ARD.RR** Simmap analysis. First, a compariston between the three different models (ARD, ER and SYM), followed by an analysis with ARD model- the best fitted model - and 1000 simulations. Output: "simmaps_2cat_1000_ARD_datedtree.bin" **2.6 02b_Explore_Simmap_habitat_use.R** Exploratory script to observed different characteristic of the simmap's output. **2.7 03_EvoModels__OUwie_habitat_use_allmorph_sizecorrectedGLS.R** Model fitting using the OUwie package to see which model best fits our data. In this analysis we performed 100 simulations. It requires a powerful machine and aprox 2-3 days of time (depending of the computer's power). The output: "03_results_ouwieMODs_shape_sizecorrectedGLS_log10trans_2cat_ARD_246sp_datedtree_5models_186_100_2.bin" which will be used in the next script (03b.Explore_EvolModels_OUwie.R). This .bin file is not included here due to its heaviness. **2.8 03_EvoModels__OUwie_Bootstrap_estimation** Bootstraping estimation to obtain the confidence interval of the estimates from the previous script. From here we obtain: 1 single ouput, which in this case is divided in two: bootstrap 2711 and bootstrap 2811. However, when running the script one single output will be produced. **2.9. 03b.Explore_EvolMod_Hab_allmorph.R** Exploratory script to look at different aspects of model fit. First, we investigate the fitness of fit (negative eigenvalues), then we determine which model is the best per morphological variable using the delta AICc, and finally we subtract the relevant indices. **3.0. 03_Explore__OUwie_Bootstrap_estimation** Exploratory script to obtain the confidence intervals of the estimates parameters of the best fit models. **3.1 05a_Convergence evolution_CT.R** Convergent analyses using convevol package. The output is showed in the Rstudio panel: 05a_Data_Groups_climbing_Ct_2.xlsx 05a_Data_Groups_grownd_dwelling_Ct_2.xlsx ### Files and variables #### File: 00ab\_all\_morph\_GLS\_resid\_complete\_datedtree\_186.bin **Description:**  .bin file containing the mean, log and size corrected data. It provides a single value per species for all morphological variables. #### File: 05a\_Data\_Groups\_climbing\_Ct\_2.xlsx **Description:** xlsx with the combined groups for convergence analysis.  #### File: 05a\_Data\_Groups\_grownd\_dwelling\_Ct\_2.xlsx **Description:** xlsx with the combined groups for convergence analysis.  #### File: Bootstrap\_models\_2711.bin **Description:** Output 1 from Bootstraping analysis.  #### File: Bootstrap\_models\_2811.bin **Description:** Output 2 from Bootstraping analysis.  #### File: Codes\_specimens\_re.xlsx **Description:** xlsx with the information for each individual and its corresponding code. Empty cells indicates absence of information.  #### File: Habitat\_Use\_data\_2cat.csv **Description:** csv. with the structural habitat information ##### Variables * species: species * habitat_use: structural habitat categories: ground dwelling and climbing #### File: 00ab\_all\_morph\_NHM\_AK\_AH\_186.csv **Description:** Raw data in mm  ##### Variables * sp: species * svl: snount-vent length * trunk: trunk * headlength: head length * headwidth: head width * headheight: head height * mouthopening: mouth length * forelimblength: forelimb length * hindlimblength: hindlimb length ## Code/software All the code is developed using R and Rstudio. The needed packages are provided in each ".R" file.  R info: ``` R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631) ``` ## Access information Other publicly accessible locations of the data: * [https://github.com/pablecastel/evolution-shape.git](https://github.com/pablecastel/evolution-shape.git)