Walking or hanging: the role of habitat use for body shape evolution in lacertid lizards
Data files
Jan 15, 2025 version files 11.48 MB
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00ab_all_morph_GLS_resid_complete_datedtree_186.bin
12.20 KB
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00ab_all_morph_NHM_AK_AH_186.csv
71.39 KB
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05a_Data_Groups_climbing_Ct_2.xlsx
10.87 KB
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05a_Data_Groups_grownd_dwelling_Ct_2.xlsx
11.60 KB
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Bootstrap_models_2711.bin
8.05 KB
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Bootstrap_models_2811.bin
1.38 KB
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Codes_specimens_re.xlsx
46.55 KB
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Habitat_Use_data_2cat.csv
7.82 KB
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Lacertidae_tree_2_2.tre
10.19 KB
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README.md
8.08 KB
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simmaps_2cat_1000_ARD_datedtree.bin
11.30 MB
Abstract
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.
README: Walking or hanging: the role of habitat use for body shape evolution in lacertid lizards
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
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals de la Universitat de Barcelona (BEECA), Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona
- Département Adaptations du Vivant, Bâtiment, UMR 7179 MECADEV C.N.R. S/M.N.H.N., d'Anatomie Comparée, Paris, France
- Department of Biology, Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium
- Department of Biology, University of Antwerp, Wilrijk 2610, Belgium
- Naturhistorisches Museum Bern, Bern 3005, Switzerland
corresponding author: 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
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: