Data and code from: Interspecific allometry of sexual shape dimorphism in small-bodied and large-bodied geckos
Data files
Dec 05, 2025 version files 2.03 MB
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Analyses.R
4 KB
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JetzTree.tre
455.94 KB
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README.md
5.04 KB
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shapedata.csv
1.50 MB
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spec.info.csv
64.29 KB
Abstract
At macroevolutionary scales and across species, levels of sexual dimorphism often covary with body size, generating allometric trends. While such patterns are most evident for sexual size dimorphism, interspecific trends in sexual shape dimorphism (SShD) remain underexamined. Furthermore, how such patterns are affected by the evolution of small body size (miniaturization) is largely unknown. In this study, we evaluated trends in SShD across 99 gecko species from two families to determine whether small body sizes were associated with increased shape dimorphism in the group. Head shape was characterized using geometric morphometrics from surface scans of nearly 600 individuals, and levels of SShD were quantified for each species. Phylogenetic comparative analyses were then used to evaluate evolutionary patterns of shape dimorphism relative to body size across species. We found considerable variation in the magnitude of SShD across taxa, with some species displaying little dimorphism and others exhibiting large sexual shape differences. Interspecific allometry of SShD differed between the two families, with strong negative allometry observed in Sphaeorodactylidae (a family with many small-bodied species), while in Phyllodactylidae (a family containing few small-bodied species) patterns were more isometric with no discernable trend. Notably, the greater SShD displayed by small-bodied species corresponded with females exhibiting more robust heads, which was consistent with sex-specific foraging strategies and dietary differences observed in this group. Our study reveals that interspecific allometry in traits other than body size can have a pervasive influence on patterns of phenotypic diversity across the tree of life.
Dataset DOI: 10.5061/dryad.ttdz08m9g
Description of the data and file structure
This dataset was generated to examine macroevolutionary patterns of sexual shape dimorphism (SShD) in geckos in relation to extreme body size. Three-dimensional head shape data were collected from 3D photogrammetry scans of nearly 600 adult geckos representing 99 species across two families: Sphaerodactylidae and Phyllodactylidae. Landmark coordinates were digitized and aligned using geometric morphometric methods to quantify variation in cranial shape. Associated metadata include species identity, sex, family, and body size (snout–vent length). A time-calibrated phylogeny, trimmed from the Tonini et al. (2016) squamate trees, provides evolutionary context for all comparative analyses. These data were used to evaluate interspecific allometry of sexual shape dimorphism and to test whether miniaturization is associated with shifts in dimorphism magnitude or direction.
Files and variables
File: Analyses.R
Description: R script reproducing all analyses presented in Glynne & Adams (2025).
The script includes data import, shape alignment, species and sex-specific mean calculations, computation of sexual size and shape dimorphism (SSD, SShD), and all phylogenetic comparative analyses (E-PGLS, family-specific allometry, SSD–SShD regression, and phylogenetic ANOVA).
All analyses were run in R v4.3+ using the packages geomorph, ape, phytools, and RRPP.
File: JetzTree.tre
Description: Time-calibrated ultrametric phylogeny for geckos, derived from the Tonini et al. (2016) fully sampled squamate tree.
This version is trimmed to the 99 species included in the present dataset.
Branch lengths are in millions of years, representing divergence times among taxa, and are used as the phylogenetic covariance structure for all comparative analyses.
File: spec.info.csv
Description: Specimen-level metadata linking each individual to species identity, sex, body size, and taxonomic family.
Used to match individuals to morphometric data and to compute species- and sex-specific means for downstream analyses.
Variables
- species_id: Species name in the format Genus_species matching tree tip labels.
- *comb**id: *Unique specimen identifier combining species and individual codes. Where each one consists of Genusspecies-Museum Specimen Number.
- Sex: Biological sex of the specimen (m = male, f = female).
- SVL: Snout–vent length (mm). Standard body size measurement.
- Family: Gecko family assignment: Phyllodactylidae or Sphaerodactylidae
File: shapedata.csv
Description: Three-dimensional landmark coordinate data representing head shape for each individual.
Landmarks were digitized from 3D photogrammetric models of gecko specimens using geometric morphometric methods.
Coordinates were Procrustes-aligned prior to analysis, and each row corresponds to a single specimen.
The dataset contains 68 landmarks (each with X, Y, Z coordinates), flattened into sequential numeric columns (V1–V204).
Variables
- Species_ID: Species identifier matching spec.info.csv
- V1–V204: Flattened 3D coordinates (68 × 3 = 204 numeric columns representing X, Y, Z positions) of each m and f average for each genus species
- V1–V3 = Landmark 1 (X, Y, Z)
- V4–V6 = Landmark 2 (X, Y, Z)
- … continuing through V202–V204 = Landmark 68 (X, Y, Z).
Code/software
All analyses were performed in R (version 4.3.2) using the following packages:
- geomorph (version 4.1.4): For Procrustes alignment, morphometric analyses, and shape visualization.
- ape (version 5.8): For phylogenetic data handling, tree manipulation, and covariance matrix computation.
- phytools (version 2.3.0): For continuous trait mapping, visualization of phylogenetic patterns, and time-scaled plotting.
- RRPP (version 1.4.1): For phylogenetic regression, MANOVA, and permutation-based hypothesis testing.
Morphometric data were derived from 3D photogrammetric models processed in meshroom (version 2021) and landmarked using Checkpoint Stratovan (version 2022).
All scripts are fully reproducible and included in the file Analyses.R.
Access information
The time-calibrated phylogeny used in this study is derived from the Tonini et al. fully-sampled squamate tree, and is publicly accessible via Dryad: https://datadryad.org/dataset/doi:10.5061/dryad.db005
License: CC0 / public domain (as per Dryad’s terms)
Specimen-level morphometric and metadata in this dataset were collected from 13 biological collections (museums). The institutional codes and catalog numbers are included in spec.info.csv (column “combid” or equivalent) to allow tracing back to original specimen vouchers. For example, collection abbreviations such as “TCWC” appear in the dataset, among others.