Data from: The effect of miniaturization on the evolution of sexual size dimorphism in geckos

https://doi.org/10.5061/dryad.kkwh70sb4

GENERAL INFORMATION & METADATA

1. Title of Dataset: Data from: The effect of miniaturization on the evolution of sexual size dimorphism in geckos
2. Author Information

Corresponding Investigator: Elizabeth Glynne, eglynne@iastate.edu, Iowa State University, Ames, Iowa

Co-investigator 1: Dean C. Adams, Iowa State University, Ames, Iowa
3. Date of data collection: 2020-2022
4. Geographic location of data collection: Ames, Iowa, United States
5. Funding Source: National Science Foundation
6. Recommended citation for this dataset: Glynne and Adams (2023), Data from: The effect of miniaturization on the evolution of sexual size dimorphism in geckos
7. Journal Name: Submitted to Evolution
8. Abstract: The evolution of miniaturization can result in dramatic alterations of morphology, physiology, and behavior; however, the effects of miniaturization on sexual dimorphism remain largely unknown. Here we investigate how miniaturization influences patterns of sexual size dimorphism (SSD) in geckos. Measuring 1,875 individuals from 131 species, we characterized patterns of SSD relative to body size across two families. We found that miniaturized species were more female-biased than nonminiaturized species. Additionally, one family, Phyllodactylidae, contained few miniaturized species and displayed an isometric trend in SSD with body size, where changes in female body size were accompanied by similar changes in male body size. By contrast, Sphaerodactylidae, which contained many miniaturized species, displayed strongly allometric patterns, where larger species were male-biased and smaller species were more female-biased. Smaller species in this lineage also produced proportionally larger eggs. Together, these observations are consistent with the hypothesis that selection for increased reproductive success in small species drives the positive SSD allometry observed in the lineage, and that selection for increased miniaturization in the clade may be offset by selection on maintaining a female size in smaller taxa that ensures reproductive success.
9. Research domain (based on OECD Fields of Science and Technology): Biological Sciences

DATA & FILE OVERVIEW

1. Description of dataset:

Linear measurements were collected from alcohol-preserved gecko specimens. All specimen measurements and MUSE_ID numbers are included in the GlAd_2023_SSDgekData.csv. The corresponding museum code key is provided in Museum_Name_Key.xls. These files can be accessed using any .csv/.xls reading programs (e.g., Excel, R).

Code for analyses can be accessed using the software program R, which can be downloaded here: https://cran.r-project.org/bin/windows/base/

Within R, the packages utilized can be installed and used with the following code:

install.packages("RRPP")

install.packages("gieger")

install.packages("phytools")

install.packages("phylolm")

install.packages("ggplot2")
2. File List:
* File Name: GlAd_2023_SSDgekData.csv = Specimen data used in analyses.
* VARIABLE DEFINITIONS & UNITS
1. X: Row number (integer)
2. ID: Unique identification number for each specimen
3. Family: Taxonomic family of the specimen (e.g., Phyllodactylidae)
4. Genus_species: Genus and species name of the specimen (e.g., Hemidactylus_turcicus)
5. Sex: Sex of the specimen (f = female, m = male)
6. SVL: Snout-to-vent length (in millimeters)
7. Hip: Hip width (in millimeters)
8. EL_min: Minimum egg length (in millimeters)
9. EL_max: Maximum egg length (in millimeters)
10. EG_min: Minimum egg girth (in millimeters)
11. EG_max: Maximum egg girth (in millimeters)
12. logSVL: Log-transformed snout-to-vent length
13. sp.sex: Species-specific sex (categorical variable indicating specific sex-related information, if any)

Note: If data was not available, it will read NA

Egg size data was translated and gathered from: Rösler, H. (2004). Kommentierte Liste der rezent, subrezent und fossil bekannten Geckotaxa (Reptilia: Gekkonomorpha). Gekkota, 4, 28-153.
* File Name: Museum_Name_Key.xls = Museum institution codes and corresponding names.
* File Name: 2023_10-SSDGekAnalyses_resub.R = This R script performs a comprehensive analysis of sexual size dimorphism (SSD) in geckos, specifically examining the effects of miniaturization. It includes loading and pruning phylogenetic data, calculating SSD indices, and testing for allometric patterns.
* Key steps and procedures include:
1. Loading and Pruning Data:
* The phylogenetic tree (JetzTree.tre) and specimen measurement data (GlAd_2023_SSDgekData.csv) are loaded.
* Data is pruned to match the phylogeny and prepare for analysis.
2. Calculating Means and Variances:
* Means and variances of snout-to-vent length (SVL) and log-transformed SVL (logSVL) are calculated for male and female specimens.
* A new dataframe (SVL.dat) is created to store these calculated values.
3. Identifying Miniaturized Species:
* Species with male and female SVL below a certain threshold are classified as miniaturized.
* A size group factor (sz.gp) is created to distinguish between miniaturized and non-miniaturized species.
4. Matching Data to Phylogeny:
* The phylogenetic tree is pruned to include only the species present in the data.
* Phylogenetic variance-covariance matrices are created for further analysis.
5. Comparing Miniature vs. Non-miniature Species:
* Linear models with random effects are used to compare SSD indices between miniaturized and non-miniaturized species.
* Phylogenetic generalized least squares (PGLS) models are fitted to account for phylogenetic relationships.
6. SSD Allometry by Family:
* Separate analyses are conducted for the Phyllodactylidae and Sphaerodactylidae families.
* Linear models with random effects are used to test for allometric patterns within each family.
7. Tests Using Intraspecific Variation:
* Additional tests are performed to compare slopes against a theoretical isometric slope of 1.0 for both families.
8. Mapping SSD on Phylogeny:
* Ancestral state reconstruction and phylogenetic mapping are performed to visualize SSD across the phylogeny.
9. Egg Size Analysis:
* Data on egg size (maximum egg length) is analyzed in relation to SVL.
* Proportional egg sizes are compared between species of different body sizes.

This script utilizes several R packages, including phytools, geiger, RRPP, phylolm, and ggplot2, for phylogenetic analysis, statistical modeling, and data visualization.
* File Name: JetzTree.tre = A .tre file that houses the phylogeny cited in the manuscript and used in the analyses. 
* File Name: phy-bootEstimates.txt = A .txt file that houses bootstrap estimates for the Phyllodactylidae family called for in the analyses.
* File Name: sph-bootEstimates.txt = A .txt file that houses bootstrap estimates for the Sphaerodactylidae family called for in the analyses.
3. METHODOLOGICAL INFORMATION

We measured body size (snout-to-vent length: SVL) from a total of 1,875 adult specimens using digital calipers, with a minimum of 3 males and 3 females per species. Measurements were log-transformed, and the mean of each species by sex combination was calculated. Egg size data were obtained from Rösler (2004) and matched to corresponding species means for females. The phylogenetic tree data used in the analyses were based on the study by Tonini et al. (2016), which provided a comprehensive phylogeny for squamates.