This repository contains all data and code used in the manuscript: "Live birth in lizards: A process-based model for the roles of temperature, behavior, and life history" by Garcia-Costoya et al., published in Evolution Letters (2025)

Description of the data and file structure.

All supplementary files are offered within the compressed folder viviparity-model-supplementary-materials.zip. Within it, the sub-folder data/contains all data used in the manuscript. Within it, there are five files:

1. adult_data.csv: Population-level data on adult characteristics. Contains columns for parity mode (Oviparity or Viviparity), species (in Genus_species format), latitude, longitude (lat, lon - in degrees), elevation (elev - in meters above sea level), adult thermal physiology traits (thermal optimum - topt_a, critical thermal minimum - ctmin_a, critical thermal maximum - ctmax_a all in ^oC), life history traits (mass of adults - za in grams, mass of hatchlings - ze  in grams, clutch/litter size - n), activity hours (activity - e.g., Diurnal, Nocturnal or Cathemeral), substrate use (substrate - Arboreal, Terrestrial, Fossorial, Saxicolous etc.), major biome (biome), timing of embryonic development (month when eggs are first seen in oviducts - eggs_seen, month when hatchlings are first seen - hatchlings_seen), nesting conditions (nest depth in cm - nest_depth, nest shade as a proportion of sun exposure as a percent - nest_shade), and source information for adult thermal physiology data (source - either b for Buckley et al. 2023 or dg for Domínguez-Guerrero et al. 2022) and for life-history trait data (source_lh, either dg for Domínguez-Guerrero et al. 2022 or sb for the SquamBase in Meiri et al. 2023). Furthermore, the columns breed_ref and nest_ref provide reference numbers for breeding phenology and nesting conditions, respectively, which can be correlated with embryo_dev_nest_conditions_citations.xlsx. For populations where no information on breeding phenology was available, we obtained data from the species that was both phylogenetically and geographically closest to the species of interest, and this species is listed in the column breed_other_species. All cases where information was missing are indicated with NA.
2. embryo_thermal_phys.csv: Species level data on embryonic thermal physiology. Contains columns for parity mode, species, embryonic critical thermal minimum (ctmin_e), embryonic thermal optimum (topt_e), and embryonic critical thermal maximum (ctmax_e). All cases where information was missing are indicated with NA.
3. ecophysiological_data.csv: Population-level data simulated via ecophysiological modelling. Contains and monthly specific information on simulated average body temperature during gestation for both adult and embryo (tg in ^oC), post-gestation body temperature for the adult (tap in ^oC), post-gestation body temperature for the embryo when laid in the ground as an egg (tep in ^oC) at different nest depths and shade coverage levels. All data is associated with each population's information (species -species, latitude - lat, longitude - lon, elevation above sea level - elev in the same format as in adult_data.csv) and an estimate of environmental temperature at a reference height of 2m under shade (tenv in ^oC). Further, the columns month (1-12) indicate the month of the year for each record, shade indicates the assumed proportion of sun exposure for the nest (0-1), and depth indicates the depth of the nest in cm.

4.model_test_data.RData: Population and month specific data to test the predictive accuracy of our model. This data contains all information also contained on adult_data.csv and ecophysiological_data.csv in addition to columns to determine whether or not a month falls within the period of embryonic development for that population (dev_check, 0 if the month does not fall within the period and 1 if it does), for the values of the parameters alpha and gamma, and for the model's prediction (opt_d) and fitness of that strategy (fitness). Note that, due to the size of this data set, it is only available in RData format and thus can only be accessed using R.

Sharing/Access information

All data and code are made publicly available via GitHub at: https://github.com/ggcostoya/viviparity-model

Data from the following sources were used in the manuscript:

1. Buckley et al. 2022: https://datadryad.org/stash/dataset/doi:10.5061/dryad.vhhmgqnwq
2. Domínguez-Guerrero et al. 2022: https://www.nature.com/articles/s41467-022-30535-w#Sec30
3. Meiri et al. 2023 (SquamBase): https://datadryad.org/stash/dataset/doi:10.5061/dryad.76hdr7t3b
4. Pettersen et al. 2023: https://osf.io/jt28v/
5. Noble et al. 2018 (Reptile development database): https://repdevo.com/database/

Code/Software

Within the viviparity-model-supplementar-materials.zip, the subfolder scripts/ contains all R scripts used to generate data and figures in the manuscript. There are six scripts:

1. adult_thermal_phys_life_history_traits_additional_info.R: Combines data from Buckley et al. 2022, Domínguez-Guerrero et al. 2022 and the SquamBase (Meiri et al. 2023) to produce adult_data.csv.
2. ecophysiological_modelling.R: Uses adult_data.csv and embryonic_thermal_phys.csv to perform the ecophysiological modelling using NicheMapR and produce eco_data.csv.
3. embryonic_thermal_physiology.R: Combines data from Pettersen et al. 2023 the reptile development database (Noble et al. 2018) to produce embryo_thermal_phys.csv.
4. fit_model_sensitivity_analysis.R: Uses adult_data.csv, eco_data.csv and embryonic_thermal_phys.csv to produce model_test_data.RData.
5. plot_figures.R: Plots all manuscript and supplementary figures using embryonic_thermal_phys.csv, adult_data.csv and model_test_data.RData.
6. supplementary_tables.R: Summarizes each data set to produce all tables within the supplementary materials and runs the three models described in the methods of the manuscript.

All analysis were performed using R version 4.2.2 (2022-10-31). The required packages are listed at the start of each script.