Data from: Generation length of the world's amphibians and reptiles
Data files
Mar 07, 2025 version files 7.60 MB
-
amphibian_full_data.csv
2.10 MB
-
generation_length_herps.csv
991.36 KB
-
README.md
8.26 KB
-
squamates_full_data.csv
4.41 MB
-
testudines_full_data.csv
87.41 KB
Mar 25, 2025 version files 8.02 MB
-
amphibian_full_data.csv
2.10 MB
-
generation_length_herps.csv
1.41 MB
-
README.md
8.65 KB
-
squamates_full_data.csv
4.41 MB
-
testudines_full_data.csv
87.41 KB
Abstract
Variation in life histories influences demographic processes, from adaptive changes to population declines leading to extinction. Among life history traits, generation length offers a critical feature to forecast species’ demographic trajectories such as population declines (widely used by the IUCN Red List) and adaptability to environmental change over time. Therefore, estimates of generation length are crucial to monitor demographic stability or predict future changes in highly threatened organisms, particularly amphibians and reptiles, which are particularly threatened among vertebrates and for which uncertainty in future impacts remains high. Despite its importance, generation length for amphibians and reptiles is largely missing. Here, we aim to fill-in this gap by modeling generation lengths for amphibians, squamates and testudines as a function of species size, climate, life history, and phylogeny using generalized additive models and phylogenetic generalized least squares. We estimated generation lengths for 5,059 (57%) amphibians, 8,722 (73%) squamates and 117 (32%) testudines. Our models performed well for most families (e.g., Bufonidae among amphibians, Lacertidae and Colubridae among squamates, and Geoemydidae among testudines), while we found high uncertainty around the prediction of a few families, notably Chamaeleonidae. Species’ body size and mean temperature were the main predictors of generation length in all groups. Although our estimates are not meant to substitute robust and validated measurements from field studies or natural history museums, they can help reduce existing biases in conservation assessments until field data will be comprehensively available.
https://doi.org/10.5061/dryad.w0vt4b93t
Description of the data and file structure
Files and variables
File: amphibian_full_data.csv
Description:
Variables
- scientificName: (character) species binomial
- generation_length_y: (numeric) average generation length in years
- source_GL: (character) source of generation length
- generation_length_y.pgls: (numeric) average generation length in years predicted by PGLS
- generation_length_y.gam: (numeric) average generation length in years predicted by GAM
- Body_mass_g: (numeric) species body mass in grams, NAs represent missing data
- source_bodymass: (character) source of body mass, NAs represent missing data
- SVL_mm: (numeric) species snout-vent length in mm, NAs represent missing data
- source_SVL: (character) source of SVL, NAs represent missing data
- bio01: (numeric) annual temperature in °C
- bio04: (numeric) temperature seasonality °C/100
- bio12: (numeric) annual precipitation in kg m-2 year-1
- bio15: (numeric) precipitation seasonality kg m-2
- life_history_mode: (character) life history modes, NAs represent missing data
- eigenV_c8: (numeric) phylogenetic eigenvector, NAs represent missing data
- eigenV_c99: (numeric) phylogenetic eigenvector, NAs represent missing data
- eigenV_c62: (numeric) phylogenetic eigenvector, NAs represent missing data
- eigenV_c71: (numeric) phylogenetic eigenvector, NAs represent missing data
- familyName: (character) species family
- family.LOO.NRMSE.gam: (numeric) NRMSE for leave one out validation for GAM, NAs only for species not used to calibrate models
- family.LOO.RMSE.gam: (numeric) RMSE for leave one out validation for GAM, NAs only for species not used to calibrate models
- family.dimension: (numeric) number of species per family in training set, NAs only for species not used to calibrate models
- family.block.RMSE.gam: (numeric) RMSE for family block validation for GAM, NAs only for species not used to calibrate models
- family.block.NRMSE.gam: (numeric) NRMSE for family block validation for GAM, NAs only for species not used to calibrate models
- family.block.RMSE.pgls: (numeric) RMSE for family block validation for PGLS, NAs only for species not used to calibrate models
- family.block.NRMSE.pgls: (numeric) NRMSE for family block validation for PGLS, NAs only for species not used to calibrate models
- family.LOO.RMSE.pgls: (numeric) RMSE for leave one out validation for PGLS, NAs only for species not used to calibrate models
- family.LOO.NRMSE.pgls: (numeric) NRMSE for leave one out validation for PGLS, NAs only for species not used to calibrate models
File: generation_length_herps.csv
Description:
Variables
- internalTaxonId: (numeric) IUCN ID for the species
- scientificName: (character) species binomial
- generation_length_y: (numeric) average generation length in years
- source_GL: (character) source of generation length
- familyName: (character) species family
- family.LOO.NRMSE.avg: (numeric) average NRMSE of PGLS and GAM leave one out validation, NAs only for species not used to calibrate models
- group: (character) species group: amphibian, squamata or testudines
File: testudines_full_data.csv
Description:
Variables
- scientificName: (character) species binomial
-
generation_length_y: (numeric) average generation length in years
-
generation_length_y.pgls: (numeric) average generation length in years predicted by PGLS
-
generation_length_y.gam: (numeric) average generation length in years predicted by GAM
- source_GL: (character) source of generation length
-
Body_mass_g: (numeric) species body mass in grams, NAs represent missing data
- bio01: (numeric) annual temperature in °C
- bio04: (numeric) temperature seasonality °C/100
- bio12: (numeric) annual precipitation in kg m-2 year-1
-
bio15: (numeric) precipitation seasonality kg m-2
- Insularity: (character) species insularity, NAs represent missing data
- Max_longevity_d: (numeric) species maximum longevity in days, NAs represent missing data
- source_MaxLongevity: (character) source of maximum longevity, NAs represent missing data
- Maturity_d: (numeric) species age at maturity in days, NAs represent missing data
- source_maturity: (character) source of age at maturity, NAs represent missing data
- familyName: (character) species family
- family.LOO.NRMSE.gam: (numeric) NRMSE for leave one out validation for GAM
- family.LOO.RMSE.gam: (numeric) RMSE for leave one out validation for GAM
- family.dimension: (numeric) number of species per family in training set, NAs only for species not used to calibrate models
- source_bodymass: (character) source of body mass, NAs represent missing data
- family.block.RMSE.gam: (numeric) RMSE for family block validation for GAM, NAs only for species not used to calibrate models
- family.block.NRMSE.gam: (numeric) NRMSE for family block validation for GAM, NAs only for species not used to calibrate models
- family.block.RMSE.pgls: (numeric) RMSE for family block validation for PGLS, NAs only for species not used to calibrate models
- family.block.NRMSE.pgls: (numeric) NRMSE for family block validation for PGLS, NAs only for species not used to calibrate models
- family.LOO.RMSE.pgls: (numeric) RMSE for leave one out validation for PGLS, NAs only for species not used to calibrate models
- family.LOO.NRMSE.pgls: (numeric) NRMSE for leave one out validation for PGLS, NAs only for species not used to calibrate models
File: squamates_full_data.csv
Description:
Variables
- scientificName: (character) species binomial
- generation_length_y: (numeric) average generation length in year
-
source_GL: (character) source of generation length
- generation_length_y.pgls: (numeric) average generation length in years predicted by PGLS
- generation_length_y.gam: (numeric) average generation length in years predicted by GAM
-
Body_mass_g: (numeric) species body mass in grams, NAs represent missing data
- bio01: (numeric) annual temperature in °C
- bio04: (numeric) temperature seasonality °C/100
-
bio12: (numeric) annual precipitation in kg m-2 year-1
-
bio15: (numeric) precipitation seasonality kg m-2
- Max_longevity_d: (numeric) species maximum longevity in days, NAs represent missing data
- source_MaxLongevity: (character) source of maximum longevity, NAs represent missing data
- Maturity_d: (numeric) species age at maturity in days, NAs represent missing data
-
source_maturity: (character) source of age at maturity, NAs represent missing data
- familyName: (character) species family
- family.LOO.NRMSE.gam: (numeric) NRMSE for leave one out validation for GAM
- family.LOO.RMSE.gam: (numeric) RMSE for leave one out validation for GAM
- family.dimension: (numeric) number of species per family in training set, NAs only for species not used to calibrate models
- eigenV_c3: (numeric) phylogenetic eigenvector, NAs represent missing data
- eigenV_c28: (numeric) phylogenetic eigenvector, NAs represent missing data
- eigenV_c22: (numeric) phylogenetic eigenvector, NAs represent missing data
- eigenV_c35: (numeric) phylogenetic eigenvector, NAs represent missing data
- eigenV_c87: (numeric) phylogenetic eigenvector, NAs represent missing data
-
eigenV_c18: (numeric) phylogenetic eigenvector, NAs represent missing data
- family.block.RMSE.gam: (numeric) RMSE for family block validation for GAM, NAs only for species not used to calibrate models
- family.block.NRMSE.gam: (numeric) NRMSE for family block validation for GAM, NAs only for species not used to calibrate models
- family.block.RMSE.pgls: (numeric) RMSE for family block validation for PGLS, NAs only for species not used to calibrate models
- family.block.NRMSE.pgls: (numeric) NRMSE for family block validation for PGLS, NAs only for species not used to calibrate models
- family.LOO.RMSE.pgls: (numeric) RMSE for leave one out validation for PGLS, NAs only for species not used to calibrate models
-
family.LOO.NRMSE.pgls: (numeric) NRMSE for leave one out validation for PGLS, NAs only for species not used to calibrate models
- Insularity: (character) species insularity, NAs represent missing data
- source_insularity: (character) source of insularity, NAs represent missing data
- source_bodymass: (character) source of body mass, NAs represent missing data
Version changes
25-mar-2025: The file generation_length_herps.csv was updated to include the Red List ID for the species and the average NRMSE of GAM and PGLS associated to the prediction.