Social environment and the evolution of delayed reproduction in birds
Data files
Aug 11, 2025 version files 161.63 KB
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data_clean.tsv
157.22 KB
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README.md
4.41 KB
Abstract
One puzzling feature of avian life histories is that individuals in many different lineages delay reproduction for several years after they finish growing. Intraspecific field studies suggest that various complex social environments—such as cooperative breeding groups, nesting colonies, and display leks—result in delayed reproduction because they require forms of sociosexual development that extend beyond physical maturation. Here, we formally propose this hypothesis and use a full suite of phylogenetic comparative methods to test it, analyzing the evolution of age at first reproduction (AFR) in females and males across 963 species of birds. Phylogenetic regressions support increased AFR in colonial females and males, cooperatively breeding males, and lekking males. Continuous Ornstein-Uhlenbeck models support distinct evolutionary regimes with increased AFR for all of the cooperative, colonial, and lekking lineages. Discrete hidden state Markov models suggest a net increase in delayed reproduction for social lineages, even when accounting for hidden state heterogeneity and the potential reverse influence of AFR on sociality. Our results support the hypothesis that the evolution of social environments reshapes the dynamics of life history evolution in birds. Comparative analyses of even the most broadly generalizable characters, such as AFR, must reckon with unique, heterogeneous, historical events in the evolution of individual lineages.
https://doi.org/10.5061/dryad.ttdz08m80
This repository contains the data (data_clean.tsv) and analysis files needed to replicate the analyses in our manuscript.
NOTE - The original version of the dataset includes full source quotation information and explanations of how every AFR value is derived from available information. These raw quotations cannot be provided in this repository due to copyright restrictions. Contact L. U. Taylor for a version of the dataset with all quotations.
Data file descriptions
data_clean.tsv
- Index_Clements: (int) Taxonomic index from the Clements v2023b Taxonomy
- Avibase_ID: (chr) AviBase ID associated with this taxon in the Clements v2023b Taxonomy
- Order_Clements: (chr) Taxonomic Order from the Clements v2023b Taxonomy
- Family_Clements: (chr) Taxonomic Family from the Clements v2023b Taxonomy
- Taxon_Clements: (chr) Genus and species binomial from the Clements v2023b Taxonomy
- Common_Clements: (chr) Common English name from the Clements v2023b Taxonomy
- Colony: (bool) Is the taxon colony-nesting? (1=yes, 0=no)
- Lek: (bool) Is the taxon cooperative breeding? (1=yes, 0=no)
- Parental_Care: (chr) Parent care code from Cockburn 2006 [! indicates revisions from that dataset]
- Social_Context: (chr) Final social category for analysis (Colony, Cooperative, Lek, Other)
- Mass: (chr) Mass (g) from the AVONET dataset.
- Min_AFR_F: (int) Minimum reported age at first reproduction (yr), females
- Min_AFR_Log_F: (dbl) Minimum reported age at first reproduction (log2 yr), females
- Min_AFR_M: (int) Minimum reported age at first reproduction (yr), males
- Min_AFR_Log_M: (dbl) Minimum reported age at first reproduction (log2 yr), males
- Min_AFR_Diff: (int) Difference between ages at first reproduction, males - females (yr)
- Source_AFR: (chr) Source for age at first reproduction data.
- BOW = Cornell's Birds of the World
- BWP = The Birds of the Western Palearctic
- HANZAB = Handbook of Australian, New Zealand, and Antarctic Birds
- BA = The Birds of Africa
- BA(M) = The Birds of Africa (Madagascar)
- Other references given with full citation information
- Tip_Label: (chr) Underscore-delimited Genus_species name for matching with tree labels
Running the code
First, create a Data/directory. Add the following files.
- data_clean.tsv
- dated_rand_sample_clements.tre (download from McTavish et al. 2024)
- tree_images.r (information for drawing PhyloPic images on the tree figures)
Next, create a Scripts/ directory. Add all .sh and .r files:
- 1_wrangle_data.sh (wrangles the main data file to a clean version for analyses). NOTE: This script was already run to produce the data_clean.tsv file provided in this repository. A raw, unformatted Excel file is not provided.
- 2_rrppanova.sh (RRPP ANOVA with Brownian covariance structures)
- 3_pgls.sh (phylogenetic generalized least squares models in nlme)
- 4_ou_models.sh (continuous evolutionary models in OUwie)
- 5-1_corhmm_F.sh and 5-2_corhmm_M.sh (discrete evolutionary models in corHMM, for parallel Female and M dataset runs)
- 6_tables_and_figures.sh (generates MS tables and figures; requires all results from Scripts 1-5)
Running the bash scripts in order will reproduce the analyses in the manuscript.
Software requirements
Scripts are written for Unix bash (Ubuntu) and R v4.4.1. See scripts and manuscript for packages and software citations. Bash scripts were originally run with Yale HPC resources (McClearly cluster) and Bowdoin HPC resources using slurm and Dead Simple Queue.
Required R packages can be installed in R with:
install.packages(c("tidyverse",
"readxl",
"ape",
"furrr",
"OUwie",
"progressr",
"corHMM",
"RRPP",
"nlme",
"broom.mixed",
"ggtree",
"ggtreeExtra",
"scales",
"patchwork"))
Secondary data collection from encyclopedia references, supplemented by additional published reports on target families or species. See the main data file for individual species references and source text quotations.
