SOCIAL CONTEXT AND THE EVOLUTION OF DELAYED REPRODUCTION IN BIRDS

Data and code repository

Liam U. Taylor and Richard O. Prum

Last updated 2023-08-02 (preprint submission version)

ABSTRACT

Classic life history theory makes generalized predictions about phenotypic correlations across large clades. Modern comparative tests of these correlations account for the underlying structure of phylogenetic trees. Yet neither life history theory nor phylogenetic comparative methods automatically specify how biological mechanisms generate correlations. This problem is evident in comparative analyses of birds. Birds show a correlation between body size and age at first reproduction, but do not actually grow larger if they delay reproduction. Instead, field studies raise the hypothesis that social contexts—especially cooperative breeding, coloniality, and lekking—generate unique demands for behavioral development, which in turn result in delayed reproduction. Here, we support that hypothesis with a comparative dataset spanning 961 species in 155 avian families. Continuous (Ornstein-Uhlenbeck), discrete (hidden state Markov), and phylogenetic regression models revealed delayed reproduction in colonial birds, a weaker signal in cooperative birds, and the consistent evolution of sexual bimaturism in polygynous, lekking birds. These results show an association between diverse social contexts, sex-specific developmental demands, and life history evolution in birds. Considering this diversity, we discuss how even statistically powerful phylogenetic correlations—whether focused on mass, lifespan, or broad social categories—can ultimately fail to model the history of life history evolution.

About this repository

This repository contains all data and code necessary to generate manuscript results and figures.

Data (in the Data/ directory):

1. data_raw_2023-07-23.xlsx (raw data, including full age sources and text quotations)
2. Clements_Taxonomy_v2022.csv (Avian taxonomy from Clements 2022)
3. AVONET_Clements_Data.csv (AVONET data, including mass, from Tobias et al. 2022)
4. Taxonomy_Dictionary_Clements_To_BirdTree.csv (dictionary to map Clements v2022 names to BirdTree phylogeny tip labels)
5. BirdTree_1000_Trees.nex (a distribution of 1,000 phylogenetic from Jetz et al. 2012 BirdTree)
6. alpha_distribution_subset.csv (example age at first reproduction distributions from well-studied species for Fig. S3)
7. tree_images.r (information for drawing PhyloPic images on the tree figures)

Analysis scripts (in the Scripts/ directory):

1. 1_wrangle_data.sh (wrangles main data file to clean version for analyses)
2. 2_ou_models.sh (continuous evolutionary models in OUwie)
3. 3_corhmm.sh (discrete evolutionary models in corHMM)
4. 4_phyanova.sh (phylogenetic ANOVAs in phytools; requires OU models results from Script 2)
5. 5_pgls.sh (phylogenetic generalized least squares models in nlme)
6. 6_tables_and_figures.sh (generates MS tables and figures; requires all results from Scripts 1-5)

Software requirements

Scripts are written for Unix bash (Ubuntu) and R v4.3.1. See scripts and manuscript for packages and software citations. Bash scripts were originally run with Yale HPC resources (McClearly cluster) 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",
                   "phytools",
                   "nlme",
                   "broom.mixed",
                   "ggtree",
                   "patchwork"))