DOI: 10.5061/dryad.r2280gbdk
title: Data and codes from: Flight hampers the evolution of weapons in birds

description: Birds are a remarkable example of how sexual selection can produce diverse
 ornaments and behaviors. Specialized fighting structures like deer’s
 antlers, in contrast, are mostly absent among birds. Here, we investigated
 if the birds’ costly mode of locomotion — powered flight — helps explain
 the scarcity of weapons among members of this clade. Our simulations of
 flight energetics predicted that the cost of bony spurs — a specialized
 avian weapon — should increase with time spent flying. Bayesian
 phylogenetic comparative analyses using a global spur dataset corroborated
 this prediction. First, extant species with flight-efficient wings (which
 presumably fly more frequently) tend to have fewer or no bony spurs.
 Second, this association likely arose because flying more leads to more
 frequent evolutionary loss of spurs. Together, these findings suggest
 that, much like pneumatic bones, absence of weaponry may be another
 feature of the avian body plan that allows birds to efficiently explore
 the aerial habitat.
description: <em>13 Jan 2022 update: adding Zenodo link to facilitate
 access to codes (affects Usage Notes and README.txt).</em>
 The files deposited here should allow anyone to rerun all
 analyses and figures in the article "Flight hampers the evolution of
 weapons in birds". All you have to do is download all files to your R
 working directory, unzip the zipped folders, and run codes as you wish.
 See README.txt for further details. Files available in Dryad:
 README.txt Detailed instructions on how to
 use Dryad files to reproduce our results and figures.
 Commented R codes (codes.html)
 <em>Available at Zenodo: https://doi.org/10.5281/zenodo.5829537</em> This HTML file contains a step-by-step guide for reproducing all analyses and figures in the article. Various ancillary files must be read in the script; all of them are available in Dryad. The files are named and organized exactly as in the codes, except that the folders are zipped. File that generates codes.html (codes.Rmd) <em>Available at Zenodo: https://doi.org/10.5281/zenodo.5829537</em> This R Markdown file is the raw version of the HTML file above. Main dataset (species_spur_data.csv) This CSV file contains the data that underlie all of our analyses and figures. It is a duplicate of the article's electronic supplement file Data S1. See README.txt for metadata. Phylogenetic trees (Jetz_trees.nex) This NEXUS file contains a sample of 100 complete bird trees based on the Hackett backbone, downloaded from http://birdtree.org on 13 August 2021. Mk-model outputs (bt3_outputs.zip) This ZIP file contains 15,300 text files with Mk-model outputs generated by BayesTraits. Our results are based on these outputs. See README.txt for further details. Mixed-model outputs (brms_outputs.zip) This ZIP file contains 11 R objects with the output of mixed models generated by the package brms in R. Our results are based on these outputs. See the codes for how these files were generated. SIMMAP outputs (simmap_outputs.zip) This ZIP file contains 10 R objects with the output of stochastic-mapping analyses generated by the package phytools in R. Our results are based on these outputs. See the codes for how these files were generated.