DOI: 10.5061/dryad.vdncjsz7z
title: Data from: Sexual dimorphism and sex-biased sampling influence analyses of trait evolution and diversity in a major songbird clade

description: Avian functional traits are widely studied in ecology and evolutionary
 biology, and these traits are often quantified from museum study skins.
 Across such studies, the sex ratio of specimens is highly variable or
 often unreported, despite knowledge that many species are sexually
 dimorphic in size and shape and that museum collections are sex-biased
 toward male specimens. Our study explicitly quantified whether sex-biased
 specimen sampling influences the answers to primary research questions
 about avian functional trait diversity and evolution. We focused on the
 songbird clade Emberizoidea, using an existing phylogenetic tree for this
 clade and a large male-specific dataset for 10 functional traits. After
 inter-measurer calibration, we collected a matching female-specific
 dataset for 408 species to assess the degree of size and shape dimorphism
 across the clade. We found that emberizoids are significantly dimorphic in
 both size and shape. We then quantified three metrics of functional trait
 diversity and found that estimated diversity differed significantly
 between male, female, and pooled datasets for all metrics. We found that
 all traits have strong significant phylogenetic signal that was of
 comparable magnitude despite differing significantly between sex-biased
 samples. We also modeled branch-specific rates of trait evolution and
 found these inferences to be more nuanced. Estimated rate shifts were
 largely congruent between sex-biased datasets, but branch-specific rates
 of size evolution were strongly impacted by both the sex ratio of the
 dataset and the choice of tool that quantified them. Thus, we found that
 sex-biased sampling can influence the answers to primary research
 questions in ecology and evolutionary biology. These issues may be avoided
 by sampling sex ratios consistently across taxa in these studies. Further,
 we recommend that these ratios should be clearly reported, and that
 researchers sample specimens in a way that makes sense given their
 questions and the biology of the organisms being studied.
description: DATA FOR: Sexual dimorphism and sex-biased sampling influence analyses of
 trait evolution and diversity in a major songbird clade Brittany M. Wu,
 Isaac G. Hemmes, and Tyler S. Imfeld TREE FILES: 1. SpeciesTree_MCC.tre A
 NEXUS formatted tree file produced by Barker et al. (2015) Auk. 2.
 SpeciesTreeMCC_pruned.tre A NEXUS formatted tree file that has been
 rarified to only include species represented with morphological data in
 the manuscript. DATA FILES: 1. Translation_Table.csv A csv file with two
 columns: "Barker" which contains the tip labels from the Barker
 et al. (2015) Auk phylogeny, and "IOC" which contains the name
 for that species on the International Ornithological Congress checklist.
 Values of NA mean that the taxon is recognized by one source and not the
 other. 2. EmbMorpho_female_All.csv A csv file containing the raw
 morphometic data measured from female study skins in this study. Mass is
 recorded in grams, and all other measurements are recorded in millimeters.
 Measurer indicates the researcher who measured that specimen, and Sex
 indicates the sex of the specimen. Abbreviations in the column names are:
 L = length, W = width, and D = depth. 3. EmbMorpho_male_All.csv A csv file
 containing the raw morphometic data measured from male study skins in this
 study. Most of these data were previously published (Imfeld & Barker
 (2024) J Evol Biol), but new specimens have been measured and added to the
 dataset. Mass is recorded in grams, and all other measurements are
 recorded in millimeters. Measurer indicates the researcher who measured
 that specimen, and Sex indicates the sex of the specimen. Abbreviations in
 the column names are: L = length, W = width, and D = depth. 4.
 EmbMorpho_spmean_All.csv A csv file containing mean morphometric data for
 each sex of each species in this study. Mass is recorded in grams, and all
 other measurements are recorded in millimeters. Sex indicates that
 sex's data. Abbreviations in the column names are: L = length, W =
 width, and D = depth. 5. 5-16. FemalePC1.txt, FemalePC2.txt,
 FemalePC3.txt, FemalePC4.txt, MalePC1.txt, MalePC2.txt, MalePC3.txt,
 MalePC4.txt, PooledPC1.txt, PooledPC2.txt, PooledPC3.txt, and
 PooledPC4.txt A series of txt files containing mean principal component
 scores for each species. The file name indicates which dataset and which
 principal component are represented in the data. These files are necessary
 to generate BAMM control files. CONTROL FILES: 1-12. FemalePC1Control.txt,
 FemalePC2Control.txt, FemalePC3Control.txt, FemalePC4Control.txt,
 MalePC1Control.txt, MalePC2Control.txt, MalePC3Control.txt,
 MalePC4Control.txt, PooledPC1Control.txt, PooledPC2Control.txt,
 PooledPC3Control.txt, and PooledPC4Control.txt A series of txt files
 generated using the BAMMtools R package. Each file configures a BAMM
 analysis, and the file name indicates which dataset and which principal
 component are analyzed. R SCRIPTS AND RDATA FILES:
 01_Dimorphism_Analysis.R An R script that performs the sexual dimorphism
 analyses. 02_Morphospace_Analysis_and_Phylo_Sig.R An R script that
 performs the subclade bootstrapping, calculates functional trait diversity
 from the subclades, and calculates phylogenetic signal from the subclades.
 02_Permutations_Complete.RData An RData file that contains the completed
 bootstrap permuations. This file can also be generated by the R script
 beginning with 02. 03_Trait_Evolution_Analysis.R An R script that
 generates the BAMM control files, analyzes the BAMM rates data, performs
 the RRphylo analysis, and analyzes the RRphylo rates data.
 03_BAMMRates.RData An RData file that contains the compiled
 branch-specific rates inferred from BAMM that are ready for analysis. This
 file can also be generated by the R script beginning with 03.
 03_RRPhyloRates.RData An RData file that contains the compiled
 branch-specific rates inferred from RRphylo that are ready for
 analysis. This file can also be generated by the R script beginning with
 03.