Data from: Sexual dimorphism and sex-biased sampling influence analyses of trait evolution and diversity in a major songbird clade
Data files
Oct 13, 2025 version files 18.62 MB
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01_Dimorphism_Analysis.R
11.76 KB
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02_Morphospace_Analysis_and_Phylo_Sig.R
26.41 KB
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02_Permutations_Complete.RData
8.81 MB
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03_BAMMRates.RData
7.74 MB
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03_RRPhyloRates.RData
576.26 KB
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03_Trait_Evolution_Analysis.R
43.44 KB
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EmbMorpho_female_All.csv
88.75 KB
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EmbMorpho_male_All.csv
213.07 KB
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EmbMorpho_spmean_All.csv
179.11 KB
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FemalePC1.txt
16.74 KB
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FemalePC1Control.txt
8.34 KB
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FemalePC2.txt
16.90 KB
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FemalePC2Control.txt
8.34 KB
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FemalePC3.txt
16.98 KB
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FemalePC3Control.txt
8.34 KB
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FemalePC4.txt
17.02 KB
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FemalePC4Control.txt
8.34 KB
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MalePC1.txt
16.74 KB
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MalePC1Control.txt
8.34 KB
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MalePC2.txt
16.87 KB
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MalePC2Control.txt
8.34 KB
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MalePC3.txt
16.97 KB
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MalePC3Control.txt
8.34 KB
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MalePC4.txt
17.02 KB
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MalePC4Control.txt
8.34 KB
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PooledPC1.txt
16.73 KB
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PooledPC1Control.txt
8.34 KB
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PooledPC2.txt
16.88 KB
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PooledPC2Control.txt
8.34 KB
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PooledPC3.txt
16.98 KB
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PooledPC3Control.txt
8.34 KB
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PooledPC4.txt
17.06 KB
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PooledPC4Control.txt
8.34 KB
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README.md
3.98 KB
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SpeciesTree_MCC.tre
570.33 KB
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SpeciesTreeMCC_pruned.tre
17.96 KB
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Translation_Table.csv
35.05 KB
Abstract
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.
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:
- SpeciesTree_MCC.tre
A NEXUS formatted tree file produced by Barker et al. (2015) Auk. - 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:
- 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. - 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. - 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. - 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. - 5-16. 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.
