Data from: The role of sexual and natural selection in shaping patterns of sexual dichromatism in the largest family of songbirds (Aves: Thraupidae)

Shultz AJ, Burns KJ

Date Published: January 31, 2017

DOI: http://dx.doi.org/10.5061/dryad.g4k83

 

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Title MCC phylogeny trimmed to data used in comparative analyses
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Description MCC phylogeny from Burns et al. (2014). The tree has been trimmed to include the species used in comparative analyses. Citation: Burns, K. J., A. J. Shultz, P. O. Title, N. A. Mason, F. K. Barker, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2014. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. MPE 75:41–77.
Download MCC_Tree_SpNames.nex (17.61 Kb)
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Title Posterior trees used in comparative analyses
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Description Set of 100 phylogenies from the posterior distribution presented in Burns et al. (2014). The tree has been trimmed to include the species used in comparative analyses. Citation: Burns, K. J., A. J. Shultz, P. O. Title, N. A. Mason, F. K. Barker, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2014. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. MPE 75:41–77.
Download Sampled_Tree_SpNames.nex (1.009 Mb)
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Title Phenotypic data
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Description Phenotypic data used in comparative analyses, corresponding to supplemental tables 1-3. Headers are: SpeciesNumsCladesHab.csv – Information on each species measured for this study. For each species we give the number of species measured for each sex, presence or absence in the Thraupidae phylogeny, subfamily, habitat designation (F = closed/forest, N = open), foraging stratum (U = understory, C = canopy, U/C = both understory and canopy, N = open), maximum color span (MaxSexDich), average color span (AvgSexDich), Male combined, non-phylogenetic PC1 scores (MalePC1), female combined, non-phylogenetic PC1 scores (FemalePC1), male combined, non-phylogenetic PC2 scores (MalePC2), female combined, non-phylogenetic PC2 scores (FemalePC2), Male separate phylogenetic PC1 scores (MalePhyloPC1), Female separate phylogenetic PC1 scores (FemalePhyloPC1), Male separate phylogenetic PC2 scores (MalePhyloPC2), and Female separate phylogenetic PC2 scores (FemalePhyloPC2). WPTCSmeasures.csv – All whole plumage tetrahedral color space measurements. The first two columns indicate species and sex, followed by average color span (AvgSpan), color span variance (VarSpan), maximum color span (MaxSpan), color volume (Volume), average hue disparity (AvgHueDisp), hue disparity variance (VarHueDisp), maximum hue disparity (MaxHueDisp), average brilliance (AvgBrill), average chroma (AvgChroma), and species abbreviations (species_abbr) to use with phylogenies. AllTristimulusColorVariables_Translated.csv – All tri-stimulus color variables calculated for each measured region of each sex. We report the species abbreviation (see Supplemental Table 2 for full name), sex, region, theta, phi, r, and normalized brilliance (NormBrill).
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Title rtetracolorspace
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Description This set of R scripts uses the set of functions implemented in tetracolorspace, a matlab package, (http://www.marycstoddard.com/#Software%20and%20tools) and implements them in R. The reference for all analysis is: Stoddard, M. C., and R. O. Prum. 2008. Evolution of avian plumage color in a tetrahedral color space: a phylogenetic analysis of New World buntings. American Naturalist 171: 755–776. Files: RtcsFunctions.R: The source code for all functions. ExampleScript.R: Examples and brief explanations of all rtcs functions. bluetitss.dat: Spectral sensitivity data from the Blue Tit (obtained from tetracolorspace). EunCamf_allpatches.csv: An example input data file of reflectance data taken from a female tanager. visualization.R: A set of functions that can be used to visualize the tetracolorspace data.
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Title R functions to perform Ancestral State Reconstructions of Color Cone Catches
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Description Functions to replicate the analyses presented by Price and Eaton (2014). See comments in file for additional information. Price, J. J., and M. D. Eaton. 2014. Reconstructing the evolution of sexual dichromatism: current color diversity does not reflect past rates of male and female change. Evolution 68:2026–2037.
Download PriceEaton2014AnalysisFunctions.R (7.15 Kb)
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When using this data, please cite the original publication:

Shultz AJ, Burns KJ (2017) The role of sexual and natural selection in shaping patterns of sexual dichromatism in the largest family of songbirds (Aves: Thraupidae). Evolution 71(4): 1061–1074. http://dx.doi.org/10.1111/evo.13196

Additionally, please cite the Dryad data package:

Shultz AJ, Burns KJ (2017) Data from: The role of sexual and natural selection in shaping patterns of sexual dichromatism in the largest family of songbirds (Aves: Thraupidae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g4k83
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