DOI: 10.5061/dryad.gmsbcc30q
title: The macroevolutionary consequences of the association between frugivory and carotenoid-dependent plumage coloration in passerine birds

description: Biotic interactions influence evolutionary pathways, impacting
 diversification positively and negatively. Here, we examine the
 coevolutionary dynamics between frugivorous diets and carotenoid-dependent
 plumage coloration in passerine birds— a highly diverse order in which
 nearly half of species exhibit carotenoids in their plumage. Plumage
 coloration is crucial for species recognition and mate choice. As birds
 cannot synthesize carotenoids, they must obtain them from the diet. We
 analyze data from 90% of passerines and explore correlations between
 frugivory, a key carotenoid source, plumage coloration, and
 diversification rates.The data used in our study includes binary
 classification of passerines based on whether they present
 carotenoid-dependent plumage coloration or not and whether fruit compose
 50% or more of the diet, also codified as a binary trait. All data come
 from published sources. Our Bayesian analysis reveals a strong
 evolutionary correlation between frugivory and the presence of carotenoid
 plumage coloration. However, Bayesian state-dependent speciation and
 extinction models (SSE) showed that neither frugivory nor carotenoid
 coloration independently correlate with heightened diversification.
 Results are unchanged when we analyze the combination of both traits,
 challenging the conventional assumption of increased speciation driven by
 frugivory in species with carotenoid-dependent plumage coloration. These
 findings underscore the complexity of trait interactions in shaping
 evolutionary trajectories and the importance of hidden states in modeling
 diversification.
description: # Trait Data Files (RevBayes & BayesTraits Input) This folder contains
 all trait matrices and phylogenetic data used in the macroevolutionary
 analyses for: **"The macroevolutionary consequences of the
 association between frugivory and carotenoid-dependent plumage coloration
 in passerine birds"** All files are formatted for use with
 **RevBayes** and **BayesTraits**. The full dataset includes **5470
 passerine species**. --- ## File Descriptions | File name | Description |
 | ---------------------------- |
 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | **bayestraits.txt** | Binary trait file formatted for BayesTraits, including frugivory and carotenoid states. | | **Carotenoids.tsv** | Trait matrix coding the presence/absence of carotenoid-dependent coloration across 5470 species. | | **Carotenoids\_Delhey.tsv** | Carotenoid coloration states derived from Delhey color scores. | | **Frugivory.tsv** | Binary matrix coding fruit consumption for each species. | | **mccBirdPasserineTree.tre** | Maximum clade credibility (MCC) tree in **NEXUS format**, representing the phylogeny of 5470 passerine species. Compatible with RevBayes and other software that support NEXUS-formatted trees. | | **Musse.tsv** | Trait file prepared for MuSSE models in RevBayes (includes frugivory and color states; States 1=F0 C0; 2=F0 C1; 3= F1 C1 A; 4= F1 C0). | | **Musse\_Delhey.tsv** | Trait matrix for MuSSE models using Delhey-based coloration values alongside frugivory states. | | **BayesTraitsTrees.nex** | File in **NEXUS format** containing the posterior distribution of 500 phylogenetic trees. These were used to generate the MCC tree (`mccBirdPasserineTree.tre`). The first 275 trees were specifically used in BayesTraits comparative analyses. | --- ## Notes * All `.tsv` files are tab-delimited and compatible with **RevBayes** trait modeling. * Trait states follow binary or multi-state codings depending on the model (e.g., MuSSE vs BiSSE). * Tree files are in **NEXUS format**, compatible with RevBayes, BayesTraits, and other comparative software. --- ## Contact For more information about trait coding or input file structure, please contact:\ **Verónica Rincón-Rubio**\ \[[veronica.rincon@ciencias.unam.mx](mailto:veronica.rincon@ciencias.unam.mx)]