The macroevolutionary consequences of the association between frugivory and carotenoid-dependent plumage coloration in passerine birds
Data files
Aug 28, 2025 version files 86.82 MB
-
bayestraits.txt
277.23 KB
-
BayesTraitsTrees.nex
85.47 MB
-
Carotenoids_Delhey.tsv
122.21 KB
-
Carotenoids.tsv
122.21 KB
-
Frugivory.tsv
122.21 KB
-
mccBirdPasserineTree.tre
446.29 KB
-
Musse_Delhey.tsv
127.67 KB
-
Musse.tsv
127.67 KB
-
README.md
3.73 KB
Abstract
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.
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
.tsvfiles 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]
