Data and code to Evolution of sexually dimorphic plumage patterns in estrildid finches

Code and data to replicate the analyses in the article "Evolution of sexually dimorphic plumage patterns in estrildid finches". Pacheco et al. (2026, Evolution).

This archive includes one R script file with code to replicate all analyses in the article, along with the datasets needed to run analyses.

Specifically, it contains:
- 'R_script_analyses.R': the complete R scripts to replicate all statistical analyses in the article. This script also contains code to import the data.
- 'males_data.txt': dataset comprising the male data per species. This dataframe includes the species ID, species code in the phylogeny, measurements of the different pigmentation patterns, colour measurements, and socio-ecological traits.
- 'females_data.txt': dataset comprising the female data per species. This dataframe includes the species ID, species code in the phylogeny, measurements of the different pigmentation patterns, colour measurements, and socio-ecological traits.
- 'Est2025_unconstrained.tree': maximum clade credibility tree from BEAST used as the phylogenetic tree in the main analyses.
- 'Est2025_unconstrained.xml': the BEAST .xml file used to generate the unconstrained tree.
- 'Est2025_constrained.tree': maximum clade credibility tree resulting from an analysis in which monophyly was constrained for 15 clades supported in the estrildid finch phylogeny reported by (Olsson & Alström, 2020, Mol. Phylog. Evol.).
- 'Est2025_unconstrained.xml': the BEAST .xml file used to generate the constrained tree.
- 'sample_names': dataframe which translates each sample in the phylogenetic tree, to the species name used in analyses. This dataframe contains “original_tree_sample_name” which is the original name of the sample in the phylogenetic tree, and “tree_sample_name_analysis” which corresponds to the species names used for the phenotypic data. This selects only one sample per species in the phylogenetic tree as multiple samples for a given species were monophyletic.

Article reference:
"Evolution of sexually dimorphic plumage patterns in estrildid finches", Evolution, 2026.
João Pacheco, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal.
Michael D. Sorenson, Department of Biology, Boston University, Boston, Massachusetts, USA.
Gonçalo C. Cardoso, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal.
Ana Cristina R. Gomes, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal; Department of Ecology and Genetics, Animal Ecology, Uppsala University, Sweden.

April 2026, João Pacheco ([e-mail]) and Ana Cristina R. Gomes ([e-mail]).