Data from: Evolutionary history of delayed plumage maturation in manakins (Aves: Pipridae)
Data files
Feb 12, 2026 version files 14.63 KB
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character_data.tsv
6.84 KB
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README.md
6.74 KB
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taxon_display_order.csv
1.06 KB
Abstract
Avian plumage maturation involves replacing feathers, via discrete molts, until reaching an iteratively-regenerated definitive plumage. In most birds, this process takes about one year. In the Neotropical lekking manakins (Pipridae), males of most species exhibit delayed plumage maturation (DPM), passing through drab predefinitive plumages for up to three years before reaching a sexually dichromatic, definitive plumage. We used a phylogenetic analysis to investigate the evolutionary history of DPM in manakins. Our unique dataset represents the developmental schedules of individual, colorful plumage patches. We found a single origin of one-year DPM, in which young males spend a year in a drab female plumage. Subsequently, there were three origins of two-year DPM, all of which featured the evolution of an intermediate plumage with colorful patches that distinguish young males from females and older males. One species evolved three-year DPM by passing through ancestral plumage stages more slowly, and two lineages have secondarily evolved sexual monochromatism by pedomorphic retention of female plumage. By detailing this complex developmental evolutionary history, we show how the iterative regeneration of bird plumages creates multiple distinct levels of ontogenetic homologies and provides new insights into the macroevolution of social signals in young birds.
A. Paper associated with this archive
Evolutionary history of delayed plumage maturation in manakins (Aves: Pipridae)
B. Originators
Liam U. Taylor and Richard Owen Prum
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
C. Contact information
Liam Taylor: l.taylor@bowdoin.edu
D. Dates of data collection
2022-3 (Synthesizing published and pers. comm. data)
2023 (Museum specimen analysis)
E. Geographic Location(s) of data collection
Museum specimen analysis included from Yale Peabody Museum of Natural History, New Haven, CT and the American Museum of Natural History, New York, New York.
F. Funding Sources
NSF GRFP (#DGE1752134)
American Society of Naturalists student research award
W. R. Coe Fund, Yale University
ACCESS INFORMATION
1. Licenses/restrictions placed on the data or code
Dryad data files (character_data.tsv and taxon_display_order.csv): CC0 waiver.
Zenodo software file (analysis.R): MIT license.
2. Data derived from other sources
Sources for initial plumage maturation descriptions available in supplemental material of the associated manuscript (Supplementary Material: Manakin plumage maturation descriptions).
As described below, several tree and tree metadata files must be drawn from other sources (Harvey et al. 2020, Berv et al. 2021, Leite et al. 2021, Moncrieff et al. 2022). Due to different licensing, those input tree files are not included here.
3. Recommended citation for this data/code archive
Taylor, L. and Prum, R. 2026. Dataset for: Evolutionary history of delayed plumage maturation in manakins (Aves: Pipridae). Dryad.
DATA & CODE FILE OVERVIEW
This repository contains the data and code to generate results and figures for the manuscript, "Evolutionary history of delayed plumage maturation in manakins (Aves: Pipridae)." This study analyzes the phylogenetic history of male delayed plumage maturation across manakins, investigating the developmental evolution of plumages and molts, the hierarchical dynamics of ontogenetic homology, and the macroevolutionary patterns of social signals in birds.
Data files and variables
character_data.tsv (Each row is a taxon, each column is either (A) associated metadata or (B) character state for a plumage character. The first two rows label and describe the 27 plumage patch characters.
| Column | Datatype | Description |
|---|---|---|
| Genus | (chr) | Genus for the taxon, following Gill et al. (2025). |
| Species | (chr) | Species (and subspecies) for the taxon, following Gill et al. (2025). |
| Data_Quality | (chr) | Data quality code as described in the supplementary material. |
| Harvey_Tip_Label | (dbl) | Tip name in the associated tree file from Harvey et al. (2020). Rooted time-calibrated tree from high-filtered (HGAPF) dataset. |
| Moncrieff_Tip_Label | (dbl) | Tip name in the associated tree file from Moncrieff et al. (2022). ML, 75% multi-SNP linked dataset. |
| Berv_Tip_Label | (dbl) | Tip name in the associated tree file from Berv et al. (2021). ML, 50% dataset UCE/Sanger dataset. |
| Leite_Tip_Label | (dbl) | Tip name in the associated tree file from Leite et al. (2021). ML, 95% dataset UCE dataset. |
| [CHARACTER COLUMNS] | (chr) | Character state for each of 27 plumage patch character |
taxon_display_order.csv (Display order for sorting manakin taxa in manuscript tables)
Other files which are needed for running the analysis code:
Tree metadata from Berv et al. (2021). Save as: BERV_all-samples.csv
Tree file from Berv et al. (2021). Save as: BERV_RAxML_bipartitions.50percent_miss
Tree file from Harvey et al. (2020) repository. Save as: HARVEY_HGAPF_complete.tre
Tree metadata from Harvey et al. (2020) repository. Save as: HARVEY_TABLES43.csv
Tree metadata from Leite et al. (2021) repository. Save as: LEITE_mafft-edge-uce-95-raxml.bipartitions.tre
Tree file from Moncrieff et al. (2022) repository. Save as: MONCRIEFF_12_IQ-TREE2_linked75_67ind.tre
Code scripts and workflow
Place the data, including all files from other repositories, into a Data/ directory. Create an empty Output/ folder. Execute the analysis.r script.
SOFTWARE VERSIONS
| Software | Version |
|---|---|
| R | 4.4.1 |
| tidyverse | 2.0.0 |
| ape | 5.0 |
| phytools | 2.0 |
| ggtree | 3.12.0 |
| gridExtra | 2.3 |
| patchwork | 1.3.0 |
References for this README
Berv, J. S., L. Campagna, T. J. Feo, I. Castro-Astor, C. C. Ribas, R. O. Prum, and I. J. Lovette. 2021. Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes. Molecular Phylogenetics and Evolution 164:107205.
Gill, F., D. Donsker, and P. Rasmussen. 2025. IOC World Bird List (v15.1). https://www.worldbirdnames.org/new/.
Harvey, M. G., G. A. Bravo, S. Claramunt, A. M. Cuervo, G. E. Derryberry, J. Battilana, G. F. Seeholzer, J. S. McKay, B. C. O’Meara, B. C. Faircloth, S. V. Edwards, J. Pérez-Emán, R. G. Moyle, F. H. Sheldon, A. Aleixo, B. T. Smith, R. T. Chesser, L. F. Silveira, J. Cracraft, R. T. Brumfield, and E. P. Derryberry. 2020. The evolution of a tropical biodiversity hotspot. Science 370:1343–1348.
Leite, R. N., R. T. Kimball, E. L. Braun, E. P. Derryberry, P. A. Hosner, G. E. Derryberry, M. Anciães, J. S. McKay, A. Aleixo, C. C. Ribas, R. T. Brumfield, and J. Cracraft. 2021. Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness. Molecular Phylogenetics and Evolution 155:107013.
Moncrieff, A. E., B. C. Faircloth, and R. T. Brumfield. 2022. Systematics of Lepidothrix manakins (Aves: Passeriformes: Pipridae) using RADcap markers. Molecular Phylogenetics and Evolution 173:107525.
