DOI: 10.5061/dryad.jsxksn0n8
title: Data from: Evolutionary history of delayed plumage maturation in manakins (Aves: <em>Pipridae</em>)

description: 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.
description: # Data from: Evolutionary history of delayed plumage maturation in
 manakins (Aves: *Pipridae*) #### 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](mailto: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](https://doi.org/10.1016/j.ympev.2021.107205)). Save as: **BERV_all-samples.csv** Tree file from Berv et al. ([2021](https://doi.org/10.1016/j.ympev.2021.107205)). Save as: **BERV_RAxML_bipartitions.50percent_miss**  Tree file from Harvey et al. ([2020](https://doi.org/10.1126/science.aaz6970)) repository. Save as: **HARVEY_HGAPF_complete.tre** Tree metadata from Harvey et al. ([2020](https://doi.org/10.1126/science.aaz6970)) repository. Save as: **HARVEY_TABLES43.csv**  Tree metadata from Leite et al. ([2021](https://doi.org/10.1016/j.ympev.2020.107013)) repository. Save as: **LEITE_mafft-edge-uce-95-raxml.bipartitions.tre** Tree file from Moncrieff et al. ([2022](https://doi.org/10.1016/j.ympev.2022.107525)) 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/](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.