DOI: 10.5061/dryad.n02v6wwvv
title: Pigmentation genes show evidence of repeated divergence and multiple bouts of introgression in <em>Setophaga</em> warblers

description: Species radiations have long served as model systems in evolutionary
 biology. However, it has only recently become possible to study the
 genetic bases of the traits responsible for diversification, and only in a
 small number of model systems. Here we use genomes of 36 species of North,
 Central, and South American warblers to highlight the role of pigmentation
 genes—involved in melanin and carotenoid processing—in the diversification
 of this group. We show that agouti signaling
 protein (ASIP) and beta-carotene oxygenase
 2 (BCO2) are predictably divergent between species that differ in
 the distribution of melanin and carotenoid in their plumages,
 respectively. Among species, sequence variation
 at ASIP broadly mirrors the species' phylogenetic
 history, consistent with repeated, independent mutations generating
 melanin-based variation. In contrast, BCO2 variation is
 highly discordant from the species tree, with evidence of cross-lineage
 introgression among species like the yellow warbler (Setophaga petechia)
 and magnolia warbler (S. magnolia) with extensive carotenoid-based
 coloration. We also detect introgression of a small part of the BCO2
 coding region (&lt;3 kb) in S.
 discolor and S. vitellina, including an amino acid
 substitution that is unique to warblers but otherwise highly conserved
 across birds. Lateral transfer of carotenoid-processing genes has been
 documented in arthropods, but introgression of BCO2 as
 demonstrated here—presumably adaptive—represents the first example of
 carotenoid gene transfer among vertebrates. These contrasting genomic
 patterns show that both independent evolution in a common set of genes and
 past gene flow have fueled plumage diversification in this colorful avian
 radiation.
description: See supplemental methods for how the genomic data was
 collected.
description: Information for samples sequenced for the study, as well as NCBI
 Accession numbers for each sample.  Column heading
 information: Genus & Species: Latin
 names based on Lovette et al. (2010;
 doi:10.1016/j.ympev.2010.07.018). ID: the unique ID
 number given to the sample. Note that the "filename" for the
 reads uploaded to NCBI may differ from this sample name.
 ID_type: either "museum voucher" (obtain additional
 sample information from the museum identified), "USGS_band"
 (additional locality and sampling information can be obtained from the
 USGS bird banding database), or "project_ID" (samples collected
 for unique projects on rare birds; contact the collector for additional
 sample information). Museum or Collector: The
 identifier of the museum or collector that contributed the
 sample. Institution: Additional information if the
 museum or collector was associated with a broader institution (such as a
 University). Accession: This is the NCBI accession
 number. Additional_ID: For CUMV samples this
 represents the additional "tissue ID" value associated with the
 sample. For blood samples collected by "David Toews" these
 represent unique record IDs, in addition to the band number.
 Original publication: DOI for which publication was the data for
 each sample was first associated with.
description: # Pigmentation genes show evidence of repeated divergence and multiple
 bouts of introgression in *Setophaga* warblers Dataset DOI:
 [10.5061/dryad.n02v6wwvv](https://doi.org/10.5061/dryad.n02v6wwvv) ##
 Description of the data and file structure Blood and tissue samples of
 warblers were sequenced using Illumina short read data. Data can be found
 on the NCBI database, and this file indicates the sample/museum catalog
 numbers associated with each sample. ### Files and variables #### File:
 Table_S1_V2.csv **Description:**  ##### Variables * Genus: Genus of
 Parulidae Species: Latin species name within Parulidae ID: Primary sample
 ID number ID_type: Type of ID number (e.g. band number, museum tissue or
 catalog number) Tissue: Tissue type (blood or tissue) Museum or Collector:
 Museum or collector name Institution: Associated institution Accession:
 NCBI SRA accession number additional_ID: Additional sample record number
 if available Original_publication: First publication associated with data
 #### File: Table_S1_V3.csv **Description:**  ##### Variables * Genus:
 Genus of Parulidae Species: Latin species name within Parulidae ID:
 Primary sample ID number ID_type: Type of ID number (e.g. band number,
 museum tissue or catalog number) Tissue: Tissue type (blood or tissue)
 Museum or Collector: Museum or collector name Institution: Associated
 institution Accession: NCBI SRA accession number additional_ID: Additional
 sample record number if available Original_publication: First publication
 associated with data Notes: In 2025, two errors were identified in the
 sample datasheet. Sample CUMV262 had an incorrect catalog number (though
 the tissue number was correct) and one sample had an incorrect species ID.
 A correction to the journal (*Current Biology*) was issued for the latter.
 ## Access information Other publicly accessible locations of the data: *
 NCBI BioProject PRJNA630247