Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers—yellow-shafted and red-shafted flickers—to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across ~7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean FST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (CYP2J19) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wings and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes.

Northern flicker reference genome (NOFL.pseudochromosomes.fasta.gz)

Gzipped file containing the northern flicker (Colaptes auratus) reference genome that was sequenced and assembled in this study. The sampled individual was a male from the yellow-shafted subspecies group.

Reference genome annotations (nofl_maker_annotation.gff.gz)

Gzipped file of the MAKER annotations of the northern flicker (Colaptes auratus) reference genome.

Northern flicker SNP dataset (RSFL-YSFL_WGS_missing80_mindepth3.vcf.gz)

Gzipped file containing the SNP dataset used in this study (7,233,334 biallelic SNPs). The data is from whole-genome re-sequencing of 10 red-shafted flickers, 10 yellow-shafted flickers, and 48 red-shafted x yellow-shafted flicker hybrids, as described in the manuscript.

Sample information (sample_info.txt)

Sample metadata to link the VCF file to individuals described in Supplementary Table 2 of the study.

Northern flicker reference genome not aligned to zebra finch (NOFL.scaffolds.fasta.gz)

gzipped file containing the scaffold version of the northern flicker reference genome that was not aligned to the zebra finch genome using Satsuma. This reference was not used in this study, but is provided to allow for use by others.

Data processing scripts are available at https://github.com/stepfanie-aguillon/. Note that file names are consistent with those used in the GitHub Repository.

Changes after Dec 22, 2020: Upon further work with these samples, we identified an error in the original sample number included for one specimen in the sample_info.txt file (CUMV 58076 was incorrectly labeled as CUMV 58075). All other listed information for this sample in the original file (locality, date, phenotype scores, etc.) were correct and have been confirmed with molecular lab notebooks, separate prep ID numbers in other files, and specimen photographs. The sample is correctly indicated in Supplemental Table 2 of the linked manuscript as CUMV 58076, so the misidentification only occurred in the included code. We have now included an updated sample_info_updated.txt file with this error corrected, but have chosen to retain the original sample_info.txt file for transparency.