Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype

Area of Science:

• Evolutionary Biology
• Genetics
• Animal Behavior

Background:

• Coloration is a key trait influenced by natural and sexual selection.
• Understanding the genetic basis of color evolution is crucial for explaining phenotypic diversity.
• Hybridizing species with distinct color differences and low genomic divergence offer tractable systems for genetic association studies.

Purpose of the Study:

• To identify the genomic underpinnings of distinct plumage coloration in North American flickers (Colaptes auratus).
• To associate specific genetic variations (SNPs) with differences in melanin and carotenoid pigment expression in six plumage patches.
• To explore novel genetic links between melanin and carotenoid pathways in coloration.

Main Methods:

• Genome-wide SNP analysis across approximately 7.25 million single nucleotide polymorphisms (SNPs) in yellow-shafted and red-shafted flickers.
• Association analysis to identify SNPs significantly linked to specific plumage color variations.
• Examination of candidate genes known for their roles in pigmentation pathways.

Main Results:

• Yellow-shafted and red-shafted flickers exhibit minimal overall genomic differentiation (mean FST = 0.008).
• 368 SNPs in highly differentiated genomic regions were significantly associated with four of the six plumage patches studied.
• The gene CYP2J19, known for yellow-to-red color transitions, was strongly linked to wing and tail feather color differences.

Conclusions:

• Plumage coloration in flickers is controlled by a small number of genomic regions with significant genetic associations.
• Novel connections between melanin and carotenoid pigmentation genes were suggested.
• Patch-specific genetic control contributes to the diversity of animal coloration through selection on gene combinations.