Plumage diversity without differential expression of pigmentation genes in a rapid avian radiation

Uncovering the molecular basis of reproductive traits is key to understanding species divergence. Capuchino Seedeaters ( Sporophila ), a radiation of genetically similar birds differing mainly in male reproductive plumage color, can be leveraged to study how such traits evolve. Outlier scans identified candidate pigmentation variants primarily in noncoding sequence, implying regulatory changes. However, RNA-seq of growing feather follicles generally did not show differential expression of pigmentation genes among different colors, with only ASIP downregulated in crown feathers. Gene expression patterns instead varied by body region. The largest difference between dimorphic sexes was the upregulation of the carotenoid-degrading gene BCO2 in males, accompanied by lower carotenoid content in male feathers. An improved genome annotation assigned 9.5% of candidate variants into coding and untranslated sequence. This suggests species-diagnostic variants lie within transcribed sequence and could act post-transcriptionally, rather than through transcript abundance, leading to a revised hypothesis for plumage divergence in this radiation.