Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters.

This article focuses on the genomic differentiation and speciation processes between two closely related Neotropical bird species, the Plumbeous Seedeater (Sporophila plumbea) and the recently described Tropeiro Seedeater (Sporophila beltoni). Despite marked phenotypic differences, especially in bill coloration, whole-genome sequencing revealed very low overall genetic differentiation between the species, attributed to ongoing gene flow over millions of generations. However, three narrow genomic regions ("islands of speciation") containing six genes—including EDN3, involved in pigmentation, and PRLR, related to breeding behavior and keratinization—showed high differentiation and signatures of reduced gene flow, suggesting these loci contribute to prezygotic reproductive isolation. The study highlights how localized genetic divergence in coloration genes can mediate species boundaries early in speciation, even amid extensive genomic homogenization.