Data from: Recent chapters of Neotropical history overlooked in phylogeography: shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins

Establishing links between phenotypic and genotypic variation is a central
goal of evolutionary biology, as they might provide important insights
into evolutionary processes shaping genetic and species diversity in
nature. One of the more intriguing possibilities is when no genetic
divergence is found to be associated with conspicuous phenotypic
divergence. In that case, speciation theory predicts that phenotypic
divergence may still occur in the presence of significant gene
flow—thereby resulting in little genomic divergence—when genetic loci
underpinning phenotypes are under strong divergent selection. However, a
finding of phenotypic distinctiveness with weak or no population genetic
structure may simply result from low statistical power to detect shallow
genetic divergences when small datasets are used. Here, we used a
subgenomic dataset of 2386 ultraconserved elements to explore genome-wide
divergence between two species of Antilophia manakins, which are
phenotypically distinct yet evidently lack strong genetic differentiation
according to previous studies based on a limited number of loci. Our
results revealed clear population structure that matches the two
phenotypes, supporting the idea that smaller datasets lacked the power to
detect this recent divergence event (likely < 100 k ya). Indeed, we
found little or no introgression between the species, as well as evidence
of genome-wide divergence. One implication of our study is that the
Araripe plateau may be a hotspot of cryptic-diverging forest Cerrado
populations. Besides their use in biogeography, subgenomic datasets may
help redefine local conservation programs by revealing cryptic population
structure that may be key to population management.