Genomic and phenotypic data of the manuscript "Divergence-with-gene-flow leads to decoupled phenotypic evolution in a passerine (Cranioleuca pyrrhophia, Furnariidae) along a dry forest gradient"

Aim: Most speciation in birds and mammals is assumed to require an allopatric phase. Yet, many studies challenge this idea and provide evidence that natural selection is the primary driver of diversification, regardless of the geographic setup (i.e., divergence-with-gene-flow). In South America, the Chaco-Andes dry forests belt spans a broad environmental gradient and provides opportunity for parapatric diversification. Our objective was to assess divergence-with-gene-flow in population evolution within a typical dry forest bird.
We studied genomic and phenotypic divergence between subspecies of Cranioleuca pyrrhophia (Aves, Furnariidae), which are distributed along the Chaco-Andes dry forest belt (Central Andes Mountains and Chaco and Pampas regions of Bolivia, Uruguay, and Argentina), and that are mostly differentiated by plumage color.
Methods: We 1) sequenced ddRAD loci of 24 samples and collected plumage and body size data of 180 specimens; 2) tested the association between genomic and phenotypic traits and elevation, geographic isolation, and climatic variation; and 3) to distinguish divergence in allopatry from divergence-with-gene-flow, compared phenotypic divergence with neutral genomic variation (S-test, PST–FST comparisons), estimated gene flow, and calculated relative (FST) and absolute (DXY) genomic divergence.
Results: In average, strongly differentiated loci also had the highest DXY values. Geographic isolation and elevation predicted phenotypic and genomic variation, with a minor unique impact of climate. Yet, these metrics better predicted plumage than body size traits. Certain phenotypic traits exceeded neutral variation (e.g., tail color), with variable divergence patterns among phenotypic traits—plumage traits being the most variable between subspecies.
Main conclusions: Phenotypic variation in C. pyrrhophia likely reflects local adaptation, shaped more by environmental factors than solely by drift. Phenotypic traits varied differently, with plumage diverging more rapidly or under stronger selection. Habitat gradients like the Chaco-Andes dry forests drive parapatric diversification, where divergence combined with local extinction of geographically intermediate populations, may lead to isolation and discontinuous variation typical of full species.

Check dataset usage in file Readme.txt