Genomic and phenotypic divergence‐with‐gene‐flow across an ecological and elevational gradient in a neotropical bird

Aim: Along with environmental gradients, some species show significant differences in morphological, ecological-related traits. Those differences are commonly related to past events of allopatry but, alternatively, could be caused by natural selection in the presence of gene flow. We aimed to explore the prevalence of the divergence-with-gene-flow model across the Chaco-Andes dry forest belt, testing competing models of evolution in a Neotropical bird. Location: Central Andes Mountain range and Chaco region of Argentina and Bolivia. Taxon: Phytotoma rutila (Aves, Cotingidae). Methods: We studied ddRADseq loci (4,893 SNPs) of 21 tissue samples and body size variation of 146 specimens. We evaluated population genetic structure and tested the effects of altitude and distance on genomic divergence. To evaluate allopatry and divergence-with-gene-flow, we compared the divergence on phenotypic traits (bill, tarsus, and wing measurements) versus neutral genomic variation, conducted coalescent analyses to estimate gene flow and divergence time among populations, and calculated relative (FST) versus absolute (DXY) genomic divergence. Results: a) there is a genomic and phenotypic differentiation in P. rutila matched the highland-lowland axis, where the altitude variation explains genomic variation; b) A larger phenotypic than neutral genomic variation was found. c) there is an asymmetric gene flow between populations; d) a pattern of relative and absolute genomic differentiation compatible with divergence-with-gene-flow. Main conclusions: The mechanism behind the morphological and genomic diversification along the Chaco-Andes dry forest belt in P. rutila is divergence‐with‐gene‐flow. Far more complex than we traditionally thought, diversification in South America implicates gene flow between populations and also natural selection along with the environmental gradients, as well as vicariance, contrasting with the idea of tropical speciation primarily based on allopatric models.