AbstractAim We test whether populations of the Mesoamerican azure‐crowned hummingbird, Amazilia cyanocephala (Trochilidae), located east and west
of the Isthmus of Tehuantepec are genetically, morphologically and environmentally differentiated and examine the relative role of drift and selection in driving diversification. Location Mexico. Methods We sequenced the mitochondrial ATPase‐6 and ATPase‐8 genes and the control region of 130 individuals collected throughout the range of
the species in Mexico. Population genetic methods and coalescent tests were used to reconstruct the phylogeography of the species. Morphological and niche variation between genetic groups of A. cyanocephala were assessed. Results The data revealed two genetic groups separated by the Isthmus of Tehuantepec in the late Pleistocene (49,300–75,800 years ago), with the split occurring in the presence of gene flow. Deviations from demographic equilibrium were
detected for the two genetic groups, indicating more recent population expansions. Amazilia cyanocephala individuals from populations on either side of the Isthmus of Tehuantepec differed in morphology and were distributed in unique environmental space. A coalescent‐based
test indicated that selection is driving the observed morphological differentiation. Main conclusions Our findings implicate the Isthmus of Tehuantepec as a permeable barrier driving
recent diversification of A. cyanocephala in the presence of gene flow. The two A. cyanocephala mitochondrial DNA (mtDNA) groups corresponding with morphological and environmental niche differences, in concert with the results of a coalescent‐based test, suggest
that selection has been strong enough to counteract the effects of gene flow.