Many hypotheses have been erected to attempt to explain the origin and maintenance of the Amazon‟s high biodiversity, although few can been tested under a phylogeographic approach. We evaluated patterns of temporal and spatial genetic diversity of two endemic bird species in the Brazilian Amazon, which have allopatric populations restricted to different areas of endemism and limited by the main rivers of the Amazon basin. Sequences of two mitochondrial genes (ND2 and cytb) and two nuclear (βf7 and G3PDH intron 11) were obtained from 30 individuals, throughout the range of the genus Phoenicircus comprising the two currently-recognised species P. carnifex and P. nigricollis. The use of phylogeographic tools, in combination with population genetics and molecular dating allowed us to reconstruct the spatial and temporal context of the diversification of this genus in the Amazon region, as well as make predictions about its evolutionary history and geographical environment. Our data revealed the existence of four genetically distinct groups, demonstrating the paraphyletic status of P. carnifex and reciprocal monophyly between the two allopatric populations of P. nigricollis. These discoveries necessitate a revision of the current two-species arrangement of the genus Phoenicircus. The group‟s evolutionary history is defined by two types of vicariant events, initially by the formation of the main rivers of the Amazon during the Plio-Pleistocene, and more recently as a result of neotectonics activity in the central Amazon, highlighting the importance of historical processes when modeling the present Amazonian biota.
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