Early stages of speciation with gene flow in the Amazilia Hummingbird (Amazilis amazilia) subspecies complex of Western South America

Disentangling the factors underlying the diversification of geographically
variable species with a wide geographical range is essential to
understanding the initial stages and drivers of the speciation process.
The Amazilia Hummingbird, Amazilis amazilia, is found along the Pacific
coast from northern Ecuador down to the Nazca Valley of Peru, and is
currently classified as six phenotypically differentiated subspecies. Our
aims were to resolve the evolutionary relationships of the six subspecies,
to assess the geographical pattern and extent of evolutionary divergence,
and to test for introgression using both a mtDNA marker and a
genome-by-sequencing dataset from 86 individuals from across the species
range. The consensus phylogenetic tree separated the six subspecies into
three distinct clades, corresponding with the Ecuador lowlands (A.
amazilia dumerilii), the Ecuador highlands (A. amazilia alticola and A.
amazilia azuay), and the Peruvian coast (A. amazilia leucophoea, A.
amazilia amazilia, and A. amazilia caeruleigularis). However, an
unresolved mtDNA network suggests that the diversification of the
subspecies was recent and rapid. We found evidence of gene flow among the
subspecies A. amazilia dumerilii, A. amazilia alticola, and A. amazilia
leucophoea, with strong genetic isolation of the subspecies A. amazilia
azuay in the isolated Yunguilla Valley of Ecuador. Finally, environmental
data from each subspecies’ capture locations were concordant with the
three distinct clades. Overall, our results suggest that both expansion
into new habitats and geographic isolation shaped the present-day
phylogeny and range of the A. amazilia subspecies, and that A. amazilia
azuay may be genetically divergent enough to be considered a separate
species.