Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex

Species with fragmented distributions are particularly useful models for investigating processes underlying biological diversification in the Neotropics. The Phaeothlypis wood-warbler complex (Aves: Parulidae) is comprised of six disjunct or parapatric populations. The geographic distribution of these six populations mirrors the classic map of Neotropical areas of endemism that were originally proposed as putative Pleistocene forest refugia, but the magnitude of mitochondrial DNA divergence between these populations suggests that they are each substantially older, with origins in the late Pliocene. Phylogenetic reconstructions based on long mtDNA coding sequences show that the Guiana Shield and Atlantic Forest populations are sister lineages, and group this combined lineage and the remaining four population-specific lineages in a five-way hard polytomy. MtDNA-based phylogenetic reconstructions provide no evidence that the three populations with conspicuous yellow rump and tail feathers currently grouped as the Buff-rumped Warbler (P. fulvicauda) form a monophyletic group. Furthermore, there is a broad discordance between mtDNA and plumage along a transect just east of the Andes, where the contact zone between highly divergent mtDNA clades is more than 1000 km north of the phenotypic hybrid zone between the bright and dark plumage forms. This discordance between mtDNA genotype and plumage phenotype is similar to patterns seen on a finer geographic scale in other avian hybrid zones and may result from asymmetric introgression of the bright plumage trait.