Abstract
The stipple-throated antwrens of the genus Epinecrophylla (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of Epinecrophylla antwrens and the first population-level genetic analyses for most species in the genus. Most of our analyses are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to confidently place the western Amazonian taxon pyrrhonota. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in the ornata group currently regarded as species, and in the haematonota and leucophthalma groups we found paraphyly at the species and subspecies levels, respectively. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group, discuss the biogeographic patterns that we uncover, and suggest areas for further study.
