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 results are robust to a diversity of
phylogenetic and population genetic methods, but we show that even with
thousands of loci we are unable to fully resolve the relationships between
some western Amazonian species in the haematonota group. 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
that are currently regarded as species, and in the haematonota and
leucophthalma groups we found paraphyly at the species and subspecies
levels, respectively. As has been found in many Amazonian taxa, our
phylogenetic results show that the major river systems of the Amazon Basin
appear to have an effect on the genetic structure and range limits within
Epinecrophylla. Our population genetics analyses showed extensive
admixture between some taxa despite their deep genetic divergence.
We present a revised taxonomy for the group and suggest areas
for further study.