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.

Alignment.zip
phylip-formatted UCE alignment for 63 Epinecrophylla samples and two outgroups. Alignment contains 2,149 loci and is 75% complete (75% of loci contain all samples). Associated charset file delimits individual loci. Data were phased in Phyluce and each individual contains two samples representing the two haplotypes, denoted with the suffixes "_0" and "_1".

Phylogenies_primary.zip
Dated phylogenies (.tre files) for UCE and mitogenome datasets. The UCE tree is illustrated in Figure 2 and dated using treePL. The mitogenome tree is illustrated in Figure S2, and estimated and dated in BEAST.

Phylogenies_supplemental.zip
Nine .tre files for phylogenies illustrated in supplemental figures S1 and S2. Please refer to the publication for details on methods used to estimate each phylogeny.

Phylogenies_SNAPP.zip
Input files and results from SNAPP. Inlcuded are input .xml files, posterior of species trees, and MCC tree. Three separate SNAPP analyses are included, with tips at different scales: clade-level (mostly subspecies), species-level, and for only clades in the haematonota group. These refer to Figure 3, Figure S3, and Figure S4.

Epinec_divergence_time_estimate_mtDNA_alignment.xml
BEAST .xml file used to estimate branch lengths with a mitochondrial molecular clock. Topology is that found in the Phylogenies.zip archive ("Figure_S1A" .tre file) and the results of this analysis are in the same archive ("Figure_2" .tre file). The mitochondrial alignment in this .xml file is that of the 13 mitochondrial protein-coding genes obtained from draft mitochondrial genomes of each individual.

illumiprocessor_conf_files.zip
.conf files for processing UCE raw reads with illumiprocessor. Raw read data are located in the Sequence Read Archive under SUB7183085.

150_most_informative_loci.txt
The 150 UCE loci with the greatest number of parsimony-informative sites. Used to estimate a phylogenetic tree in a fully partitioned analysis in STACEY.

UCE_gene_trees-RAxML.tre
UCE gene trees estimated in RAxML for use in ASTRAL-III