DOI: 10.5061/dryad.r2280gb9n
title: Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla)

description: 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.
description: Alignment.zip<br> 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<br> 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<br> 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<br> 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
 <i>haematonota</i> group. These refer to Figure 3, Figure S3,
 and Figure S4.
 Epinec_divergence_time_estimate_mtDNA_alignment.xml<br>
 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<br>
 .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<br> 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<br> UCE gene trees estimated in
 RAxML for use in ASTRAL-III