DOI: 10.5061/dryad.rn8pk0p90
title: Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

description: The family Thamnophilidae is a species-rich Neotropical radiation of
 passerine birds. Current classification of its 235 species is mostly based
 on morphological similarities, but recent studies integrating
 comprehensive phenotypic and phylogenetic data have redefined taxonomic
 limits of several taxa. Here, we assess generic relationships of
 Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using
 DNA sequences from the mitochondrion, nuclear exons, and ultraconserved
 elements (UCEs), with further attention to interspecific relationships
 within Herpsilochmus. We show that Herpsilochmus and Sakesphorus are not
 monophyletic. We resolve H. sellowi as a deep-branch sister species to the
 monotypic genus Biatas and S. cristatus as sister to a clade comprising
 Herpsilochmus sensu stricto and Dysithamnus. These results are consistent
 across loci, obtained via concatenation and coalescent-based analyses, and
 supported by likelihood-ratio tests of the distribution of our sampled
 coalescent histories. The phenotypic distinctiveness of both H. sellowi
 and Biatas argues against merging them into a single genus. Because no
 generic name is available for H. sellowi, we describe a monotypic genus.
 The polyphyly of Sakesphorus warrants recognition of the available generic
 name Sakesphoroides for the distinctive and monotypic S. cristatus.
 Furthermore, we recover six well-supported species groups within
 Herpsilochmus sensu stricto. Within the context of the family as a whole,
 the ubiquity of long terminal branches representing monotypic genera
 points to extinction events among ancestors of these lineages. We suggest
 that retention of ancestral characters or random genetic drift coupled
 with extensive extinction could explain the high degree of morphological
 and ecological similarity across these taxa, but we highlight the
 potential role of the environment in driving adaptive phenotypic
 convergence. Finally, our results send a cautionary message against the
 blind use of phylogenies containing imputed data based on taxonomy due to
 the increasingly frequent mismatches between traditional taxonomic
 classification and molecular phylogenies.
description: This data repository contains sequence alignments, gene trees,
 species phylogenies, and morphometric data used in the study
 below: <strong>Bravo, G. A. et al. Phylogenomic
 analyses reveal non-monophyly of the antbird genera
 <i>Herpsilochmus</i> and <i>Sakesphorus</i>
 (Thamnophilidae), with description of a new genus for
 <i>Herpsilochmus sellowi. </i>Ornithology. In
 press.</strong>  Specifically, the data contained
 here is as follows: 1.
 <strong><em>UCEs_exons_concatenated.phy</em></strong>: FASTA alignment containing concatenated sequences for 2,142 regions flanking UCEs (36 individuals; 1,415,745 bp; average of 661 bp/locus) and 27 exons (36; individuals; 14,484 bp; average of 536 bp/locus) that were used in phylogenomic analyses aiming at assessing generic relationships of the antbird genera <i>Herpsilochmus</i>, <i>Sakesphorus</i>, <i>Thamnophilus</i>, <i>Biatas</i>, and <i>Dysithamnus.</i> 2. <em><strong>PartitionFile_UCEs_concatenated.txt</strong></em>: Partition file of the FASTA file above to run a partitioned concatenated analysis or separate gene alignments needed for subsequent coalescent-based phylogenetic methods. 3. <strong><em>UCEs_exons_concatenated.tre</em></strong>: Tree file resulting from the partitioned concatenated analysis using RAxML. 4. <strong><em>All_gene_trees.tre</em></strong>: Unrooted gene trees for all 2,169 loci obtained using IQ-TREE. 5. <em><strong>All_gene_trees_no_toepad.tre</strong></em>: Tree file containing 2,169 unrooted gene trees with one toepad sample removed (<i>Herpsilochmus axillaris senex</i> ANSP 158009) to be used in ASTRAL.  6. <em><strong>Astral_notoepad_nobs.tre</strong></em>: Tree file resulting from running ASTRAL. 7. <em><strong>Reduced_genetrees_coalescent_tests.tre</strong></em>: Tree file containing 1,683 gene trees built on a reduced subset of 9 individuals to run coalescent-based tests of alternative genus-level topologies. 8. <em><strong>ND2_all.FASTA:</strong></em> Fasta alignment of the complete mitochondrial gene ND2 (1,041 bp) for 103 thamnophilids. 9. <strong><em>ND2.treefile.tre</em></strong>: Tree file containing ND2 gene tree file obtained using IQ-TREE. 10. <strong><em>Morphometric_data.txt</em></strong>: Tab-delimited file containing raw data for 11 morphological variables (242 individuals) used in multivariate morphometric analyses. <em>Note: This is the same table as Table S2 in the manuscript.</em> <strong>Raw UCE and exon data are available at NCBI BioProject PRJNA655842 (See Supplemental Material Table S1 in the manuscript for SRA numbers).</strong>