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Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Citation

Bravo, Gustavo et al. (2022), Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi, Dryad, Dataset, https://doi.org/10.5061/dryad.rn8pk0p90

Abstract

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.

Methods

This data repository contains sequence alignments, gene trees, species phylogenies, and morphometric data used in the study below:

Bravo, G. A. et al. Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi. Ornithology. In press. 

Specifically, the data contained here is as follows:

1. UCEs_exons_concatenated.phy: 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 Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus.

2. PartitionFile_UCEs_concatenated.txt: 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. UCEs_exons_concatenated.tre: Tree file resulting from the partitioned concatenated analysis using RAxML.

4. All_gene_trees.tre: Unrooted gene trees for all 2,169 loci obtained using IQ-TREE.

5. All_gene_trees_no_toepad.tre: Tree file containing 2,169 unrooted gene trees with one toepad sample removed (Herpsilochmus axillaris senex ANSP 158009) to be used in ASTRAL. 

6. Astral_notoepad_nobs.tre: Tree file resulting from running ASTRAL.

7. Reduced_genetrees_coalescent_tests.tre: 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. ND2_all.FASTA: Fasta alignment of the complete mitochondrial gene ND2 (1,041 bp) for 103 thamnophilids.

9. ND2.treefile.tre: Tree file containing ND2 gene tree file obtained using IQ-TREE.

10. Morphometric_data.txt: Tab-delimited file containing raw data for 11 morphological variables (242 individuals) used in multivariate morphometric analyses. Note: This is the same table as Table S2 in the manuscript.

Raw UCE and exon data are available at NCBI BioProject PRJNA655842 (See Supplemental Material Table S1 in the manuscript for SRA numbers).

Funding

National Science Foundation, Award: DEB-1011435

National Science Foundation, Award: DBI-0400797

National Science Foundation, Award: DEB-0841729

National Science Foundation, Award: DEB-1136423

Fundação de Amparo à Pesquisa do Estado de São Paulo, Award: 2012/23852-0

Conselho Nacional de Desenvolvimento Científico e Tecnológico, Award: 132893/2009-6

Conselho Nacional de Desenvolvimento Científico e Tecnológico, Award: 141823/2011-9

Conselho Nacional de Desenvolvimento Científico e Tecnológico, Award: 457974-2014-1

Conselho Nacional de Desenvolvimento Científico e Tecnológico, Award: 571334/2008-3