DOI: 10.5061/dryad.k57430s
title: Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting

description: Resolving patterns of ancient and rapid diversifications is one of the
 most challenging tasks in evolutionary biology. These difficulties arise
 from confusing phylogenetic signals that are associated with the interplay
 of incomplete lineage sorting and homoplasy. Phylogenomic analyses of
 hundreds, or even thousands, of loci offer the potential to resolve such
 contentious relationships. Yet, how much useful phylogenetic information
 these large data sets contain remains uncertain and often goes untested.
 Here, we assess the utility of different data filtering approaches to
 maximize phylogenetic information and minimize noise when reconstructing
 an ancient radiation of Neotropical electric knifefishes (Order
 Gymnotiformes) using ultraconserved elements. We found two contrasting
 hypotheses of gymnotiform evolutionary relationships depending on whether
 phylogenetic inferences were based on concatenation or coalescent methods.
 In the first case, all analyses inferred a previously—and
 commonly—proposed hypothesis, where the family Apteronotidae was found as
 the sister group to all other gymnotiform families. In contrast,
 coalescent-based analyses suggested a novel hypothesis where families
 producing pulse-type (viz., Gymnotidae, Hypopomidae and Rhamphichthyidae)
 and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were
 reciprocally monophyletic. Nodal support for this second hypothesis
 increased when analyzing loci with the highest phylogenetic information
 content and further increased when data were pruned using targeted
 filtering methods that maximized phylogenetic informativeness at the
 deepest nodes of the Gymnotiformes. Bayesian concordance analyses and
 topology tests of individual gene genealogies demonstrated that the
 difficulty of resolving this radiation was likely due to high gene-tree
 incongruences that resulted from incomplete lineage sorting. We show that
 data filtering reduces gene tree heterogeneity and increases nodal support
 and consistency of species trees using coalescent methods; however, we
 failed to observe the same effect when using concatenation methods.
 Furthermore, the targeted filtering strategies applied here support the
 use of “gene data interrogation” rather than “gene genealogy
 interrogation” approaches in phylogenomic analyses, to extract
 phylogenetic signal from intractable portions of the Tree of Life.
description: Online Appendix
 1Extended Methods section
 including: DNA Extraction and Library Preparation, and Target Enrichment
 and Sequencing of UCEs.Aldaetal_SystBio_Appendix1.pdfOnline Appendix 2Extended Methods section including: Assembly and Alignment of Sequence Capture Data.Aldaetal_SystBio_Appendix2.pdfgymno_full_dataset_min75_completeIndividual UCE loci alignments that are common to at least 75% of taxa in the full dataset of Gymnotiformes (966 loci, 47 taxa). Codes for individual names in README.gymno_reduced_dataset_min75_completeIndividual UCE loci alignments that are common to at least 75% of taxa in the reduced dataset of Gymnotiformes (1472 loci, 11 taxa). Name codes in README.txt.gymno_reduced_dataset_100_completeIndividual UCE loci alignments that are common to 100% of taxa in the reduced dataset of Gymnotiformes (368 loci, 11 taxa). Codes for individual names in README.gymno_full_dataset_min75_concatenated.nexConcatenated matrix of UCE loci in common to at least 75% of taxa in the Gymnotiformes full dataset. Code names in README.txt.gymno_reduced_dataset_min75_concatenatedConcatenated matrix of UCE loci in common to at least 75% of taxa in the Gymnotiformes reduced dataset. Code names in README.txt.gymno_reduced_dataset_100_concatenatedConcatenated matrix of UCE loci in common to at least 100% of taxa in the Gymnotiformes reduced dataset. Code names in README.txt.Aldaetal_SystBio_SupplMatSupplementary Tables S1-S4, and Supplementary Figures S1-S16.all_gene_treesAll gene trees (best and bootstrapped) inferred in RAxML for each individual UCE locus for the full and reduced taxon sets. Contents in README.pruned_gene_treesAll gene trees (best and bootstrapped) inferred in RAxML for all the filtered datasets. Contents in README.