Dataset
Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting
Dryad
12/04/2018
DOI: 10.5061/dryad.k57430s
Abstract
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.
Details
- Title: Subtitle
- Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting
- Creators
- Fernando Alda - University of Tennessee at ChattanoogaVictor A. Tagliacollo - Universidade de São PauloMaxwell J. Bernt - University of Louisiana at LafayetteBrandon T. Waltz - University of Louisiana at LafayetteWilliam B. Ludt - Louisiana State University of AlexandriaBrant C. Faircloth - Louisiana State University of AlexandriaMichael E. Alfaro - University of California, Los AngelesJames S. Albert - University of Louisiana at LafayetteProsanta Chakrabarty - Louisiana State University of Alexandria
- Resource Type
- Dataset
- DOI
- 10.5061/dryad.k57430s
- Publisher
- Dryad
- Grant note
- DEB-1242260, DEB-0614334, DEB-0741450, DEB-1354511, DEB-0916695, DEB-1354149 / National Science Foundation (https://ror.org/021nxhr62)
- Language
- English
- Date published
- 12/04/2018
- Academic Unit
- Biology
- Record Identifier
- 9984936495802771
Metrics
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