ArticleMolecular phylogenetics and evolution2018
Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.
Article in Molecular phylogenetics and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 21 citations in OpenAlex.
- PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model.Nature communications · 2025Article
- A region of suppressed recombination misleads neoavian phylogenomics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae).Genome biology and evolution · 2023Article
- Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction.Systematic biology · 2021Article
- Unraveling the Global Phylodynamic and Phylogeographic Expansion ofPathogens (Basel, Switzerland) · 2020Article
- Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets.Genome biology and evolution · 2020Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.
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