ArticleMolecular phylogenetics and evolution2015
Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.
Article in Molecular phylogenetics and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed.
- Evaluating Probe Design for Phylogenomics Across Taxonomic Scales: First Steps for Applying Ultraconserved Elements in an Understudied Class (Mollusca: Polyplacophora).Molecular ecology resources · 2026Article
- Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River.Systematic biology · 2025Article
- Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non-Model Nematodes.Molecular ecology resources · 2025Article
- Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes.International journal of molecular sciences · 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
- Placing human gene families into their evolutionary context.Human genomics · 2022Review
- Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous.Nature ecology & evolution · 2022Article
- Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby,Animals : an open access journal from MDPI · 2022Article
- Perfect and imperfect views of ultraconserved sequences.Nature reviews. Genetics · 2022Review
- Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree.Genome biology and evolution · 2021Article
- Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes).Systematic biology · 2021Article
- Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data.Molecular biology and evolution · 2021Article
- Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity.Proceedings. Biological sciences · 2020Article
- Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements.Scientific reports · 2020Article
- Article
- Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes.Ecology and evolution · 2019Article
- Gene markers for exon capture and phylogenomics in ray-finned fishes.Ecology and evolution · 2019Article
- Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.Molecular phylogenetics and evolution · 2018Article
- Article
- Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata.PloS one · 2018Article
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Authors and funding
7 authors.
Funding
Abstract
Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life.
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