ArticlePloS one2013
A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs).
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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105 citing papers in PubMed.
- An ontological morphological phylogenetic framework for living and extinct ray-finned fishes (Actinopterygii).Anatomical record (Hoboken, N.J. : 2007) · 2026Article
- Phylogenomic blind spots: the limits of UCE and BUSCO loci in the presence of gene flow.Molecular biology and evolution · 2026Article
- Searching for shared epigenetic clocks: evaluating ultra-conserved markers in a de novo genome assembly of the albacore tuna.GeroScience · 2026Article
- SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation.Molecular ecology resources · 2026Article
- Mining for Mitochondria: 68 Mitogenomes for Wrasses and Parrotfishes (F: Labridae) From Off-Target UCE Data.Ecology and evolution · 2026Article
- Ancient DNA reconstruction of late holocene ecosystems within the Carpathian basin from paleo-meanders and archaeological deposits.Scientific reports · 2026Article
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- Secondary neurulation mechanisms likely arose in vertebrates during mesenchymal tailbud extension.Frontiers in cell and developmental biology · 2026Article
- Genomic Organization, Evolutionary Conservation and Expression ofBiomedicines · 2025Article
- 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
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- Novel complete mitochondrial genomes of eight riverineMitochondrial DNA. Part B, Resources · 2025Article
- The Evolution of Ultraconserved Elements in Vertebrates.Molecular biology and evolution · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- High-throughput sequencing and fatty acid profile analyses of the Black Amur bream (Ecology and evolution · 2024Article
- Phylogenomic analysis and molecular identification of true fruit flies.Frontiers in genetics · 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
- Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England.Animal microbiome · 2023Article
- Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome ofLife (Basel, Switzerland) · 2023Article
- Phylogenomics and Diversification of the Schistosomatidae Based on Targeted Sequence Capture of Ultra-Conserved Elements.Pathogens (Basel, Switzerland) · 2022Article
45 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.
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