ArticleGenome research2012
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers, 1 of them a synthesis that pooled it.
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Who cites it
113 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Type Genomics: A Framework for Integrating Genomic Data into Biodiversity and Taxonomic Research.Systematic biology · 2025Guideline
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- Phylogenomic blind spots: the limits of UCE and BUSCO loci in the presence of gene flow.Molecular biology and evolution · 2026Article
- A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.Molecular ecology resources · 2026Review
- Unlocking the Past to Protect the Future: Forensic DNA and Historical Specimens Reveal the Origins of Smuggled Yellow-Headed Parrots.Evolutionary applications · 2026Article
- Evaluating Probe Design for Phylogenomics Across Taxonomic Scales: First Steps for Applying Ultraconserved Elements in an Understudied Class (Mollusca: Polyplacophora).Molecular ecology resources · 2026Article
- Sequencing Ultraconserved Elements (UCEs) for Marine Population Genomics: A Proof-of-Concept Using a Deep-Sea Mussel Species.Evolutionary applications · 2026Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- Covering All Bases: A Universal Metazoan UCE Probe Set to Democratize Phylogenomics.Genome biology and evolution · 2025Article
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop.BMC ecology and evolution · 2024Article
- The Evolution of Ultraconserved Elements in Vertebrates.Molecular biology and evolution · 2024Article
- The role of biogeographical barriers on the historical dynamics of passerine birds with a circum-Amazonian distribution.Ecology and evolution · 2024Article
- Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).BMC biology · 2024Article
- Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials.Zoological research · 2023Article
- Phylogeny ofInsects · 2023Article
- Whole-genome Analyses Reveal Past Population Fluctuations and Low Genetic Diversities of the North Pacific Albatrosses.Molecular biology and evolution · 2023Article
- Improving quartet graph construction for scalable and accurate species tree estimation from gene trees.Genome research · 2023Article
- Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae).Systematic biology · 2023Article
- Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome ofLife (Basel, Switzerland) · 2023Article
53 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals. In broad outline, our phylogeny agrees with recent phylogenomic studies of mammals, including several formerly controversial relationships. Our results also inform two outstanding questions in placental mammal phylogeny involving rapid speciation, where species-tree methods are particularly needed. Contrary to most phylogenomic studies, our study supports a first-diverging placental mammal lineage that includes elephants and tenrecs (Afrotheria). The level of conflict among gene histories is consistent with this basal divergence occurring in or near a phylogenetic "anomaly zone" where a failure to account for coalescent stochasticity will mislead phylogenetic inference. Addressing a long-standing phylogenetic mystery, we find some support from a high genomic coverage data set for a traditional placement of bats (Chiroptera) sister to a clade containing Perissodactyla, Cetartiodactyla, and Carnivora, and not nested within the latter clade, as has been suggested recently, although other results were conflicting. One of the most remarkable findings of our study is that ultraconserved elements and their flanking DNA are a rich source of phylogenetic information with strong potential for application across Amniotes.
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