2024
Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells
Church S, Mah J, Dunn C. Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells. PLOS Biology 2024, 22: e3002633. PMID: 38787797, PMCID: PMC11125556, DOI: 10.1371/journal.pbio.3002633.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineageEvolution, MolecularHumansPhylogenySequence Analysis, RNASingle-Cell AnalysisSpecies SpecificityConceptsScRNA-seqPhylogenetic comparative approachCellular gene expressionScRNA-seq analysisSingle-cell RNA sequencingRNA sequencing analysisGene treesSpecies treeCell phylogenyPhylogenetic approachPhylogenetic treeEvolutionary historyPairwise alignmentSingle-cell RNA sequencing analysisSequence analysisCellular lifeRNA sequencingGene expressionGenesCell evolutionCell lineagesPhylogenySpeciesCell functionCells
2005
Molecular Phylogenetics of the Siphonophora (Cnidaria), with Implications for the Evolution of Functional Specialization
Dunn C, Pugh P, Haddock S. Molecular Phylogenetics of the Siphonophora (Cnidaria), with Implications for the Evolution of Functional Specialization. Systematic Biology 2005, 54: 916-935. PMID: 16338764, DOI: 10.1080/10635150500354837.Peer-Reviewed Original ResearchConceptsRibosomal RNA genesRNA genesNuclear small subunit ribosomal RNA geneLarge subunit ribosomal RNA geneFunctional specializationSmall subunit ribosomal RNA geneMitochondrial large subunit ribosomal RNA geneFree-living animalsMolecular phylogeneticsOutgroup taxaColonial hydrozoansParsimony reconstructionsMolecular dataBudding processMorphological dataTaxaFunctional typesSiphonophoresMajor groupsPhylogenyDeep seaMedusaeGenesLiving animalsScuba diving
2004
Adaptive evolution of HoxA11 and HoxA13 at the origin of the uterus in mammals
Lynch V, Roth J, Takahashi K, Dunn C, Nonaka D, Stopper G, Wagner G. Adaptive evolution of HoxA11 and HoxA13 at the origin of the uterus in mammals. Proceedings Of The Royal Society B 2004, 271: 2201-2207. PMID: 15539344, PMCID: PMC1691855, DOI: 10.1098/rspb.2004.2848.Peer-Reviewed Original ResearchConceptsAdaptive evolutionTranscription factorsMolecular evolutionHoxa-11Hoxa-13Cis-regulatory evolutionAdaptive molecular evolutionEvolution of developmentMammalian female reproductive systemStrong positive selectionCis-regulatory elementsAmniote taxaDevelopmental genesStem lineageDevelopmental evolutionEvolutionary changeEutherian mammalsSpatial regulationPositive selectionMorphological charactersFemale reproductive organsGenesFemale reproductive systemReproductive organsMammals