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 ResearchConceptsScRNA-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 functionCellsCell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data
Mah J, Dunn C. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nature Ecology & Evolution 2024, 8: 325-338. PMID: 38182680, DOI: 10.1038/s41559-023-02281-9.Peer-Reviewed Original ResearchSingle-cell datasetsCell typesSingle-cell RNA sequencing dataFundamental evolutionary questionsCell type evolutionSister cell typesGene expression dynamicsRNA sequencing dataSingle-cell dataEvolutionary relationshipsEvolutionary questionsEvolutionary historyEvolutionary biologyExpression dynamicsPhylogenetic methodsPhylogenetic charactersMarker genesPhylogenySequencing dataEye cellsCladeType evolutionSpeciesCellsNon-myelinating Schwann cells
2014
Animal Phylogeny and Its Evolutionary Implications
Dunn C, Giribet G, Edgecombe G, Hejnol A. Animal Phylogeny and Its Evolutionary Implications. Annual Review Of Ecology Evolution And Systematics 2014, 45: 1-25. DOI: 10.1146/annurev-ecolsys-120213-091627.Peer-Reviewed Original ResearchAnimal phylogenyAnimal treeEvolution of developmentEvolutionary radiationEvolutionary implicationsMore homoplasyFossil recordPhylogenySpiraliaDeep branchLate NeoproterozoicEarly CambrianRemarkable patternAnimal relationshipsAlternative hypothesisTreesXenacoelomorphaBilateriaEcdysozoaMonophylyProtostomiaGenomeHomoplasyRecent progressNervous system
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