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 functionCellsGiants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores
Ahuja N, Cao X, Schultz D, Picciani N, Lord A, Shao S, Jia K, Burdick D, Haddock S, Li Y, Dunn C. Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores. Genome Biology And Evolution 2024, 16: evae048. PMID: 38502059, PMCID: PMC10980510, DOI: 10.1093/gbe/evae048.Peer-Reviewed Original ResearchConceptsK-mer spectraMitochondrial genomeGenomic diversityK-mersNuclear genomeEstimate nuclear genome sizesMitochondrial gene orderNuclear genome sizeGenome assembly projectsRearranged mitochondrial genomesK-mer countingGenome skimmingGene orderGenome sizeRead coverageSequencing depthPhylogenetic samplingIllumina sequencingCnidarian speciesGenomeAssembly projectsSiphonophoresZooplankton communityAbundant predatorsSpecies
2018
Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals
PUGH P, DUNN C, HADDOCK S. Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals. Zootaxa 2018, 4415: 452-472. PMID: 30313611, DOI: 10.11646/zootaxa.4415.3.3.Peer-Reviewed Original Research
2013
The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes
Bracken-Grissom H, Collins A, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien S, Paulay G, Putnam N, Ravasi T, Rouse G, Ryan J, Schulze A, Wörheide G, Adamska M, Bailly X, Breinholt J, Browne W, Diaz M, Evans N, Flot J, Fogarty N, Johnston M, Kamel B, Kawahara A, Laberge T, Lavrov D, Michonneau F, Moroz L, Oakley T, Osborne K, Pomponi S, Rhodes A, Santos S, Satoh N, Thacker R, Van de Peer Y, Voolstra C, Welch D, Winston J, Zhou X. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal Of Heredity 2013, 105: 1-18. PMID: 24336862, PMCID: PMC4072906, DOI: 10.1093/jhered/est084.Peer-Reviewed Original ResearchConceptsGenome/transcriptome sequencingInvertebrate genomesMetazoan speciesPhyletic diversityMarine taxaPhylogenetic placementTaxonomic spectrumTranscriptome sequencingStudy taxaWhole genomeGenomeConservation researchInvertebratesSpeciesTaxaSequencingComparative approachPlacozoaCnidariaTranscriptomeCtenophoraPoriferaHuman healthArthropodaGenomics
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