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 predatorsSpeciesCell 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
2021
The Evolutionary History of Siphonophore Tentilla: Novelties, Convergence, and Integration
Damian-Serrano A, Haddock S, Dunn C. The Evolutionary History of Siphonophore Tentilla: Novelties, Convergence, and Integration. Integrative Organismal Biology 2021, 3: obab019. PMID: 34355122, PMCID: PMC8331849, DOI: 10.1093/iob/obab019.Peer-Reviewed Original ResearchEvolutionary historyMorphological diversityComplex evolutionary historyBroad morphological diversityEvolutionary gainPhenotypic integrationEvolutionary timeHydrozoan cnidariansMorphological convergenceFunctional diversityMorphological charactersStructured diversityCharacter correlationsFeeding habitsPrey captureUnique biological structureSiphonophore speciesNematocyst typesTentillaDiversityKinematic diversitySpeciesBiological structuresNematocyst dischargeCnidarians
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
2016
Comparative genomics and the diversity of life
Dunn C, Munro C. Comparative genomics and the diversity of life. Zoologica Scripta 2016, 45: 5-13. DOI: 10.1111/zsc.12211.Peer-Reviewed Original ResearchGenomic analysisComparative genome analysisComparative genomic analysisNumber of speciesDiversity of lifeGenome functionGene duplicationComparative genomicsOrganism's phenotypeLaboratory model systemPhylogenetic analysisGene homologyGenome sequenceGenome analysisMore speciesBiodiversity researchGenomicsNomenclatural systemSpeciesModel systemCentral roleSystematicsOrthologsPhylogeneticsPowerful window
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
A re-examination of siphonophore terminology and morphology, applied to the description of two new prayine species with remarkable bio-optical properties
Haddock S, Dunn C, Pugh P. A re-examination of siphonophore terminology and morphology, applied to the description of two new prayine species with remarkable bio-optical properties. Marine Biodiversity Records 2005, 85: 695-707. DOI: 10.1017/s0025315405011616.Peer-Reviewed Original Research