2017
Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification
Richardson JB, Lee KY, Mireji P, Enyaru J, Sistrom M, Aksoy S, Zhao H, Caccone A. Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification. PLOS Neglected Tropical Diseases 2017, 11: e0005949. PMID: 28961238, PMCID: PMC5636163, DOI: 10.1371/journal.pntd.0005949.Peer-Reviewed Original ResearchConceptsAfrican trypanosomesHigh genetic similarityMaximum likelihood phylogenyStrain identificationGenomic resourcesGenetic structureEvolutionary relationshipsGenetic clustersPhylogenetic analysisGenomic analysisSingle nucleotide polymorphismsTaxonomic classificationGenetic similarityLarge comparative analysisGenetic markersHigh similarityGeographic originEvansi strainsSNPsNucleotide polymorphismsT. brucei bruceiPhylogenyTrypanosomesTrypanosomaTrypanozoon
2012
Genetic isolation within the malaria mosquito Anopheles melas
Deitz K, Athrey G, Reddy M, Overgaard H, Matias A, Jawara M, della Torre A, Petrarca V, Pinto J, Kiszewski A, Kengne P, Costantini C, Caccone A, Slotman M. Genetic isolation within the malaria mosquito Anopheles melas. Molecular Ecology 2012, 21: 4498-4513. PMID: 22882458, PMCID: PMC4067978, DOI: 10.1111/j.1365-294x.2012.05724.x.Peer-Reviewed Original ResearchConceptsMicrosatellite dataIsland populationsGambiae complexMaximum likelihood phylogenetic analysisBp of mtDNALevel of divergenceLast glaciation periodA. gambiae complexMalaria vectorsSalt marsh grassAnopheles gambiae complexAnopheles melasMajor malaria vectorApproximate Bayesian analysisMtDNA divergenceGenetic differentiationGenetic divergenceGenetic isolationMainland populationsPhylogenetic analysisPopulation structureMicrosatellite markersLarval habitatsA. gambiaeGlaciation period
2008
Characterization of a Nonclassical Class I MHC Gene in a Reptile, the Galápagos Marine Iguana (Amblyrhynchus cristatus)
Glaberman S, Du Pasquier L, Caccone A. Characterization of a Nonclassical Class I MHC Gene in a Reptile, the Galápagos Marine Iguana (Amblyrhynchus cristatus). PLOS ONE 2008, 3: e2859. PMID: 18682845, PMCID: PMC2483932, DOI: 10.1371/journal.pone.0002859.Peer-Reviewed Original ResearchConceptsGalápagos marine iguanasClass I MHC genesMHC genesMarine iguanasLarge taxonomic gapsClassical class I genesGenomic sequence dataClassical MHC genesMajor histocompatibility complex (MHC) genesPeptide-binding residuesClass I genesMHC evolutionNonclassical genesVertebrate taxaDiverse orderClass I sequencesMHC organizationCytoplasmic domainPhylogenetic analysisGenomic sequencesTaxonomic gapsConserved characterI geneSequence dataI sequences
2006
Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids
Poulakakis N, Parmakelis A, Lymberakis P, Mylonas M, Zouros E, Reese D, Glaberman S, Caccone A. Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids. Biology Letters 2006, 2: 451-454. PMID: 17148428, PMCID: PMC1686204, DOI: 10.1098/rsbl.2006.0467.Peer-Reviewed Original ResearchConceptsEvolutionary historyDNA sequencesAncient DNA studiesDNA fragmentsMultiple displacement amplification (MDA) methodPygmy mammothsIndependent historyShort DNA sequencesB-DNA fragmentEastern MediterraneanMediterranean islandsPhylogenetic analysisMolecular dataMainland samplesCretan sampleDNA studiesHistoryElephantidsDiagnostic sitesElephasPrevailing viewIslandsMammothsMammuthusSequenceMitochondrial DNA from Hemlock Woolly Adelgid (Hemiptera: Adelgidae) Suggests Cryptic Speciation and Pinpoints the Source of the Introduction to Eastern North America
Havill N, Montgomery M, Yu G, Shiyake S, Caccone A. Mitochondrial DNA from Hemlock Woolly Adelgid (Hemiptera: Adelgidae) Suggests Cryptic Speciation and Pinpoints the Source of the Introduction to Eastern North America. Annals Of The Entomological Society Of America 2006, 99: 195-203. DOI: 10.1603/0013-8746(2006)099[0195:mdfhwa]2.0.co;2.Peer-Reviewed Original ResearchEastern North AmericaWestern North AmericaMitochondrial DNANatural rangeA. tsugaeNorth AmericaCryptic speciationMitochondrial lineagesHemlock Woolly AdelgidTsuga speciesPhylogenetic analysisSingle haplotypeT. sieboldiiIntroduced pestMultiple haplotypesAdelges tsugae AnnandAdelgidWoolly AdelgidGeographic originMolecular methodsSouthern JapanLineagesHigher elevationsSevere mortalityT. diversifolia
2005
Short report: Phylogenetic relationships of the anthropophilic Plasmodium falciparum malaria vectors in Africa.
Marshall J, Powell J, Caccone A. Short report: Phylogenetic relationships of the anthropophilic Plasmodium falciparum malaria vectors in Africa. American Journal Of Tropical Medicine And Hygiene 2005, 73: 749-52. PMID: 16222020, DOI: 10.4269/ajtmh.2005.73.749.Peer-Reviewed Original ResearchConceptsNumber of speciesMalaria vectorsAfrican mosquito vectorsMosquito vectorsNuclear genesParaphyletic relationshipSubgenus CelliaPhylogenetic relationshipsPhylogenetic analysisAdditional speciesStatistical supportSpeciesPlasmodium falciparumP. falciparumCausative agentCelliaFalciparumGenesHistorical associationVectorBayesian methods
2003
Xantusiid “night” lizards: a puzzling phylogenetic problem revisited using likelihood-based Bayesian methods on mtDNA sequences
Vicario S, Caccone A, Gauthier J. Xantusiid “night” lizards: a puzzling phylogenetic problem revisited using likelihood-based Bayesian methods on mtDNA sequences. Molecular Phylogenetics And Evolution 2003, 26: 243-261. PMID: 12565035, DOI: 10.1016/s1055-7903(02)00313-5.Peer-Reviewed Original ResearchConceptsDivergence time estimatesXantusia riversianaCytochrome b geneMaximum parsimony analysisCalifornia Channel IslandsLikelihood-based Bayesian methodsIsland endemicsMitochondrial genesLizard evolutionAncestral stateScleroglossan lizardsRibosomal genesMtDNA sequencesPhylogenetic problemsCrown cladeAdditional cladesPhylogenetic analysisNeighbor-JoiningParsimony analysisB geneBoundary bolide impactRock crevicesCladeMaximum likelihoodXantusiaPhylogeography and molecular rates of subterranean aquatic Stenasellid Isopods with a peri‐Tyrrhenian distribution
Ketmaier V, Argano R, Caccone A. Phylogeography and molecular rates of subterranean aquatic Stenasellid Isopods with a peri‐Tyrrhenian distribution. Molecular Ecology 2003, 12: 547-555. PMID: 12535105, DOI: 10.1046/j.1365-294x.2003.01734.x.Peer-Reviewed Original ResearchConceptsMtDNA cytochrome oxidase IInteresting disjunct distributionCytochrome oxidase ICombination of vicarianceSardinia-Corsica microplateThird codon positionMultiple phylogenetic analysesPresent distribution patternAllozyme dataCOI fragmentOxidase ISubterranean isopodDispersal capacityDispersal eventsDisjunct distributionRelated taxaPhylogenetic analysisMolecular dataMolecular ratesCodon positionsPeri-Tyrrhenian areaDistant groupsMultiple populationsIsopodsCrustaceans
2002
The evolutionary origin of Indian Ocean tortoises (Dipsochelys)
Palkovacs E, Gerlach J, Caccone A. The evolutionary origin of Indian Ocean tortoises (Dipsochelys). Molecular Phylogenetics And Evolution 2002, 24: 216-227. PMID: 12144758, DOI: 10.1016/s1055-7903(02)00211-7.Peer-Reviewed Original ResearchConceptsWestern Indian Ocean islandsGiant tortoisesIndian Ocean islandsIndian Ocean giant tortoisesIndian OceanCyt b geneDNA substitution ratesOcean islandsShort generation timeSmall body sizeSource of colonizationMalagasy lineagesEvolutionary originWestern Indian OceanWild populationsMitochondrial DNAPhylogenetic analysisSequence evolutionB geneSubstitution ratesBody sizeOcean currentsEast coastGeneration timeTortoises
1998
Multiple Origins of Cytologically Identical Chromosome Inversions in the Anopheles gambiae Complex
Caccone A, Min G, Powell J. Multiple Origins of Cytologically Identical Chromosome Inversions in the Anopheles gambiae Complex. Genetics 1998, 150: 807-814. PMID: 9755210, PMCID: PMC1460344, DOI: 10.1093/genetics/150.2.807.Peer-Reviewed Original ResearchConceptsA. merusAnopheles gambiae complexA. gambiaePolytene chromosomesA. arabiensisGambiae complexDNA sequence analysisPhylogenetic historySister taxaChromosomal inversionsChromosome inversionsPhylogenetic analysisParallel evolutionImportant genesDNA sequencesCommon ancestryMultiple originsSequence analysisAssumption of monophylyImmediate ancestorsImportant vectorGambiaeChromosomesFirst clear evidenceParticular inversion