2018
Giant tortoise genomes provide insights into longevity and age-related disease
Quesada V, Freitas-Rodríguez S, Miller J, Pérez-Silva J, Jiang Z, Tapia W, Santiago-Fernández O, Campos-Iglesias D, Kuderna L, Quinzin M, Álvarez M, Carrero D, Beheregaray L, Gibbs J, Chiari Y, Glaberman S, Ciofi C, Araujo-Voces M, Mayoral P, Arango J, Tamargo-Gómez I, Roiz-Valle D, Pascual-Torner M, Evans B, Edwards D, Garrick R, Russello M, Poulakakis N, Gaughran S, Rueda D, Bretones G, Marquès-Bonet T, White K, Caccone A, López-Otín C. Giant tortoise genomes provide insights into longevity and age-related disease. Nature Ecology & Evolution 2018, 3: 87-95. PMID: 30510174, PMCID: PMC6314442, DOI: 10.1038/s41559-018-0733-x.Peer-Reviewed Original ResearchConceptsGiant tortoisesAge-related diseasesNew genome sequencesAldabra giant tortoiseDNA repair genesGiant tortoise populationLonesome GeorgeRelated speciesGenome sequenceEvolutionary informationVertebrate animalsGenomic determinantsTortoise populationsGenomeExcellent modelRepair genesCancer developmentTortoisesSupervised analysisGenesEvolutionary strategyGlobal analysisImportant resourceLast memberLongevityUncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes
Gloria-Soria A, Dunn WA, Yu X, Vigneron A, Lee KY, Li M, Weiss BL, Zhao H, Aksoy S, Caccone A. Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. G3: Genes, Genomes, Genetics 2018, 8: 887-897. PMID: 29343494, PMCID: PMC5844309, DOI: 10.1534/g3.117.300493.Peer-Reviewed Original ResearchConceptsGenomic resourcesRelated speciesCandidate genesNonmodel organismsTranscript librariesFunctional genomicsTranscriptome assemblyFunctional annotationWild populationsPhysiological traitsGenomic regionsDNA regulationMost speciesRNAseq experimentsGenetic basisLaboratory coloniesGenesFunctional studiesPolymorphic sitesSpeciesTrypanosome infection statusGenomeNew assemblyTrypanosoma infectionFlies
2010
Anopheles Immune Genes and Amino Acid Sites Evolving Under the Effect of Positive Selection
Parmakelis A, Moustaka M, Poulakakis N, Louis C, Slotman MA, Marshall JC, Awono-Ambene PH, Antonio-Nkondjio C, Simard F, Caccone A, Powell JR. Anopheles Immune Genes and Amino Acid Sites Evolving Under the Effect of Positive Selection. PLOS ONE 2010, 5: e8885. PMID: 20126662, PMCID: PMC2811201, DOI: 10.1371/journal.pone.0008885.Peer-Reviewed Original ResearchConceptsPositive selectionImmune genesGambiae complexDN/dS ratiosLineage-specific evolutionPopulation genetics frameworkAmino acid sitesAnopheles gambiae complexSpecific amino acidsInnate immunity genesAncestral polymorphismComparative phylogeneticsGene diversityEvolutionary historyNatural populationsGenetic diversityGenetic frameworkNatural selectionImmunity genesVector biologyDS ratiosGenesAmino acidsDiversityGenetic knowledge
2009
Characterization and evolution of MHC class II B genes in Galápagos marine iguanas (Amblyrhynchus cristatus)
Glaberman S, Moreno M, Caccone A. Characterization and evolution of MHC class II B genes in Galápagos marine iguanas (Amblyrhynchus cristatus). Developmental & Comparative Immunology 2009, 33: 939-947. PMID: 19454336, DOI: 10.1016/j.dci.2009.03.003.Peer-Reviewed Original ResearchConceptsClass II B genesGalápagos marine iguanasB geneMarine iguanasMHC class II B genesAvian MHC evolutionInterlocus gene conversionAncestral locusEvolutionary forcesMHC evolutionBird speciesGene conversionGene groupsPositive selectionCDNA sequenceClass II genesLocus groupsVertebratesGenesMammalsShort tractsBeta 2 domainAdaptive immune systemMajor groupsSquamates
2008
The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex
Parmakelis A, Slotman MA, Marshall JC, Awono-Ambene PH, Antonio-Nkondjio C, Simard F, Caccone A, Powell JR. The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex. BMC Ecology And Evolution 2008, 8: 79. PMID: 18325105, PMCID: PMC2288592, DOI: 10.1186/1471-2148-8-79.Peer-Reviewed Original ResearchConceptsInsect innate immune systemAnopheles gambiae speciesLevel of polymorphismAnopheles gambiae complexSpecific adaptive responsesAncestral polymorphismPhylogenetic frameworkMolecular evolutionSuch genesGambiae speciesPositive selectionImmunity genesSelection pressureCandidate genesImmune genesMosquito's abilityGambiae complexStudied genesGenesInnate immune systemAdaptive responseMalaria parasitesPlasmodium parasitesEase of manipulationSpecies
2007
Patterns of Selection in Anti-Malarial Immune Genes in Malaria Vectors: Evidence for Adaptive Evolution in LRIM1 in Anopheles arabiensis
Slotman MA, Parmakelis A, Marshall JC, Awono-Ambene PH, Antonio-Nkondjo C, Simard F, Caccone A, Powell JR. Patterns of Selection in Anti-Malarial Immune Genes in Malaria Vectors: Evidence for Adaptive Evolution in LRIM1 in Anopheles arabiensis. PLOS ONE 2007, 2: e793. PMID: 17726523, PMCID: PMC1945087, DOI: 10.1371/journal.pone.0000793.Peer-Reviewed Original ResearchConceptsAdaptive evolutionPrimary malaria vectorMalaria vectorsPatterns of selectionNon-vector speciesAnopheles gambiae complexMcDonald-KreitmanReplacement substitutionsPositive selectionGenetic variationMalaria vector AnLRIM1Immune genesSelection showGambiae complexGenesAdjacent codonsProtein differentiationLevel of resistanceAdaptive responsePlasmodium speciesCEC1Vector AnMaximum likelihood testSpecies
2006
Genetic Divergence of Connecticut Melanoplus femurrubrum Populations
Lee J, Marshall J, Schmitz O, Caccone A. Genetic Divergence of Connecticut Melanoplus femurrubrum Populations. Journal Of Heredity 2006, 97: 290-293. PMID: 16598036, DOI: 10.1093/jhered/esj027.Peer-Reviewed Original ResearchConceptsGenetic diversityHigh mitochondrial diversityNuclear gene regionsAT-rich genesHigh sequence divergenceFixation index analysisMultiple genetic markersPhylogeographic patternsMitochondrial diversityMolecular varianceGenetic divergenceSequence divergenceEqual diversityGenetic variationLittle divergenceGene regionGenetic markersPopulation-level studiesITS1 geneGenesDiversityDivergenceSmall geographic areasND2Species
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
2004
Variation in an intron sequence of the voltage‐gated sodium channel gene correlates with genetic differentiation between Anopheles gambiae s.s. molecular forms
Gentile G, Santolamazza F, Fanello C, Petrarca V, Caccone A, Della Torre A. Variation in an intron sequence of the voltage‐gated sodium channel gene correlates with genetic differentiation between Anopheles gambiae s.s. molecular forms. Insect Molecular Biology 2004, 13: 371-377. PMID: 15271209, DOI: 10.1111/j.0962-1075.2004.00494.x.Peer-Reviewed Original ResearchConceptsVoltage-gated sodium channel geneSodium channel geneGenetic differentiationGenetic variationChannel genesPossible selective sweepMajor haplotypesSingle mutational stepAnopheles gambiae MRDNA sitesGene flowSelective sweepsMutational stepsTaxonomic statusIntron sequencesGambiae MMolecular formsIntron ISingle localityIntronic regionsAnopheles gambiae s.Additional haplotypesGambiae s.HaplotypesGenes
2003
Analysis of a Shift in Codon Usage in Drosophila
Powell JR, Sezzi E, Moriyama EN, Gleason JM, Caccone A. Analysis of a Shift in Codon Usage in Drosophila. Journal Of Molecular Evolution 2003, 57: s214-s225. PMID: 15008418, DOI: 10.1007/s00239-003-0030-3.Peer-Reviewed Original ResearchConceptsCodon usageD. melanogasterMutation biasSaltans species groupAmino acidsFour-fold degenerate sitesRelaxed selectionD. willistoniExtant speciesDrosophila willistoniSpecies groupsPosttranscriptional modificationsWobble positionDegenerate sitesFrozen accidentWillistoniLineagesRelative abundanceMelanogasterSpeciesTRNAGenesC compositionFurther insightDrosophila
1999
Characterization of the soluble guanylyl cyclase β‐subunit gene in the mosquito Anopheles gambiae
Caccone A, Garcia B, Mathiopoulos K, Min G, Moriyama E, Powell J. Characterization of the soluble guanylyl cyclase β‐subunit gene in the mosquito Anopheles gambiae. Insect Molecular Biology 1999, 8: 23-30. PMID: 9927171, DOI: 10.1046/j.1365-2583.1999.810023.x.Peer-Reviewed Original ResearchConceptsAnopheles gambiaeDeduced amino acid sequenceA. gambiae genomeMosquito Anopheles gambiaeThird codon positionInternal stop codonBeta-subunit geneAmino acid sequenceGambiae genomeGambiae genesGene structureTransposable elementsFifth intronCodon positionsNoncoding regionsSubunit geneAcid sequenceFlanking regionsC-terminusFunctional domainsGenomic DNAStop codonHigh similarityGenesFirst detailed description
1993
Rates of DNA evolution in Drosophila depend on function and developmental stage of expression.
Powell J, Caccone A, Gleason J, Nigro L. Rates of DNA evolution in Drosophila depend on function and developmental stage of expression. Genetics 1993, 133: 291-298. PMID: 8094697, PMCID: PMC1205319, DOI: 10.1093/genetics/133.2.291.Peer-Reviewed Original ResearchConceptsComplementary DNADNA-DNA hybridization experimentsTotal single-copy DNALineage-specific shiftsSingle-copy genomeDivergence of genesSpecies of DrosophilaDevelopmental stagesDNA sequence divergenceGreater evolutionary distanceSingle-copy DNADifferent developmental stagesDNA evolutionEvolutionary distanceCodon usageCDNA sequenceSequence dataHybridization experimentsDegree of relatednessDrosophilaEmbryonic stagesSilent substitutionsGenesSpeciesDNA
1992
Evolutionary divergence in Dolichopoda cave crickets: A comparison of single copy DNA hybridization data with allozymes and morphometric distances
Allegrucci G, Caccone A, Cesaroni D, Sbordoni V. Evolutionary divergence in Dolichopoda cave crickets: A comparison of single copy DNA hybridization data with allozymes and morphometric distances. Journal Of Evolutionary Biology 1992, 5: 121-148. DOI: 10.1046/j.1420-9101.1992.5010121.x.Peer-Reviewed Original ResearchDolichopoda cave cricketsNuclear genesGenetic divergenceCave cricketsOverall genetic divergenceDNA hybridization dataDNA-DNA hybridizationDolichopoda speciesMorphological divergenceEvolutionary divergenceAllozyme frequenciesMolecular clockEvolutionary factorsMolecular dataMorphological charactersHybridization dataMorphological differentiationMorphometric distancesAllozymesDivergenceMolecular changesAppendage morphologyGenesDNA hybridizationEstimates of time