2021
Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises
Jensen E, Gaughran S, Garrick R, Russello M, Caccone A. Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises. Molecular Ecology 2021, 30: 6325-6339. PMID: 34510620, DOI: 10.1111/mec.16176.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsEvolution, MolecularGenetics, PopulationHumansPopulation DensityTurtlesWhole Genome SequencingConceptsGalapagos giant tortoisesPopulation genetics theoryGiant tortoisesWhole-genome sequencingMolecular evolutionWhole genomeGenetic theoryGenome sequencingPopulation genetic summary statisticsGiant tortoise speciesPopulation genetic predictionsLife-history traitsSignals of selectionPatterns of diversityMutation accumulation ratesGenetic summary statisticsEvolutionary distinctivenessRecent radiationExtant lineagesPhylogeographic studiesHistory traitsPopulation genomicsEvolutionary historyMutation accumulationDemographic history
2019
Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians
Valero K, Marshall J, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller M, Pabijan M, Russello M, Sinervo B, Werneck F, Sites J, , Wiens J, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes 2019, 10: 646. PMID: 31455040, PMCID: PMC6769790, DOI: 10.3390/genes10090646.Peer-Reviewed Original ResearchMeSH KeywordsAmphibiansAnimalsEcosystemEvolution, MolecularGenetic SpeciationReptilesSelection, GeneticConceptsEcological speciationSpeciation researchIntegrative taxonomyGenetics of speciationProcess of speciationSouth American lizardsSpeciation ratesPhenotypic evolutionEvolutionary forcesClimatic nicheEuropean salamandersPhenotypic traitsGenetic mechanismsEcological aspectsBiogeographyReptilesSpeciationAmphibiansCase studyGenomicsLizardsGeneticsTaxonomyFinal case studySalamanders
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 ResearchMeSH KeywordsAgingAnimalsDNA RepairEvolution, MolecularGenomeHEK293 CellsHumansInflammation MediatorsMaleNeoplasmsPhylogenyPopulation DensityTurtlesConceptsGiant 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 memberLongevity
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 bruceiPhylogenyTrypanosomesTrypanosomaTrypanozoonMultiple evolutionary origins of Trypanosoma evansi in Kenya
Kamidi CM, Saarman NP, Dion K, Mireji PO, Ouma C, Murilla G, Aksoy S, Schnaufer A, Caccone A. Multiple evolutionary origins of Trypanosoma evansi in Kenya. PLOS Neglected Tropical Diseases 2017, 11: e0005895. PMID: 28880965, PMCID: PMC5605091, DOI: 10.1371/journal.pntd.0005895.Peer-Reviewed Original ResearchConceptsT. brucei strainsDifferent genetic backgroundsEvolutionary originGenetic diversityBrucei strainsMultiple evolutionary originsGenetic backgroundTsetse fly vectorT. evansiLethal human diseaseIndependent originsPolymorphic microsatellitesT. bruceiEvansi isolatesGenetic unitsHuman diseasesObligate linkBruceiEvansi strainsT. brucei bruceiTsetse fliesFly vectorsFliesDiversityBrucei bruceiGenomic insights into the ancient spread of Lyme disease across North America
Walter KS, Carpi G, Caccone A, Diuk-Wasser MA. Genomic insights into the ancient spread of Lyme disease across North America. Nature Ecology & Evolution 2017, 1: 1569-1576. PMID: 29185509, PMCID: PMC6431794, DOI: 10.1038/s41559-017-0282-8.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArachnid VectorsBorrelia burgdorferiCanadaEvolution, MolecularGenetic VariationGenome, BacterialIxodesLyme DiseaseUnited StatesConceptsHistory of spreadEvolutionary historyNorth AmericaLyme disease epidemicLast Glacial MaximumAncient spreadLyme disease bacteriaComplex evolutionary historyPast centuryGlacial MaximumHistoryGenomic insightsEvolutionary changeAmericaUndocumented levelB. burgdorferi s.Large collectionSensu strictoBurgdorferi s.Vector-borne diseasesSouthern CanadaLand use changeBorrelia burgdorferi sensu strictoCenturyDisease bacteria
2016
Global population divergence and admixture of the brown rat (Rattus norvegicus)
Puckett EE, Park J, Combs M, Blum MJ, Bryant JE, Caccone A, Costa F, Deinum EE, Esther A, Himsworth CG, Keightley PD, Ko A, Lundkvist Å, McElhinney LM, Morand S, Robins J, Russell J, Strand TM, Suarez O, Yon L, Munshi-South J. Global population divergence and admixture of the brown rat (Rattus norvegicus). Proceedings Of The Royal Society B 2016, 283: 20161762. PMID: 27798305, PMCID: PMC5095384, DOI: 10.1098/rspb.2016.1762.Peer-Reviewed Original ResearchMeSH KeywordsAfricaAnimalsAustralasiaChinaEuropeEvolution, MolecularGenetics, PopulationHumansMongoliaNorth AmericaPolymorphism, Single NucleotideRatsRussiaConceptsEvolutionary clustersColonization of EuropeRat eradication programmeAgricultural settlementsWestward expansionEastward expansionSoutheast AsiaSouthward expansionAleutian ArchipelagoExpansion routesAstonishing degreeRecent migrantsGlobal population structureGlobal phylogeographyBlack ratsGlobal tradeCommensal rodentsEuropeDe Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense
Sistrom M, Evans B, Benoit J, Balmer O, Aksoy S, Caccone A. De Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense. PLOS ONE 2016, 11: e0147660. PMID: 26910229, PMCID: PMC4766357, DOI: 10.1371/journal.pone.0147660.Peer-Reviewed Original ResearchConceptsGenome assemblyGenetic recombinationT. bruceiPentatricopeptide repeat-containing proteinGenome-wide similarityDe novo genome assemblyHybrid de novo assemblyComparative genomic analysisRepeat-containing proteinVariant surface glycoprotein (VSG) coatComplete genome assemblyDe novo assemblyNovo genome assemblyGenomic differentiationSignificant epidemiological consequencesWhole-genome sequencingGene familyPutative genesEukaryotic pathogensNovo assemblySerum resistance associated geneHuman infective strainsGenomic analysisSingle geneAlcohol oxidoreductase
2015
Mitochondrial DNA sequence divergence and diversity of Glossina fuscipes fuscipes in the Lake Victoria basin of Uganda: implications for control
Kato AB, Hyseni C, Okedi LM, Ouma JO, Aksoy S, Caccone A, Masembe C. Mitochondrial DNA sequence divergence and diversity of Glossina fuscipes fuscipes in the Lake Victoria basin of Uganda: implications for control. Parasites & Vectors 2015, 8: 385. PMID: 26197892, PMCID: PMC4511262, DOI: 10.1186/s13071-015-0984-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDNA, MitochondrialEvolution, MolecularGene FlowGenetic VariationInsect ControlLakesPhylogenyTsetse FliesUgandaConceptsMicrosatellite loci dataDemographic historyGenetic differentiationMicrosatellite dataLoci dataMitochondrial DNA (mtDNA) cytochrome oxidase II geneGenetic variationMitochondrial DNA sequence divergenceCytochrome oxidase II geneWeak genetic differentiationDNA sequence divergenceLake Victoria basinGenetic structuringGene flowDemographic testsGenetic divergenceMtDNA dataSequence divergenceGenetic diversityGeographic distanceVictoria basinGenetic analysisSampling sitesMutation ratePopulation clusters
2014
Lineage fusion in Galápagos giant tortoises
Garrick R, Benavides E, Russello M, Hyseni C, Edwards D, Gibbs J, Tapia W, Ciofi C, Caccone A. Lineage fusion in Galápagos giant tortoises. Molecular Ecology 2014, 23: 5276-5290. PMID: 25223395, DOI: 10.1111/mec.12919.Peer-Reviewed Original ResearchConceptsLineage fusionGiant tortoise speciesGalápagos giant tortoisesWidespread introgressive hybridizationLong generation timesWolf VolcanoCryptic lineagesReticulate evolutionIntrogressive hybridizationLineage splittingMicrosatellite dataGalápagos tortoisesPopulation geneticsEvolutionary phenomenaMate selectivityTortoise speciesGiant tortoisesLineagesGeneration timeRapid extinctionTortoisesPurebred femalesFusionIslandsHistorical reconstruction
2013
HUMAN IMPACTS HAVE SHAPED HISTORICAL AND RECENT EVOLUTION IN AEDES AEGYPTI, THE DENGUE AND YELLOW FEVER MOSQUITO
Brown JE, Evans BR, Zheng W, Obas V, Barrera‐Martinez L, Egizi A, Zhao H, Caccone A, Powell JR. HUMAN IMPACTS HAVE SHAPED HISTORICAL AND RECENT EVOLUTION IN AEDES AEGYPTI, THE DENGUE AND YELLOW FEVER MOSQUITO. Evolution 2013, 68: 514-525. PMID: 24111703, PMCID: PMC3946797, DOI: 10.1111/evo.12281.Peer-Reviewed Original ResearchMeSH KeywordsAedesAnimalsEvolution, MolecularGenes, InsectHuman MigrationHumansPhylogeographyPolymorphism, Single NucleotideSelection, GeneticConceptsYellow fever mosquitoSingle nucleotide polymorphism (SNP) markersHuman trade routesPatterns of domesticationArthropod disease vectorsDomestic formsNuclear genesEcological overlapEvolutionary historyDomestic AePolymorphism markersNovel nichesDNA sequencesGenetic dataEvolutionary processesDisease vectorsGenetic studiesSuch speciesLater invasionDNA sequencingNew WorldSpeciesAnthropogenic impactsHuman impactAnthropogenic forces
2010
Population Genetic Structure of Aldabra Giant Tortoises
Balmer O, Ciofi C, Galbraith D, Swingland I, Zug G, Caccone A. Population Genetic Structure of Aldabra Giant Tortoises. Journal Of Heredity 2010, 102: 29-37. PMID: 20805288, DOI: 10.1093/jhered/esq096.Peer-Reviewed Original ResearchConceptsGenetic structurePopulation structureGiant tortoisesMitochondrial DNA control region sequencesPopulation genetic structureSignificant population structureControl region sequencesAldabra giant tortoisePrevious ecological studiesAllopatric divergenceNuclear lociPopulation subdivisionHabitat variationMtDNA sequencesMicrosatellite lociPopulation geneticsUnsuitable habitatGenetic variabilityAllelic variationRegion sequencesEcological factorsTerrestrial ecosystemsPopulation dynamicsAldabra AtollGeographical barriersGenetic Differentiation between Marine Iguanas from Different Breeding Sites on the Island of Santa Fé (Galápagos Archipelago)
Lanterbecq D, Glaberman S, Vitousek M, Steinfartz S, Benavides E, Wikelski M, Caccone A. Genetic Differentiation between Marine Iguanas from Different Breeding Sites on the Island of Santa Fé (Galápagos Archipelago). Journal Of Heredity 2010, 101: 663-675. PMID: 20538757, DOI: 10.1093/jhered/esq067.Peer-Reviewed Original ResearchConceptsMarine iguanasGenetic diversitySex-biased dispersalMitochondrial control regionMitochondrial DNA markersGalápagos marine iguanasSanta FéDifferent breeding sitesSouthern sitesGenetic differentiationEvolutionary signalGenetic structureMicrosatellite lociDNA markersControl regionGenetic variationGenetic patternsBreeding sitesLittle differentiationBase pairsNeighboring islandsIguanasDiversitySampling sitesDifferentiation
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
Colonization and diversification of Galpagos terrestrial fauna: a phylogenetic and biogeographical synthesis
Parent C, Caccone A, Petren K. Colonization and diversification of Galpagos terrestrial fauna: a phylogenetic and biogeographical synthesis. Philosophical Transactions Of The Royal Society B Biological Sciences 2008, 363: 3347-3361. PMID: 18782729, PMCID: PMC2607378, DOI: 10.1098/rstb.2008.0118.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiodiversityEcosystemEcuadorEvolution, MolecularGenetic SpeciationGeographyPhylogenyPopulation DynamicsSpecies SpecificityConceptsTerrestrial faunaPhylogenetic studiesDivergence of populationsSimilar geological historyDistinct evolutionary historiesMolecular phylogenetic studiesRemote oceanic islandsRange of organismsStudy of diversificationHabitat specializationBiogeographical synthesisGeological historyLow vagilityDiverse habitatsEvolutionary historyGeological formationsOceanic islandsGroup of islandsGalápagos IslandsRemarkable settingUnique assemblageComparable climateEvolutionary processesFaunaIslandsSpecies-specific evolution of class I MHC genes in iguanas (Order: Squamata; Subfamily: Iguaninae)
Glaberman S, Caccone A. Species-specific evolution of class I MHC genes in iguanas (Order: Squamata; Subfamily: Iguaninae). Immunogenetics 2008, 60: 371-382. PMID: 18488213, DOI: 10.1007/s00251-008-0298-y.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsEvolution, MolecularGenes, MHC Class IGenetic VariationIguanasMolecular Sequence DataPhylogenySpecies SpecificityConceptsMarine iguanasSpecies-specific evolutionGalápagos land iguanasGalápagos marine iguanasDifferent phylogenetic historiesNon-avian reptilesSpecies-specific mannerClass I MHC genesMajor histocompatibility complexConservation geneticsPhylogenetic historySquamate speciesVertebrate taxaDiversified orderGenetic diversityNatural selectionMHC researchDNA dataGenetic basisLand iguanasMultiple lociMHC genesMHC studiesHost resistanceIguanasThe 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
Independent evolutionary origins of landlocked alewife populations and rapid parallel evolution of phenotypic traits
PALKOVACS E, DION K, POST D, CACCONE A. Independent evolutionary origins of landlocked alewife populations and rapid parallel evolution of phenotypic traits. Molecular Ecology 2007, 17: 582-597. PMID: 18179439, DOI: 10.1111/j.1365-294x.2007.03593.x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsConnecticutDNA, MitochondrialEvolution, MolecularFishesGeographyMicrosatellite RepeatsMolecular Sequence DataSequence Analysis, DNAConceptsLandlocked populationsAnadromous populationsAlewife populationSmaller adult body sizeRapid parallel evolutionLife history divergenceFreshwater ancestorsIndependent evolutionary originsDivergence time estimatesLife-history variantsGill raker spacingMicrosatellite mutation ratesMtDNA control regionAdult body sizeRate of evolutionSmall prey itemsAnadromous ancestorsForaging traitsPopulation divergenceAllele frequency dataDivergence timesEvolutionary ratesMicrosatellite dataAnadromous formEvolutionary originPatterns 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 ResearchMeSH KeywordsAnimalsAnophelesEvolution, MolecularFemaleGenetic VariationInsect ProteinsInsect VectorsPlasmodium falciparumSelection, GeneticConceptsAdaptive 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 testSpeciesGiant Galápagos tortoises; molecular genetic analyses identify a trans-island hybrid in a repatriation program of an endangered taxon
Milinkovitch MC, Monteyne D, Russello M, Gibbs JP, Snell HL, Tapia W, Marquez C, Caccone A, Powell JR. Giant Galápagos tortoises; molecular genetic analyses identify a trans-island hybrid in a repatriation program of an endangered taxon. BMC Ecology And Evolution 2007, 7: 2. PMID: 17302982, PMCID: PMC1820773, DOI: 10.1186/1472-6785-7-2.Peer-Reviewed Original ResearchConceptsMolecular genetic analysisGenetic analysisIsland of EspañolaEffective population sizeGalápagos tortoisesGenetic integrityConservation significanceReproductive successHuman transportMicrosatellite allelesPopulation sizeTaxaSex ratioRepatriation programMajor islandsTortoisesFemale tortoisesSingle contaminationBreedersFurther contaminationIslandsHybridsPinzónContaminationLinage