2022
The Galapagos giant tortoise Chelonoidis phantasticus is not extinct
Jensen E, Gaughran S, Fusco N, Poulakakis N, Tapia W, Sevilla C, Málaga J, Mariani C, Gibbs J, Caccone A. The Galapagos giant tortoise Chelonoidis phantasticus is not extinct. Communications Biology 2022, 5: 546. PMID: 35681083, PMCID: PMC9184544, DOI: 10.1038/s42003-022-03483-w.Peer-Reviewed Original ResearchConceptsGalapagos giant tortoisesGiant tortoisesMitochondrial DNA phylogenyDNA phylogenyMonophyletic groupCarapace morphologyPhylogeny GroupSame lineagePopulation sizeSpeciesTortoisesLineagesFemale tortoisesSingle specimenSingle individualPhylogenyCladeGenomeExtinctSaddlebackContinued existenceIslandsDiscoveryA new lineage of Galapagos giant tortoises identified from museum samples
Jensen E, Quinzin M, Miller J, Russello M, Garrick R, Edwards D, Glaberman S, Chiari Y, Poulakakis N, Tapia W, Gibbs J, Caccone A. A new lineage of Galapagos giant tortoises identified from museum samples. Heredity 2022, 128: 261-270. PMID: 35217806, PMCID: PMC8987048, DOI: 10.1038/s41437-022-00510-8.Peer-Reviewed Original ResearchConceptsGalapagos giant tortoisesMitochondrial control regionGiant tortoisesSingle nucleotide polymorphismsControl regionMuseum samplesGenome-wide single nucleotide polymorphismsDivergent mitochondrial lineagesSingle mitochondrial haplotypeContemporary populationsIconic radiationMitochondrial lineagesAdditional lineagesMitochondrial haplotypesNuclear markersSan CristóbalSecond lineageMicrosatellite lociNew lineagePinta IslandSame cladeEvolutionary processesLineagesGalapagos ArchipelagoEarly evolution
2019
Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern Europe
Pichler V, Kotsakiozi P, Caputo B, Serini P, Caccone A, della Torre A. Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern Europe. PLOS Neglected Tropical Diseases 2019, 13: e0007554. PMID: 31437154, PMCID: PMC6705758, DOI: 10.1371/journal.pntd.0007554.Peer-Reviewed Original ResearchConceptsDouble digest Restriction-site Associated DNAHistorical contextMultiple independent invasionsSouth East AsiaRestriction-site Associated DNAPopulation genomic structureInvasive Aedes albopictusInvasion historyWorldwide expansionSouthern EuropeFirst countryHistoryAnimal invasionsItalyEuropeAlbaniaSuccessful historyRecent invasionMigration patternsHuman arbovirusesComplex interplayMultiple geographic locationsIndependent invasionsColonistsInvasive range
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 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 bruceiPhylogenyTrypanosomesTrypanosomaTrypanozoon
2016
Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States
Carpi G, Walter KS, Mamoun CB, Krause PJ, Kitchen A, Lepore TJ, Dwivedi A, Cornillot E, Caccone A, Diuk-Wasser MA. Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States. BMC Genomics 2016, 17: 888. PMID: 27821055, PMCID: PMC5100190, DOI: 10.1186/s12864-016-3225-x.Peer-Reviewed Original ResearchConceptsStrong population structurePopulation structureGenome-wide diversityDifferentiated genetic clustersRecent population expansionB. microti samplesTick-borne apicomplexan parasiteB. microtiNortheastern USAGene flowEvolutionary originApicomplexan parasitesApicoplast genomeGenetic clustersGenomic variationPopulation expansionGeographic rangeRange expansionGenomic signaturesCurrent diversityHuman-derived samplesInfectious phenotypeTick vectorCapture strategyDiversityWas Frozen Mammoth or Giant Ground Sloth Served for Dinner at The Explorers Club?
Glass J, Davis M, Walsh T, Sargis E, Caccone A. Was Frozen Mammoth or Giant Ground Sloth Served for Dinner at The Explorers Club? PLOS ONE 2016, 11: e0146825. PMID: 26840445, PMCID: PMC4740485, DOI: 10.1371/journal.pone.0146825.Peer-Reviewed Original ResearchMeSH KeywordsAlaskaAnimalsCytochromes bDNA, MitochondrialFood, PreservedHumansMammothsMeatPhylogenySlothsConceptsGiant ground slothGround slothsYale Peabody MuseumValue of museumsPeabody MuseumArchival materialFrozen mammothsWoolly mammothQuaternary extinctionsLong historyPublicity stuntMammothsExotic foodsMuseumExtraordinary claimsAnnual traditionInstantaneous freezingClubsGeneral publicPublicDinnerSlothsLegendTraditionMegatherium
2015
Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island
Poulakakis N, Edwards D, Chiari Y, Garrick R, Russello M, Benavides E, Watkins-Colwell G, Glaberman S, Tapia W, Gibbs J, Cayot L, Caccone A. Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island. PLOS ONE 2015, 10: e0138779. PMID: 26488886, PMCID: PMC4619298, DOI: 10.1371/journal.pone.0138779.Peer-Reviewed Original ResearchConceptsMultiple independent evolutionary lineagesGiant tortoise speciesIndependent evolutionary lineagesCompelling genetic evidenceGalapagos tortoisesRank of speciesSanta Cruz IslandGenetic distinctivenessAnalysis of DNAEvolutionary lineagesEvolutionary relationshipsNatural populationsDNA charactersDistinct lineagesIsland of originTaxonomic revisionMorphological charactersMuseum specimensNew speciesGenetic evidenceTortoise speciesLineagesSpeciesTortoisesType specimenMitochondrial 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 ResearchConceptsMicrosatellite 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 clustersHybridization masks speciation in the evolutionary history of the Galápagos marine iguana
MacLeod A, Rodríguez A, Vences M, Orozco-terWengel P, García C, Trillmich F, Gentile G, Caccone A, Quezada G, Steinfartz S. Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana. Proceedings Of The Royal Society B 2015, 282: 20150425. PMID: 26041359, PMCID: PMC4590447, DOI: 10.1098/rspb.2015.0425.Peer-Reviewed Original ResearchConceptsGalápagos marine iguanasEvolutionary historyMarine iguanasIncipient speciationStrong population structureGenome-wide analysisGalápagos land iguanasCommon gene poolDepth genome-wide analysisSpeciation eventsIsland speciationSister lineageEvolutionary potentialFrequent hybridizationExtant populationsLocal adaptationPhylogenetic treeGene poolSister groupPopulation structureVariable markersLand iguanasEvolutionary processesSame islandNearby islands
2013
Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics
Symula RE, Alam U, Brelsfoard C, Wu Y, Echodu R, Okedi LM, Aksoy S, Caccone A. Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics. BMC Ecology And Evolution 2013, 13: 31. PMID: 23384159, PMCID: PMC3574847, DOI: 10.1186/1471-2148-13-31.Peer-Reviewed Original ResearchConceptsMtDNA haplotypesDifferent WolbachiaGenetic diversityHost haplotypesSequence diversityMultiple WolbachiaArthropod host reproductionPopulation genetic differentiationComplex evolutionary dynamicsMitochondrial DNA haplotypesAssociation of WolbachiaLow reproductive outputHost population geneticsHost genetic diversityTsetse fliesMulti-locus sequence typingMost WolbachiaHost genetic compositionGenetic differentiationWolbachia evolutionWolbachia associationsHost reproductionDNA haplotypesMtDNA groupsΑ-proteobacteria
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
2011
Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises
POULAKAKIS N, RUSSELLO M, GEIST D, CACCONE A. Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises. Molecular Ecology 2011, 21: 160-173. PMID: 22098061, DOI: 10.1111/j.1365-294x.2011.05370.x.Peer-Reviewed Original ResearchConceptsGiant Galápagos tortoisesHuman-mediated dispersal eventsVicariant eventsGalápagos tortoisesMainland South AmericaHuman activitiesIndependent evolutionary unitsAvailable geological dataSimple linear trendRecent human activitiesIsland lifeEvolutionary unitsEndangered taxaColonization eventsExtant speciesDispersal eventsEvolutionary historyGeological dataMultiple colonizationsExtinct speciesOcean islandsDNA dataOlder islandsYounger islandsOceanic islands
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 barriersPhylogeography and Population Structure of Glossina fuscipes fuscipes in Uganda: Implications for Control of Tsetse
Beadell JS, Hyseni C, Abila PP, Azabo R, Enyaru JC, Ouma JO, Mohammed YO, Okedi LM, Aksoy S, Caccone A. Phylogeography and Population Structure of Glossina fuscipes fuscipes in Uganda: Implications for Control of Tsetse. PLOS Neglected Tropical Diseases 2010, 4: e636. PMID: 20300518, PMCID: PMC2838784, DOI: 10.1371/journal.pntd.0000636.Peer-Reviewed Original ResearchConceptsGene flowPopulation structureLarge-scale genetic structureDivergent mitochondrial lineagesCurrent gene flowScale genetic structureBayesian assignment testsLittle gene flowHistorical colonization eventsZone of contactSouthern lineagesMitochondrial lineagesAssignment testsGenetic structureArea-wide controlMainland populationsColonization eventsMicrosatellite dataPopulation geneticsPhylogeographic analysisRiverine speciesIsland populationsAppropriate geographical scaleGenetic analysisMicrosatellite structureAnopheles 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
Morphometrics Parallel Genetics in a Newly Discovered and Endangered Taxon of Galápagos Tortoise
Chiari Y, Hyseni C, Fritts T, Glaberman S, Marquez C, Gibbs J, Claude J, Caccone A. Morphometrics Parallel Genetics in a Newly Discovered and Endangered Taxon of Galápagos Tortoise. PLOS ONE 2009, 4: e6272. PMID: 19609441, PMCID: PMC2707613, DOI: 10.1371/journal.pone.0006272.Peer-Reviewed Original ResearchConceptsGalápagos tortoisesGenetic variationGenetic distinctionTortoise populationsNon-neutral lociStrong genetic differentiationComplex heritable traitsDiagnostic morphological charactersShell morphologyShell shape variationGenetic differentiationMitochondrial dataMonophyletic lineageMorphological charactersGiant tortoisesHeritable traitGenetic dataMost islandsSanta CruzMolecular studiesShell shapeTurtle shellTortoisesLineagesParallel Genetic
2008
Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise
Poulakakis N, Glaberman S, Russello M, Beheregaray LB, Ciofi C, Powell JR, Caccone A. Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 15464-15469. PMID: 18809928, PMCID: PMC2563078, DOI: 10.1073/pnas.0805340105.Peer-Reviewed Original ResearchConceptsMuseum specimensHistorical DNA analysisDiversification of organismsCaptive breeding programsIsland of FloreanaModern DNA techniquesMicrosatellite dataGalápagos tortoisesConservation biologyMitochondrial DNANatural selectionExtinct speciesExtinct taxaBreeding programsGiant tortoisesIntense harvestingGenetic analysisGenetic dataGalápagos ArchipelagoTortoise populationsDNA techniquesHuman exploitationNearby islandsEnough individualsSpeciesColonization 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 ResearchConceptsTerrestrial 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 ResearchConceptsMarine 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 resistanceIguanas