2024
A genotyping array for the globally invasive vector mosquito, Aedes albopictus
Cosme L, Corley M, Johnson T, Severson D, Yan G, Wang X, Beebe N, Maynard A, Bonizzoni M, Khorramnejad A, Martins A, Lima J, Munstermann L, Surendran S, Chen C, Maringer K, Wahid I, Mukherjee S, Xu J, Fontaine M, Estallo E, Stein M, Livdahl T, Scaraffia P, Carter B, Mogi M, Tuno N, Mains J, Medley K, Bowles D, Gill R, Eritja R, González-Obando R, Trang H, Boyer S, Abunyewa A, Hackett K, Wu T, Nguyễn J, Shen J, Zhao H, Crawford J, Armbruster P, Caccone A. A genotyping array for the globally invasive vector mosquito, Aedes albopictus. Parasites & Vectors 2024, 17: 106. PMID: 38439081, PMCID: PMC10910840, DOI: 10.1186/s13071-024-06158-z.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingLow-coverage whole-genome sequencingSNP chipRepetitive elementsGenomic analysisNative rangePatterns of genomic variationWhole-genome sequencing dataSNP chip genotypesPopulation genomic analysesProtein-coding genesLevels of admixtureOrigin of invasionNon-coding regionsPercentage of repetitive elementsGenotyping of samplesChip genotypesGenetic clustersAncestry analysisGenomic variationGenotyping arraysGenotyping platformsMendelian genesGenetic variationGenotyping methods
2022
Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program
Gray R, Fusco N, Miller J, Tapia W, Mariani C, Caccone A, Jensen E. Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program. Integrative And Comparative Biology 2022, 62: 1864-1871. PMID: 35906184, DOI: 10.1093/icb/icac129.Peer-Reviewed Original ResearchConceptsCaptive breeding programsBreeding programsEffective population sizeGalapagos giant tortoisesCaptive breedingGenetic diversityGenetic trackingReproductive outputSpecies restorationGiant tortoisesConservation managersBreeding outcomesMicrosatellite markersGenetic analysisMore foundersBreeding cyclePopulation sizeBreeding facilitiesTortoisesValue of hybridsParentageOffspringGenomeHybridsBreedingApplication of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin gene
George S, Suwondo P, Akorli J, Otchere J, Harrison LM, Bilguvar K, Knight JR, Humphries D, Wilson MD, Caccone A, Cappello M. Application of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin gene. Scientific Reports 2022, 12: 11459. PMID: 35794459, PMCID: PMC9259660, DOI: 10.1038/s41598-022-15718-1.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsPeriodic mass drug administrationHigh-risk groupCross-sectional studyDrug resistance markersMass drug administrationResistance-associated mutationsHookworm Necator americanusPost-treatment samplesIsotype-1 β-tubulin geneHookworm infectionPersistent infectionResistance markersDrug AdministrationNecator americanusInfection statusVeterinary nematodesInfectionMarkersNucleotide polymorphismsSensitive toolBenzimidazole drugsNucleotide allelesThe 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 evolutionReal‐time geographic settling of a hybrid zone between the invasive winter moth (Operophtera brumata L.) and the native Bruce spanworm (O. bruceata Hulst)
Andersen J, Havill N, Boettner G, Chandler J, Caccone A, Elkinton J. Real‐time geographic settling of a hybrid zone between the invasive winter moth (Operophtera brumata L.) and the native Bruce spanworm (O. bruceata Hulst). Molecular Ecology 2022, 31: 6617-6633. PMID: 35034394, DOI: 10.1111/mec.16349.Peer-Reviewed Original ResearchConceptsInvasive winter mothClinal hybrid zoneHybrid zoneWinter mothBruce spanwormNon-native speciesNon-native organismsLow dispersal ratesProbability of establishmentMosaic hybrid zoneCases of hybridizationNative congenerNovel habitatsLong Island SoundEnvironmental variablesO. bruceataDispersal ratesCoastal ConnecticutMicrosatellite dataOperophtera brumataHybrid fitnessWinter cold temperaturesPopulation densityWinter temperaturesEvolutionary trajectories
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 ResearchConceptsGalapagos 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 historyFour times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America
Andersen J, Havill N, Caccone A, Elkinton J. Four times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America. Molecular Ecology 2021, 30: 3439-3452. PMID: 34033202, DOI: 10.1111/mec.15983.Peer-Reviewed Original ResearchConceptsWinter mothNortheastern United StatesNorth AmericaInvasive winter mothNon-native speciesPopulation genetic dataAmount of diversityInvasion successSerial invasionInvaded regionsWidespread defoliationGenetic bottleneckBayesian assignmentOperophtera brumataMicrosatellite lociApproximate Bayesian computation methodsIndependent introductionsNorthern FennoscandiaCentral EuropeGenetic dataHybridization eventsBritish ColumbiaGeographic originNova ScotiaAmericaA machine-learning approach to map landscape connectivity in Aedes aegypti with genetic and environmental data
Pless E, Saarman NP, Powell JR, Caccone A, Amatulli G. A machine-learning approach to map landscape connectivity in Aedes aegypti with genetic and environmental data. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2003201118. PMID: 33619083, PMCID: PMC7936321, DOI: 10.1073/pnas.2003201118.Peer-Reviewed Original Research
2020
Improved reference genome of the arboviral vector Aedes albopictus
Palatini U, Masri RA, Cosme LV, Koren S, Thibaud-Nissen F, Biedler JK, Krsticevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux AB, Pischedda E, Marconcini M, Ghurye J, Rhie A, Sharma A, Karagodin DA, Jenrette J, Gamez S, Miesen P, Masterson P, Caccone A, Sharakhova MV, Tu Z, Papathanos PA, Van Rij RP, Akbari OS, Powell J, Phillippy AM, Bonizzoni M. Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology 2020, 21: 215. PMID: 32847630, PMCID: PMC7448346, DOI: 10.1186/s13059-020-02141-w.Peer-Reviewed Original ResearchConceptsArboviral vector Aedes albopictusSex-determining locusFirst physical mapAsian tiger mosquito Aedes albopictusTiger mosquito Aedes albopictusMosquito Aedes albopictusAedes albopictusPiRNA clustersDiverse AeGenome assemblyInnovative control measuresReference genomeAccurate DNA sequencesNovel microRNAsImmunity genesPhysical mapDNA sequencesGenetic manipulationViral insertionVector Aedes albopictusExpression dataGenomeAlbopictus populationsSequencing methodsAdaptation potentialEvolution of kdr haplotypes in worldwide populations of Aedes aegypti: Independent origins of the F1534C kdr mutation
Cosme LV, Gloria-Soria A, Caccone A, Powell JR, Martins AJ. Evolution of kdr haplotypes in worldwide populations of Aedes aegypti: Independent origins of the F1534C kdr mutation. PLOS Neglected Tropical Diseases 2020, 14: e0008219. PMID: 32298261, PMCID: PMC7188295, DOI: 10.1371/journal.pntd.0008219.Peer-Reviewed Original ResearchPhylogeography and population structure of the tsetse fly Glossina pallidipes in Kenya and the Serengeti ecosystem
Bateta R, Saarman NP, Okeyo WA, Dion K, Johnson T, Mireji PO, Okoth S, Malele I, Murilla G, Aksoy S, Caccone A. Phylogeography and population structure of the tsetse fly Glossina pallidipes in Kenya and the Serengeti ecosystem. PLOS Neglected Tropical Diseases 2020, 14: e0007855. PMID: 32092056, PMCID: PMC7058365, DOI: 10.1371/journal.pntd.0007855.Peer-Reviewed Original Research
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 ResearchConceptsEcological speciationSpeciation researchIntegrative taxonomyGenetics of speciationProcess of speciationSouth American lizardsSpeciation ratesPhenotypic evolutionEvolutionary forcesClimatic nicheEuropean salamandersPhenotypic traitsGenetic mechanismsEcological aspectsBiogeographyReptilesSpeciationAmphibiansCase studyGenomicsLizardsGeneticsTaxonomyFinal case studySalamandersComplex 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 rangeSpatio-temporal distribution of Spiroplasma infections in the tsetse fly (Glossina fuscipes fuscipes) in northern Uganda
Schneider DI, Saarman N, Onyango MG, Hyseni C, Opiro R, Echodu R, O’Neill M, Bloch D, Vigneron A, Johnson TJ, Dion K, Weiss BL, Opiyo E, Caccone A, Aksoy S. Spatio-temporal distribution of Spiroplasma infections in the tsetse fly (Glossina fuscipes fuscipes) in northern Uganda. PLOS Neglected Tropical Diseases 2019, 13: e0007340. PMID: 31369548, PMCID: PMC6692048, DOI: 10.1371/journal.pntd.0007340.Peer-Reviewed Original ResearchGenetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise
Quinzin M, Sandoval‐Castillo J, Miller J, Beheregaray L, Russello M, Hunter E, Gibbs J, Tapia W, Villalva F, Caccone A. Genetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise. Conservation Biology 2019, 33: 1404-1414. PMID: 30901116, DOI: 10.1111/cobi.13319.Peer-Reviewed Original ResearchConceptsOverall genetic diversityGenetic diversityExtinct speciesC. nigerFloreana IslandExtinct taxaCaptive breeding strategiesCaptive breeding programsSmall breeding groupsGalapagos tortoisesSpecies restoration programsHigh ancestrySpecies biologyExtant speciesGenetic integrityCaptive breedingGenomic representationAdaptive potentialSpecies conservationBreeding strategiesSpecies recoveryGenotypic dataEndemic rangeBiodiversity conservationEcosystem restorationGenetic Markers of Benzimidazole Resistance among Human Hookworms (Necator americanus) in Kintampo North Municipality, Ghana.
Orr AR, Quagraine JE, Suwondo P, George S, Harrison LM, Dornas FP, Evans B, Caccone A, Humphries D, Wilson MD, Cappello M. Genetic Markers of Benzimidazole Resistance among Human Hookworms (Necator americanus) in Kintampo North Municipality, Ghana. American Journal Of Tropical Medicine And Hygiene 2019, 100: 351-356. PMID: 30734697, PMCID: PMC6367626, DOI: 10.4269/ajtmh.18-0727.Peer-Reviewed Original ResearchConceptsMass drug administrationSoil-transmitted helminthsKintampo North MunicipalitySchool-aged childrenSingle nucleotide polymorphismsPolymerase chain reactionEffectiveness of MDAWild-type SNPsInfected study subjectsPeriodic mass drug administrationResistance-associated single nucleotide polymorphismsCross-sectional studyResistance-associated mutationsWorld Health OrganizationHookworm infectionDrug exposureHookworm eggsUnreported associationStudy subjectsDrug AdministrationPosttreatment samplesChemotherapeutic approachesGrowth delayHuman hookwormHealth OrganizationThe population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda
Saarman NP, Opiro R, Hyseni C, Echodu R, Opiyo EA, Dion K, Johnson T, Aksoy S, Caccone A. The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda. Molecular Ecology 2019, 28: 66-85. PMID: 30471158, PMCID: PMC9642080, DOI: 10.1111/mec.14957.Peer-Reviewed Original ResearchConceptsAdmixture zonePopulation genomicsHybrid zoneMitochondrial cytochrome oxidase IGenome-wide admixtureProcess of speciationCytochrome oxidase IPatterns of divergenceMaternal inheritance patternDivergent lineagesReproductive barriersSecondary contactOxidase IEvolutionary biologyApproximate Bayesian computationGenetic lineagesParental typesGenetic markersInheritance patternGenomicsLineagesMultiple generationsBayesian computationSpeciationRiver network
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 memberLongevityEditing nature: Local roots of global governance
Kofler N, Collins JP, Kuzma J, Marris E, Esvelt K, Nelson MP, Newhouse A, Rothschild LJ, Vigliotti VS, Semenov M, Jacobsen R, Dahlman JE, Prince S, Caccone A, Brown T, Schmitz OJ. Editing nature: Local roots of global governance. Science 2018, 362: 527-529. PMID: 30385564, DOI: 10.1126/science.aat4612.Peer-Reviewed Original ResearchConceptsLocal communitiesGene-editing techniquesContext-dependent impactsMost policy discussionsEcological disturbancesIsland habitatsCollective oversightClimate changeEvolutionary resistanceWild speciesLocal inputGene editingTarget mutationsSpeciesCommunityCRISPREnvironmental applicationsEcosystemsHabitatsResponsible applicationExtinctionProfound benefitsInternational levelUnprecedented capacityPolicy discussions