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
Application 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 evolution
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 historyA 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
2019
Genetic 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 Organization
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 memberLongevityGenetic Differentiation of Glossina pallidipes Tsetse Flies in Southern Kenya.
Okeyo WA, Saarman NP, Bateta R, Dion K, Mengual M, Mireji PO, Ouma C, Okoth S, Murilla G, Aksoy S, Caccone A. Genetic Differentiation of Glossina pallidipes Tsetse Flies in Southern Kenya. American Journal Of Tropical Medicine And Hygiene 2018, 99: 945-953. PMID: 30105964, PMCID: PMC6159567, DOI: 10.4269/ajtmh.18-0154.Peer-Reviewed Original ResearchConceptsGenetic differentiationPopulation dynamicsDispersal patternsTsetse fliesLow genetic diversityGreater genetic differentiationEvidence of admixtureWestern clusterEastern clusterRecent anthropogenic influencesAnimal African trypanosomiasisGenetic connectivityWestern relativesGenetic diversityMicrosatellite lociPopulation structureGenotypic dataWidespread signalDisease vectorsMajor vectorVector control effortsGreat Rift ValleyDemographic parametersFliesVector control programs
2017
Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya
Okeyo WA, Saarman NP, Mengual M, Dion K, Bateta R, Mireji PO, Okoth S, Ouma JO, Ouma C, Ochieng J, Murilla G, Aksoy S, Caccone A. Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya. Parasites & Vectors 2017, 10: 471. PMID: 29017572, PMCID: PMC5635580, DOI: 10.1186/s13071-017-2415-y.Peer-Reviewed Original ResearchConceptsTemporal genetic differentiationGenetic diversityGenetic differentiationGenetic bottleneckGenetic variationNational ParkTemporal genetic variationExtensive control measuresAnimal African trypanosomiasisAllelic richnessPairwise FSTGenetic driftNe estimatesHabitat alterationPopulation geneticsTemporal differentiationMicrosatellite markersRuma National ParkClosest sampling sitesG. pallidipesMajor vectorTsetse fliesVector populationsDifferentiationDiversityIdentification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provides Founders for Species Restoration Program
Miller J, Quinzin M, Poulakakis N, Gibbs J, Beheregaray L, Garrick R, Russello M, Ciofi C, Edwards D, Hunter E, Tapia W, Rueda D, Carrión J, Valdivieso A, Caccone A. Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provides Founders for Species Restoration Program. Scientific Reports 2017, 7: 11471. PMID: 28904401, PMCID: PMC5597637, DOI: 10.1038/s41598-017-11516-2.Peer-Reviewed Original ResearchConceptsGiant tortoisesGalápagos giant tortoisesHuman-driven environmental changesCaptive breeding programsCaptive breeding centerSpecies restoration programsHigh ancestryFloreana IslandSpecies todayIsland ecosystemsBreeding programsGalápagos IslandsGenetic analysisBreeding CenterEnvironmental changesRestoration programsTortoisesSpeciesEcosystemsDistinctive morphologyAncestryUnprecedented rateIslandsTranslocationUnique opportunityMultiple 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 brucei
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 strategyDiversityGlobal 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 ResearchConceptsEvolutionary clustersColonization of EuropeRat eradication programmeAgricultural settlementsWestward expansionEastward expansionSoutheast AsiaSouthward expansionAleutian ArchipelagoExpansion routesAstonishing degreeRecent migrantsGlobal population structureGlobal phylogeographyBlack ratsGlobal tradeCommensal rodentsEuropePotential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors
Guevara EE, Veilleux CC, Saltonstall K, Caccone A, Mundy NI, Bradley BJ. Potential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors. American Journal Of Biological Anthropology 2016, 161: 181-185. PMID: 27393125, DOI: 10.1002/ajpa.23046.Peer-Reviewed Original ResearchConceptsSweet proteinNew sequence dataAmino acid sitesSeed dispersersProtein evolutionAccelerated evolutionBiochemical mimicryPrimate lineageGorilla lineagePositive selectionSequence dataGorilla dietCaloric gainArms raceWestern gorillasBrazzeinAfrican primatesProteinLineagesCoevolutionPentadiplandra brazzeanaLocal plantsSpeciesSweet signalsMutationsComparative genomics of drug resistance in Trypanosoma brucei rhodesiense
Graf F, Ludin P, Arquint C, Schmidt R, Schaub N, Kunz Renggli C, Munday J, Krezdorn J, Baker N, Horn D, Balmer O, Caccone A, de Koning H, Mäser P. Comparative genomics of drug resistance in Trypanosoma brucei rhodesiense. Cellular And Molecular Life Sciences 2016, 73: 3387-3400. PMID: 26973180, PMCID: PMC4967103, DOI: 10.1007/s00018-016-2173-6.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAquaporinsComparative Genomic HybridizationDNA, ProtozoanDrug ResistanceGenome, ProtozoanHeterozygoteHumansMaleMelarsoprolNucleoside Transport ProteinsParasitic Sensitivity TestsPentamidinePhenotypePolymorphism, Single NucleotideProtozoan ProteinsRNA-Binding ProteinsSequence AlignmentTrypanocidal AgentsTrypanosoma brucei rhodesienseTrypanosomiasis, AfricanDe 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 oxidoreductaseWas 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 ResearchConceptsGiant ground slothGround slothsYale Peabody MuseumValue of museumsPeabody MuseumArchival materialFrozen mammothsWoolly mammothQuaternary extinctionsLong historyPublicity stuntMammothsExotic foodsMuseumExtraordinary claimsAnnual traditionInstantaneous freezingClubsGeneral publicPublicDinnerSlothsLegendTraditionMegatherium
2015
Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi
Carpi G, Walter KS, Bent SJ, Hoen AG, Diuk-Wasser M, Caccone A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics 2015, 16: 434. PMID: 26048573, PMCID: PMC4458057, DOI: 10.1186/s12864-015-1634-x.Peer-Reviewed Original ResearchConceptsWhole-genome captureGenome captureGenomic studiesPopulation genomic studiesArthropod vectorsPathogen DNABorrelia burgdorferi genomeNext-generation sequencing technologiesWhole genome sequencesMixed DNA templatesCulture-independent methodsGeneration sequencing technologyPathogen sequence dataFine-resolution studiesGenome sequenceVector-borne pathogensMixed DNA samplesSingle nucleotide polymorphismsComplete genomeEvolutionary dynamicsSequence dataSequencing technologiesDisease vectorsStudy systemDNA templateGenetic Diversity and Population Structure of Trypanosoma brucei in Uganda: Implications for the Epidemiology of Sleeping Sickness and Nagana
Echodu R, Sistrom M, Bateta R, Murilla G, Okedi L, Aksoy S, Enyioha C, Enyaru J, Opiyo E, Gibson W, Caccone A. Genetic Diversity and Population Structure of Trypanosoma brucei in Uganda: Implications for the Epidemiology of Sleeping Sickness and Nagana. PLOS Neglected Tropical Diseases 2015, 9: e0003353. PMID: 25695634, PMCID: PMC4335064, DOI: 10.1371/journal.pntd.0003353.Peer-Reviewed Original Research