2024
Whole-genome sequencing confirms multiple species of Galapagos giant tortoises
Gaughran S, Gray R, Ochoa A, Jones M, Fusco N, Miller J, Poulakakis N, de Queiroz K, Caccone A, Jensen E. Whole-genome sequencing confirms multiple species of Galapagos giant tortoises. Evolution 2024, qpae164. PMID: 39548869, DOI: 10.1093/evolut/qpae164.Peer-Reviewed Original ResearchInbreeding avoidance, competition and natal dispersal in a pair-living, genetically monogamous mammal, Azara’s owl monkey (Aotus azarae)
Corley M, de la Chica A, van der Heide G, Rotundo M, Caccone A, Fernandez-Duque E. Inbreeding avoidance, competition and natal dispersal in a pair-living, genetically monogamous mammal, Azara’s owl monkey (Aotus azarae). Royal Society Open Science 2024, 11: 240379. PMID: 39113772, PMCID: PMC11305132, DOI: 10.1098/rsos.240379.Peer-Reviewed Original ResearchAzara's owl monkeysNatal dispersalInbreeding avoidanceMating systemPair-livingPotential matesNatal groupMaintenance of social organizationTiming of natal dispersalLife history stagesPopulation structureGenetic dataMonogamous mammalsWild populationsParental careIndividual fitnessEcological factorsRegulating dispersalAotus azaraeDispersal patternsInbreedingStep-parentsAgonistic conflictsMatingMammalsA 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
2023
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)
Fusco N, Cosentino B, Gibbs J, Allen M, Blumenfeld A, Boettner G, Carlen E, Collins M, Dennison C, DiGiacopo D, Picard A, Edmonson J, Fisher‐Reid M, Fyffe R, Gallo T, Grant A, Harbold W, Heard S, Lafferty D, Lehtinen R, Marino S, McDonald J, Mortelliti A, Murray M, Newman A, Oswald K, Ott‐Conn C, Richardson J, Rimbach R, Salaman P, Steele M, Stothart M, Urban M, Vandegrift K, Vanek J, Vanderluit S, Vezina L, Caccone A. Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis). Molecular Ecology 2023, 33: e17230. PMID: 38078558, DOI: 10.1111/mec.17230.Peer-Reviewed Original ResearchGalapagos giant tortoise trafficking case demonstrates the utility and applications of long‐term comprehensive genetic monitoring
Quinzin M, Bishop A, Miller J, Poulakakis N, Tapia W, Torres‐Rojo F, Sevilla C, Caccone A. Galapagos giant tortoise trafficking case demonstrates the utility and applications of long‐term comprehensive genetic monitoring. Animal Conservation 2023, 26: 826-838. DOI: 10.1111/acv.12870.Peer-Reviewed Original ResearchGalapagos giant tortoisesGiant tortoisesIllegal wildlife tradeGenetic analysisNuclear microsatellite markersGenetic repositoryBreeding CenterStandard genetic markersComprehensive genetic characterizationWild speciesIsland of originGenetic monitoringMicrosatellite markersGenetic markersGenetic characterizationSpecies protectionGalapagos IslandsLa conservaciónWildlife tradeSpeciesJuvenile tortoisesTortoisesSan CristobalJuvenilesFirst documentation
2022
Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA
Gloria-Soria A, Shragai T, Ciota A, Duval T, Alto B, Martins A, Westby K, Medley K, Unlu I, Campbell S, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham P, Caccone A, Armstrong P. Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 2022, 78: 99-127. PMID: 37408738, PMCID: PMC10321554, DOI: 10.3897/neobiota.78.84986.Peer-Reviewed Original ResearchPopulations of AeGenetic structureGenetic diversityPopulation geneticsGenetic cladesMicrosatellite markersAsian tiger mosquitoNortheastern USARange northwardsNorthern rangeAlbopictus populationsFounder effectPopulation turnoverVector suppressionEast coastTiger mosquitoEastern USAInvasive mosquito vectorsMosquito vectorsAedes albopictusLocal populationWarming conditionsAlbopictusCold wintersConsecutive yearsTemporal 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 hybridsParentageOffspringGenomeHybridsBreedingMultiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps
Vavassori L, Honnen A, Saarman N, Caccone A, Müller P. Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps. Ecology And Evolution 2022, 12: e9138. PMID: 35903757, PMCID: PMC9313497, DOI: 10.1002/ece3.9138.Peer-Reviewed Original ResearchDouble-digest restriction site-associated DNA sequencingRestriction site-associated DNA sequencingWeak genetic structurePopulation genomic dataAsian native rangeGenome-wide SNPsHuman-aided dispersalBiogeographic barriersGenetic structureNative rangeGenetic clustersInvasive speciesRecent invasionGenetic patternsGenomic dataSNP dataGenetic admixtureMultiple introductionsDisease vectorsNorthward expansionDNA sequencingMosquito populationsAedes albopictusProgressive invasionFull siblingsApplication 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 historyAuthor Correction: 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. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology 2021, 22: 205. PMID: 34253230, PMCID: PMC8274027, DOI: 10.1186/s13059-021-02431-x.Peer-Reviewed Original ResearchFour 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 integrating genetic and ecological data in tsetse flies (Glossina pallidipes) for spatially explicit vector control planning
Bishop AP, Amatulli G, Hyseni C, Pless E, Bateta R, Okeyo WA, Mireji PO, Okoth S, Malele I, Murilla G, Aksoy S, Caccone A, Saarman NP. A machine learning approach to integrating genetic and ecological data in tsetse flies (Glossina pallidipes) for spatially explicit vector control planning. Evolutionary Applications 2021, 14: 1762-1777. PMID: 34295362, PMCID: PMC8288027, DOI: 10.1111/eva.13237.Peer-Reviewed Original ResearchGenetic dataVectors of humanLake Victoria basinAnimal African trypanosomiasisGenetic connectivityVector-borne disease transmissionFuture monitoring effortsMicrosatellite lociHabitat useImportant environmental predictorsHabitat suitabilityFuture climatic changesDispersal patternsVictoria basinEcological dataEnvironmental predictorsVector systemTsetse fliesTsetse speciesClimatic shiftsFliesClimatic changesSampling sitesMonitoring effortsVector controlNorthern Fennoscandia via the British Isles: evidence for a novel post-glacial recolonization route by winter moth (Operophtera brumata)
Andersen J, Havill N, Griffin B, Jepsen J, Hagen S, Klemola T, Barrio I, Kjeldgaard S, Høye T, Murlis J, Baranchikov Y, Selikhovkin A, Vindstad O, Caccone A, Elkinton J. Northern Fennoscandia via the British Isles: evidence for a novel post-glacial recolonization route by winter moth (Operophtera brumata). Frontiers Of Biogeography 2021, 13 DOI: 10.21425/f5fbg49581.Peer-Reviewed Original ResearchA 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 ResearchChapter 7 Evolution and phylogenetics
Caccone A. Chapter 7 Evolution and phylogenetics. 2021, 117-138. DOI: 10.1016/b978-0-12-817554-5.00019-8.Peer-Reviewed Original ResearchGalapagos giant tortoisesGiant tortoise populationChapter 7 EvolutionEvolutionary historyRepopulation programsCaptive breedingGenetic diversityGiant tortoisesTortoise populationsDifferent islandsConservation programsPhylogeneticsTortoisesPhylogeographyHuman activitiesPhylogenyBreedingData helpYears of researchSpeciesNatural eventsDiversityCurrent patternsGalapagosEvolution
2020
Species delimitation and invasion history of the balsam woolly adelgid, Adelges (Dreyfusia) piceae (Hemiptera: Aphidoidea: Adelgidae), species complex
Havill N, Griffin B, Andersen J, Foottit R, Justesen M, Caccone A, D'Amico V, Elkinton J. Species delimitation and invasion history of the balsam woolly adelgid, Adelges (Dreyfusia) piceae (Hemiptera: Aphidoidea: Adelgidae), species complex. Systematic Entomology 2020, 46: 186-204. DOI: 10.1111/syen.12456.Peer-Reviewed Original Research