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
Multiple 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 siblings
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 bruceiPhylogenyTrypanosomesTrypanosomaTrypanozoonGenetic diversity of Glossina fuscipes fuscipes along the shores of Lake Victoria in Tanzania and Kenya: implications for management
Manangwa O, Nkwengulila G, Ouma JO, Mramba F, Malele I, Dion K, Sistrom M, Khan F, Aksoy S, Caccone A. Genetic diversity of Glossina fuscipes fuscipes along the shores of Lake Victoria in Tanzania and Kenya: implications for management. Parasites & Vectors 2017, 10: 268. PMID: 28558831, PMCID: PMC5450392, DOI: 10.1186/s13071-017-2201-x.Peer-Reviewed Original ResearchGenetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: Implications for vector control
Opiro R, Saarman NP, Echodu R, Opiyo EA, Dion K, Halyard A, Dunn AW, Aksoy S, Caccone A. Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: Implications for vector control. PLOS Neglected Tropical Diseases 2017, 11: e0005485. PMID: 28453513, PMCID: PMC5425221, DOI: 10.1371/journal.pntd.0005485.Peer-Reviewed Original ResearchConceptsAnimal African trypanosomiasisGenetic clustersEffective population size estimatesLake KyogaRecent population bottleneckMitochondrial DNA markersDistinct genetic clustersPolymorphic microsatellite lociNile drainagePopulation size estimatesGenetic structurePopulation bottlenecksMain haplogroupsGenetic diversityMicrosatellite lociGenetic assignmentDNA markersPopulation structureMtDNA analysisGenetic admixtureSampling sitesGenetic unitsMost populationsTrypanosoma parasitesHuman African trypanosomiasisPostglacial recolonization shaped the genetic diversity of the winter moth (Operophtera brumata) in Europe
Andersen J, Havill N, Caccone A, Elkinton J. Postglacial recolonization shaped the genetic diversity of the winter moth (Operophtera brumata) in Europe. Ecology And Evolution 2017, 7: 3312-3323. PMID: 28515868, PMCID: PMC5433974, DOI: 10.1002/ece3.2860.Peer-Reviewed Original ResearchDistinct glacial refugiaWinter mothPostglacial recolonizationGene flowGlacial refugiaGenetic diversityOngoing gene flowObserved genetic patternsQuaternary climatic oscillationsLong-distance dispersalResult of dispersalPolymorphic microsatellite lociMajor genetic clustersNorthern puritySouthern richnessSecondary contactHybrid zoneSpecies diversityNorthern populationsSouthern populationsGenetic clustersMicrosatellite lociWestern PalearcticGenetic lineagesGenetic patterns
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 strategyDiversity
2014
Cryptic structure and niche divergence within threatened Galápagos giant tortoises from southern Isabela Island
Edwards D, Garrick R, Tapia W, Caccone A. Cryptic structure and niche divergence within threatened Galápagos giant tortoises from southern Isabela Island. Conservation Genetics 2014, 15: 1357-1369. DOI: 10.1007/s10592-014-0622-z.Peer-Reviewed Original ResearchSouthern Isabela IslandGalápagos giant tortoisesGenetic clustersIsabela IslandGiant tortoisesMorphological diversityRecent gene flowBiodiversity lossConservation managementEcological divergenceSignificant unitsNiche divergenceFeral animalsEcological factorsGenetic differentiationEcological nichesGene flowCryptic structureMicrosatellite lociManagement successSpatial distributionCurrent taxonomyTortoisesManagement programDiversity
2013
Urban population genetics of slum‐dwelling rats (Rattus norvegicus) in Salvador, Brazil
Kajdacsi B, Costa F, Hyseni C, Porter F, Brown J, Rodrigues G, Farias H, Reis MG, Childs JE, Ko AI, Caccone A. Urban population genetics of slum‐dwelling rats (Rattus norvegicus) in Salvador, Brazil. Molecular Ecology 2013, 22: 5056-5070. PMID: 24118116, PMCID: PMC3864905, DOI: 10.1111/mec.12455.Peer-Reviewed Original ResearchConceptsGenetic structurePopulation genetic structureComplex genetic structureSmall geographical distancesGene flowGenetic clustersGenetic diversityMicrosatellite lociPopulation geneticsUrban landscapeGenetic variationPopulation ecologyGenetic dataHeterogeneous urban landscapesDistinct sampling sitesGeographical distanceRodent control measuresRodent control strategiesZoonotic pathogensR. norvegicusSampling sitesSpatial connectivityRat populationsOvergrown vegetationBayesian analysisGeographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest‐savannah biome transition as a barrier to gene flow
J P, A E, JL V, B G, F S, M M, JD C, F S, N E, D W, MJ D, A C, A D. Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest‐savannah biome transition as a barrier to gene flow. Evolutionary Applications 2013, 6: 910-924. PMID: 24062800, PMCID: PMC3779092, DOI: 10.1111/eva.12075.Peer-Reviewed Original ResearchGene flowPopulation structurePopulation substructureAfrican malaria vector Anopheles gambiaeMalaria vector Anopheles gambiaeGeographic population structureComplex population structureChromosomal arrangementsBiome transitionsGenetic clustersMicrosatellite lociAnopheles gambiae sensu strictoGambiae sensu strictoAnopheles gambiaeSensu strictoRainforest beltDistinct westAdditional populationsS formMolecular formsGambiaeBiomeLociSpeciesStricto
2009
Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus)
Steinfartz S, Glaberman S, Lanterbecq D, Russello M, Rosa S, Hanley T, Marquez C, Snell H, Snell H, Gentile G, Dell'Olmo G, Powell A, Caccone A. Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus). BMC Ecology And Evolution 2009, 9: 297. PMID: 20028547, PMCID: PMC2807874, DOI: 10.1186/1471-2148-9-297.Peer-Reviewed Original ResearchConceptsComplete mitochondrial control regionMarine iguanasGene flowPopulation structureMarine iguana populationsHistorical gene flowNuclear gene flowMicrosatellite genetic diversityStrong genetic differentiationMale-biased dispersalMitochondrial control regionRecent population expansionBayesian cluster analysisGalápagos marine iguanasHaplotype distribution patternsDistinct genetic clustersPast genetic studiesGenetic differentiationWestern islandsFST estimatesIguana populationsFounder eventsFST analysisDifferent inheritance patternsGenetic clusters