2018
Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities
Combs M, Byers K, Ghersi B, Blum M, Caccone A, Costa F, Himsworth C, Richardson J, Munshi-South J. Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities. Proceedings Of The Royal Society B 2018, 285: 20180245. PMID: 29875297, PMCID: PMC6015871, DOI: 10.1098/rspb.2018.0245.Peer-Reviewed Original ResearchConceptsGene flowGenome-wide single nucleotide polymorphismsSpatial population genomicsGenome-wide diversityShortest distance classesGenerality of predictionsPopulation genomicsGenetic discontinuityLimited dispersalNeutral evolutionSingle nucleotide polymorphismsMultiple speciesPest managementSame speciesBrown ratsDifferent biomesDistance classesNucleotide polymorphismsAnimal movementSpeciesGenomicsMajor waterwaysCoancestryClustering analysisDispersal
2017
Postglacial 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
2015
Mitochondrial 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 clusters
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
Habitat fragmentation and the genetic structure of the Amazonian palm Mauritia flexuosa L.f. (Arecaceae) on the island of Trinidad
Federman S, Hyseni C, Clement W, Oatham M, Caccone A. Habitat fragmentation and the genetic structure of the Amazonian palm Mauritia flexuosa L.f. (Arecaceae) on the island of Trinidad. Conservation Genetics 2013, 15: 355-362. DOI: 10.1007/s10592-013-0543-2.Peer-Reviewed Original ResearchIsland of TrinidadGenetic structureAnimal-mediated seed dispersalSmall-scale spatial genetic structureLand use changeNearest-neighbor matingSpatial genetic structureTemporal genetic patternsMauritia flexuosa L.fHabitat fragmentationSuccessful conservationSeed dispersalAnthropogenic changesScientific ReserveMauritia flexuosaGenetic differentiationManagement planGene flowGenetic patternsStudy sitesGenetic diversitySmall collection areaGenetic exchangeWild populationsPopulation's abilityUrban 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 analysisGlossina fuscipes populations provide insights for human African trypanosomiasis transmission in Uganda
Aksoy S, Caccone A, Galvani AP, Okedi LM. Glossina fuscipes populations provide insights for human African trypanosomiasis transmission in Uganda. Trends In Parasitology 2013, 29: 394-406. PMID: 23845311, PMCID: PMC3772539, DOI: 10.1016/j.pt.2013.06.005.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiodiversityDNA, MitochondrialFemaleGene FlowGenetics, PopulationHost-Pathogen InteractionsHumansInsect VectorsMaleMicrobiotaMicrosatellite RepeatsPest Control, BiologicalSymbiosisTrypanosoma brucei gambienseTrypanosoma brucei rhodesienseTrypanosomiasis, AfricanTsetse FliesUgandaConceptsOccurrence of polyandryGene flowPopulation geneticsPopulation structureGenetic applicationsHuman African trypanosomiasisMajor vectorMicrobiome compositionTsetse control programsTrypanosomiasis transmissionRecent spreadPotential rolePresent knowledgeGlossinaAfrican trypanosomiasisPolyandryHuman African trypanosomiasis transmissionInfection outcomesGeneticsFuscipesDiversityPopulationGeographic 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
2011
Isolation of 13 novel highly polymorphic microsatellite loci for the Amazonian Palm Mauritia flexuosa L.f. (Arecaceae)
Federman S, Hyseni C, Clement W, Caccone A. Isolation of 13 novel highly polymorphic microsatellite loci for the Amazonian Palm Mauritia flexuosa L.f. (Arecaceae). Conservation Genetics Resources 2011, 4: 355-357. DOI: 10.1007/s12686-011-9547-8.Peer-Reviewed Original ResearchGenetic diversity and population structure of Glossina pallidipes in Uganda and western Kenya
Ouma JO, Beadell JS, Hyseni C, Okedi LM, Krafsur ES, Aksoy S, Caccone A. Genetic diversity and population structure of Glossina pallidipes in Uganda and western Kenya. Parasites & Vectors 2011, 4: 122. PMID: 21711519, PMCID: PMC3146932, DOI: 10.1186/1756-3305-4-122.Peer-Reviewed Original ResearchConceptsSex-biased dispersalGenetic diversityPopulation structureSource populationModern gene flowHigh genetic diversityMean genetic distanceAnalysis of mtDNAGene flowNuclear markersBayesian assignmentRelict populationsMtDNA haplotypesGenetic distanceMicrosatellite genotypesG. pallidipesGenetic variationPairwise relatednessMicrosatellite allelesMicrosatellite analysisDispersalSoutheastern UgandaFall populationPopulation comparisonsEffective control efforts
2010
Phylogeography 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 structure
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 clustersIn situ population structure and ex situ representation of the endangered Amur tiger
HENRY P, MIQUELLE D, SUGIMOTO T, McCULLOUGH D, CACCONE A, RUSSELLO M. In situ population structure and ex situ representation of the endangered Amur tiger. Molecular Ecology 2009, 18: 3173-3184. PMID: 19555412, DOI: 10.1111/j.1365-294x.2009.04266.x.Peer-Reviewed Original ResearchConceptsGenetic variationPopulation genetic variationRecent population bottleneckPopulation genetic structurePotential gene flowEffective population sizeAmur tigersPostglacial colonizationWild tiger populationsGene flowGenetic structurePopulation bottlenecksNative rangeWild populationsDemographic historyGenetic diversityCaptive populationsPopulation structureDemographic contractionGene variantsHistorical contractionGenetic signaturesEcological connectivityPopulation sizeTiger populations
2007
Multiple Origins of Knockdown Resistance Mutations in the Afrotropical Mosquito Vector Anopheles gambiae
Pinto J, Lynd A, Vicente J, Santolamazza F, Randle N, Gentile G, Moreno M, Simard F, Charlwood J, do Rosário V, Caccone A, della Torre A, Donnelly M. Multiple Origins of Knockdown Resistance Mutations in the Afrotropical Mosquito Vector Anopheles gambiae. PLOS ONE 2007, 2: e1243. PMID: 18043750, PMCID: PMC2080755, DOI: 10.1371/journal.pone.0001243.Peer-Reviewed Original ResearchConceptsResistance allelesMutation eventsMosquito vector Anopheles gambiaeVoltage-gated sodium channel geneNatural insect populationsEvolution of resistanceInsecticide resistance mutationsIndependent mutation eventsGambiae S formSodium channel geneMalaria vector AnophelesKnockdown resistance alleleKnockdown resistance (kdr) mutationsGene flowMolecular evolutionNeutrality testsSelective sweepsMalaria vector control programmesAdaptive traitsMultiple mutation eventsInsect populationsGenomic regionsHaplotype compositionKdr locusLocal selectionGenetic population structure of Anopheles gambiae in Equatorial Guinea
Moreno M, Salgueiro P, Vicente J, Cano J, Berzosa P, de Lucio A, Simard F, Caccone A, Do Rosario V, Pinto J, Benito A. Genetic population structure of Anopheles gambiae in Equatorial Guinea. Malaria Journal 2007, 6: 137. PMID: 17937805, PMCID: PMC2100067, DOI: 10.1186/1475-2875-6-137.Peer-Reviewed Original ResearchConceptsGenetic differentiationMicrosatellite lociPopulation structureMainland samplesGenetic diversity parametersGenetic population structureGambiae s.A. gambiae s.Incipient speciationPopulation differentiationGene flowGenetic structureGenetic isolationS formMicrosatellite dataGenomic islandsContinental Equatorial GuineaDiversity parametersMosquito vector populationsChromosome 3Anopheles gambiaeIsland samplesAnopheles gambiae s.Shallow differentiationIsland of Bioko
2006
Genetic differentiation between the BAMAKO and SAVANNA chromosomal forms of Anopheles gambiae as indicated by amplified fragment length polymorphism analysis.
Slotman M, Mendez M, Torre A, Dolo G, Touré Y, Caccone A. Genetic differentiation between the BAMAKO and SAVANNA chromosomal forms of Anopheles gambiae as indicated by amplified fragment length polymorphism analysis. American Journal Of Tropical Medicine And Hygiene 2006, 74: 641-8. PMID: 16606999, DOI: 10.4269/ajtmh.2006.74.641.Peer-Reviewed Original ResearchConceptsChromosomal formsAnopheles gambiaeSavanna chromosomal formsRibosomal DNA locusFragment length polymorphism (AFLP) primer combinationsPolymorphism primer combinationsGenetic differentiationGene flowDNA lociAFLP analysisFragment length polymorphism analysisPrimer combinationsMolecular markersDiagnostic differencesRecent originLength polymorphism analysisSavannaGambiaePolymorphism analysisMain vectorSympatryGenomeLociDifferentiationMoptiPhylogeographic History and Gene Flow Among Giant Galápagos Tortoises on Southern Isabela Island
Ciofi C, Wilson GA, Beheregaray LB, Marquez C, Gibbs JP, Tapia W, Snell HL, Caccone A, Powell JR. Phylogeographic History and Gene Flow Among Giant Galápagos Tortoises on Southern Isabela Island. Genetics 2006, 172: 1727-1744. PMID: 16387883, PMCID: PMC1456292, DOI: 10.1534/genetics.105.047860.Peer-Reviewed Original ResearchConceptsDispersal eventsMitochondrial DNA control region sequencesGalápagos giant tortoisesLimited dispersal abilityRecent dispersal eventsControl region sequencesGiant Galápagos tortoisesMultilocus genotyping methodsLand bridge formationMovement of organismsEffects of vicarianceRapid population declineIslands of IsabelaLineage sortingClade analysisPhylogeographic historyGene flowDispersal abilityGenetic divergenceGalápagos tortoisesMicrosatellite lociPhylogeographic inferenceSouthern Isabela IslandTaxonomic distinctionGiant tortoises
2004
Variation in an intron sequence of the voltage‐gated sodium channel gene correlates with genetic differentiation between Anopheles gambiae s.s. molecular forms
Gentile G, Santolamazza F, Fanello C, Petrarca V, Caccone A, Della Torre A. Variation in an intron sequence of the voltage‐gated sodium channel gene correlates with genetic differentiation between Anopheles gambiae s.s. molecular forms. Insect Molecular Biology 2004, 13: 371-377. PMID: 15271209, DOI: 10.1111/j.0962-1075.2004.00494.x.Peer-Reviewed Original ResearchConceptsVoltage-gated sodium channel geneSodium channel geneGenetic differentiationGenetic variationChannel genesPossible selective sweepMajor haplotypesSingle mutational stepAnopheles gambiae MRDNA sitesGene flowSelective sweepsMutational stepsTaxonomic statusIntron sequencesGambiae MMolecular formsIntron ISingle localityIntronic regionsAnopheles gambiae s.Additional haplotypesGambiae s.HaplotypesGenesGiant tortoises are not so slow: Rapid diversification and biogeographic consensus in the Galápagos
Beheregaray L, Gibbs J, Havill N, Fritts T, Powell J, Caccone A. Giant tortoises are not so slow: Rapid diversification and biogeographic consensus in the Galápagos. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 6514-6519. PMID: 15084743, PMCID: PMC404076, DOI: 10.1073/pnas.0400393101.Peer-Reviewed Original ResearchConceptsGiant Galápagos tortoisesGalápagos tortoisesGreat natural laboratoryGenetic variationDivergent monophyletic cladesHistory of diversificationIsolated oceanic archipelagoPatterns of colonizationBiogeographic predictionsEvolutionary diversificationGene flowEndemic haplotypesExtant populationsLimited dispersalOceanic archipelagosBiogeographic patternsEvolutionary eventsBiological diversificationMonophyletic cladeMtDNA sequencesRapid diversificationGenetic interchangeRange expansionOlder islandsGiant tortoises