2024
Inbreeding 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 conflictsMatingMammals
2018
Genetic 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 programsPopulation genomics through time provides insights into the consequences of decline and rapid demographic recovery through head‐starting in a Galapagos giant tortoise
Jensen E, Edwards D, Garrick R, Miller J, Gibbs J, Cayot L, Tapia W, Caccone A, Russello M. Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head‐starting in a Galapagos giant tortoise. Evolutionary Applications 2018, 11: 1811-1821. PMID: 30459831, PMCID: PMC6231475, DOI: 10.1111/eva.12682.Peer-Reviewed Original ResearchGiant tortoisesBottleneck eventsGenetic diversityGenetic variationPopulation declineTortoise populationsPopulation sizeCurrent genetic diversityEffective population sizePopulation genetics theoryWide single nucleotide polymorphism dataCaptive breeding programsRapid demographic recoveryRecent population declineSingle nucleotide polymorphism dataGalapagos giant tortoisesNucleotide polymorphism dataRapid population declineLarge population sizesPopulation genomicsSpecies restorationLong-term persistencePopulation structureGenetic patternsGenetic theoryGenome-Wide Assessment of Diversity and Divergence Among Extant Galapagos Giant Tortoise Species
Miller J, Quinzin M, Edwards D, Eaton D, Jensen E, Russello M, Gibbs J, Tapia W, Rueda D, Caccone A. Genome-Wide Assessment of Diversity and Divergence Among Extant Galapagos Giant Tortoise Species. Journal Of Heredity 2018, 109: 611-619. PMID: 29986032, DOI: 10.1093/jhered/esy031.Peer-Reviewed Original ResearchConceptsGiant tortoise speciesMitochondrial DNA sequencesSingle nucleotide polymorphismsTortoise speciesGenetic diversityMicrosatellite lociDNA sequencesGenotypic dataMicrosatellite genotypic dataNuclear microsatellite lociGenome-wide markersEstimates of diversityGenome-wide assessmentGalapagos giant tortoisesSpecies radiationEvolutionary geneticsSignificant unitsMitochondrial DNAPopulation structureSpecies conservationGenetic lineagesGiant tortoisesPopulation delineationTortoise populationsDNA sequencing
2017
Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study
Gaughran S, Quinzin M, Miller J, Garrick R, Edwards D, Russello M, Poulakakis N, Ciofi C, Beheregaray L, Caccone A. Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study. Evolutionary Applications 2017, 11: 1084-1093. PMID: 30026799, PMCID: PMC6050186, DOI: 10.1111/eva.12551.Peer-Reviewed Original ResearchGalápagos giant tortoisesSingle nucleotide polymorphismsGenetic differentiationPopulation structureGiant tortoisesRecent single nucleotide polymorphismGenomewide single nucleotide polymorphismsGenomic single nucleotide polymorphismsGiant tortoise speciesHigh-throughput DNA sequencingStructured natural populationsHundreds of SNPsThousands of SNPsPopulation genetics theoryTraditional genetic markersAge of genomicsMitochondrial DNA analysisNonmodel organismsNonmodel speciesEvolutionary historyNatural populationsGenetic theoryTortoise speciesUnnatural groupingGenomic dataGenetic 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 trypanosomiasis
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
Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana
MacLeod A, Rodríguez A, Vences M, Orozco-terWengel P, García C, Trillmich F, Gentile G, Caccone A, Quezada G, Steinfartz S. Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana. Proceedings Of The Royal Society B 2015, 282: 20150425. PMID: 26041359, PMCID: PMC4590447, DOI: 10.1098/rspb.2015.0425.Peer-Reviewed Original ResearchConceptsGalápagos marine iguanasEvolutionary historyMarine iguanasIncipient speciationStrong population structureGenome-wide analysisGalápagos land iguanasCommon gene poolDepth genome-wide analysisSpeciation eventsIsland speciationSister lineageEvolutionary potentialFrequent hybridizationExtant populationsLocal adaptationPhylogenetic treeGene poolSister groupPopulation structureVariable markersLand iguanasEvolutionary processesSame islandNearby islands
2013
Glossina 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
2012
Genetic isolation within the malaria mosquito Anopheles melas
Deitz K, Athrey G, Reddy M, Overgaard H, Matias A, Jawara M, della Torre A, Petrarca V, Pinto J, Kiszewski A, Kengne P, Costantini C, Caccone A, Slotman M. Genetic isolation within the malaria mosquito Anopheles melas. Molecular Ecology 2012, 21: 4498-4513. PMID: 22882458, PMCID: PMC4067978, DOI: 10.1111/j.1365-294x.2012.05724.x.Peer-Reviewed Original ResearchConceptsMicrosatellite dataIsland populationsGambiae complexMaximum likelihood phylogenetic analysisBp of mtDNALevel of divergenceLast glaciation periodA. gambiae complexMalaria vectorsSalt marsh grassAnopheles gambiae complexAnopheles melasMajor malaria vectorApproximate Bayesian analysisMtDNA divergenceGenetic differentiationGenetic divergenceGenetic isolationMainland populationsPhylogenetic analysisPopulation structureMicrosatellite markersLarval habitatsA. gambiaeGlaciation period
2011
Genetic 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
Population Genetic Structure of Aldabra Giant Tortoises
Balmer O, Ciofi C, Galbraith D, Swingland I, Zug G, Caccone A. Population Genetic Structure of Aldabra Giant Tortoises. Journal Of Heredity 2010, 102: 29-37. PMID: 20805288, DOI: 10.1093/jhered/esq096.Peer-Reviewed Original ResearchConceptsGenetic structurePopulation structureGiant tortoisesMitochondrial DNA control region sequencesPopulation genetic structureSignificant population structureControl region sequencesAldabra giant tortoisePrevious ecological studiesAllopatric divergenceNuclear lociPopulation subdivisionHabitat variationMtDNA sequencesMicrosatellite lociPopulation geneticsUnsuitable habitatGenetic variabilityAllelic variationRegion sequencesEcological factorsTerrestrial ecosystemsPopulation dynamicsAldabra AtollGeographical barriersPhylogeography 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
Genetic 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
Polymorphic microsatellite markers for studies of Aedes aegypti (Diptera: Culicidae), the vector of dengue and yellow fever
SLOTMAN M, KELLY N, HARRINGTON L, KITTHAWEE S, JONES J, SCOTT T, CACCONE A, POWELL J. Polymorphic microsatellite markers for studies of Aedes aegypti (Diptera: Culicidae), the vector of dengue and yellow fever. Molecular Ecology Resources 2006, 7: 168-171. DOI: 10.1111/j.1471-8286.2006.01533.x.Peer-Reviewed Original ResearchMicrosatellite lociA. aegypti genomePopulation genetic studiesPolymorphic microsatellite lociField-collected specimensPolymorphic microsatellite markersAedes aegyptiAegypti genomePopulation structureGenetic variationVariable markersImportant speciesMicrosatellite markersGenetic studiesLaboratory coloniesLociVector of dengueAllelesAegyptiGenomeMarkersGeneticsSpeciesDengue vectorsYellow fever
2003
Genetic structure of Mesoamerican populations of Big‐leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis
Novick R, Dick C, Lemes M, Navarro C, Caccone A, Bermingham E. Genetic structure of Mesoamerican populations of Big‐leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis. Molecular Ecology 2003, 12: 2885-2893. PMID: 14629370, DOI: 10.1046/j.1365-294x.2003.01951.x.Peer-Reviewed Original ResearchConceptsGenetic structurePhylogeographic structureStrong phylogeographic structureNeotropical tree speciesVariable microsatellite lociHigh-resolution markersBig-leaf mahoganyMahogany populationsGenetic differentiationCosta RicaBiogeographic historyNeotropical treeGenetic divergenceRegional biogeographyNative rangeNorthern populationsGenetic distanceGenetic diversityMicrosatellite lociAtlantic populationsPopulation structureAmerican treesMesoamerican populationsSwietenia macrophylla KingUnrooted dendrogram
1999
Population structure, speciation, and introgression in the Anopheles gambiae complex.
Powell JR, Petrarca V, della Torre A, Caccone A, Coluzzi M. Population structure, speciation, and introgression in the Anopheles gambiae complex. Parassitologia 1999, 41: 101-13. PMID: 10697841.Peer-Reviewed Original ResearchConceptsAnopheles gambiae complexGambiae complexPopulation structureAdaptive genetic variationPresence of introgressionChromosome inversion polymorphismsDistribution of karyotypesMicro-geographic scaleGambiae s.Major environmental variablesDistinct genetic formsCryptic taxaPanmictic unitInversion polymorphismPhylogenetic dataChromosome inversionsLevels of aridityPhylogenetic studiesEvolutionary dynamicsGenetic variationWest African populationsImportant vectorKaryotype studiesMolecular studiesEnvironmental variables