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
2018
Population 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 theoryGenetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island
Miller J, Quinzin M, Scheibe E, Ciofi C, Villalva F, Tapia W, Caccone A. Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island. Journal Of Heredity 2018, 109: 620-630. PMID: 29490038, DOI: 10.1093/jhered/esy010.Peer-Reviewed Original ResearchConceptsReproductive skewGalapagos giant tortoisesBreeding programsFloreana IslandGiant tortoisesAssortative matingSelf-sustaining wild populationsGenetic pedigree analysisMajority of progenyCaptive breeding programsSmall breeding groupsOrigin of individualsPedigree analysisLarge breeding programsFounding individualsWild populationsAllelic diversityGenetic diversityExtinct tortoisesGenetic variationGenetic analysisC. nigerPopulation sizeRelated individualsBreeding groups
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 populationsDifferentiationDiversity
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 clustersGenetics of a head-start program to guide conservation of an endangered Galápagos tortoise (Chelonoidis ephippium)
Jensen E, Tapia W, Caccone A, Russello M. Genetics of a head-start program to guide conservation of an endangered Galápagos tortoise (Chelonoidis ephippium). Conservation Genetics 2015, 16: 823-832. DOI: 10.1007/s10592-015-0703-7.Peer-Reviewed Original ResearchGalápagos tortoisesEx situ conservation strategiesEx situ conservation programsWild populationsMicrosatellite genotypic dataSitu conservation strategiesSitu conservation programsGenetic variationGiant Galápagos tortoisesSignificant genetic differentiationPopulation genetic variationEx situ approachesConservation strategiesConservation interventionsConservation programsWildlife speciesCaptive foundersPinzón IslandCaptive populationsGenetic differentiationBreadth of diversityIntensive managementGiant tortoisesPrivate allelesManagement decisions
2014
Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex
Sistrom M, Evans B, Bjornson R, Gibson W, Balmer O, Mäser P, Aksoy S, Caccone A. Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex. Genome Biology And Evolution 2014, 6: 2811-2819. PMID: 25287146, PMCID: PMC4224348, DOI: 10.1093/gbe/evu222.Peer-Reviewed Original ResearchConceptsT. brucei complexGenomic variationLife historyVariable life historiesAverage linkage disequilibriumTrypanosoma brucei complexGenome-wide studiesMeiotic reciprocal recombinationWhole genome sequencesMultiple genetic backgroundsHuman pathogenicityNumber of subspeciesHuman-infective parasiteNuclear genomeComparative genomicsChromosome sizeEukaryotic parasitesGenomic regionsHuman African trypanosomiasisRegulatory genesTaxonomic designationsDiverse hostsSingle nucleotide polymorphismsGenetic variationReciprocal recombination
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 analysis
2012
Recovery of a nearly extinct Galápagos tortoise despite minimal genetic variation
Milinkovitch MC, Kanitz R, Tiedemann R, Tapia W, Llerena F, Caccone A, Gibbs JP, Powell JR. Recovery of a nearly extinct Galápagos tortoise despite minimal genetic variation. Evolutionary Applications 2012, 6: 377-383. PMID: 23467700, PMCID: PMC3586625, DOI: 10.1111/eva.12014.Peer-Reviewed Original ResearchEspañola IslandGenetic variationEffective population sizeUnequal reproductive successMinimal genetic variationMolecular genetic analysisGalápagos tortoisesReproductive successCaptive populationsNonrandom matingBreeding regimesParental populationsGenetic analysisMorphological dataPopulation sizeTortoise sizeSpeciesCaptivityNumber of animalsTortoisesIslandsInbreedingGalápagosMatingRepatriation efforts
2011
Influence of Host Phylogeographic Patterns and Incomplete Lineage Sorting on Within-Species Genetic Variability in Wigglesworthia Species, Obligate Symbionts of Tsetse Flies
Symula RE, Marpuri I, Bjornson RD, Okedi L, Beadell J, Alam U, Aksoy S, Caccone A. Influence of Host Phylogeographic Patterns and Incomplete Lineage Sorting on Within-Species Genetic Variability in Wigglesworthia Species, Obligate Symbionts of Tsetse Flies. Applied And Environmental Microbiology 2011, 77: 8400-8408. PMID: 21948847, PMCID: PMC3233068, DOI: 10.1128/aem.05688-11.Peer-Reviewed Original ResearchConceptsObligate symbiontsHost speciesGenetic variationMultiple host populationsIncongruence length difference testIncomplete lineage sortingHost-symbiont combinationsSingle host speciesPopulation-level processesIncomplete lineageLineage sortingPhylogeographic patternsSouthern lineagesSymbiont lineagesHost mtDNAWigglesworthia glossinidiaMolecular varianceBacterial symbiontsEvolutionary associationEvolutionary historySouthern populationsMitochondrial DNA haplogroupsVariable lociSymbiontsGenetic variabilityGenetic 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
Genetic Differentiation between Marine Iguanas from Different Breeding Sites on the Island of Santa Fé (Galápagos Archipelago)
Lanterbecq D, Glaberman S, Vitousek M, Steinfartz S, Benavides E, Wikelski M, Caccone A. Genetic Differentiation between Marine Iguanas from Different Breeding Sites on the Island of Santa Fé (Galápagos Archipelago). Journal Of Heredity 2010, 101: 663-675. PMID: 20538757, DOI: 10.1093/jhered/esq067.Peer-Reviewed Original ResearchConceptsMarine iguanasGenetic diversitySex-biased dispersalMitochondrial control regionMitochondrial DNA markersGalápagos marine iguanasSanta FéDifferent breeding sitesSouthern sitesGenetic differentiationEvolutionary signalGenetic structureMicrosatellite lociDNA markersControl regionGenetic variationGenetic patternsBreeding sitesLittle differentiationBase pairsNeighboring islandsIguanasDiversitySampling sitesDifferentiation
2009
In 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 populationsMorphometrics Parallel Genetics in a Newly Discovered and Endangered Taxon of Galápagos Tortoise
Chiari Y, Hyseni C, Fritts T, Glaberman S, Marquez C, Gibbs J, Claude J, Caccone A. Morphometrics Parallel Genetics in a Newly Discovered and Endangered Taxon of Galápagos Tortoise. PLOS ONE 2009, 4: e6272. PMID: 19609441, PMCID: PMC2707613, DOI: 10.1371/journal.pone.0006272.Peer-Reviewed Original ResearchConceptsGalápagos tortoisesGenetic variationGenetic distinctionTortoise populationsNon-neutral lociStrong genetic differentiationComplex heritable traitsDiagnostic morphological charactersShell morphologyShell shape variationGenetic differentiationMitochondrial dataMonophyletic lineageMorphological charactersGiant tortoisesHeritable traitGenetic dataMost islandsSanta CruzMolecular studiesShell shapeTurtle shellTortoisesLineagesParallel Genetic
2007
Patterns of Selection in Anti-Malarial Immune Genes in Malaria Vectors: Evidence for Adaptive Evolution in LRIM1 in Anopheles arabiensis
Slotman MA, Parmakelis A, Marshall JC, Awono-Ambene PH, Antonio-Nkondjo C, Simard F, Caccone A, Powell JR. Patterns of Selection in Anti-Malarial Immune Genes in Malaria Vectors: Evidence for Adaptive Evolution in LRIM1 in Anopheles arabiensis. PLOS ONE 2007, 2: e793. PMID: 17726523, PMCID: PMC1945087, DOI: 10.1371/journal.pone.0000793.Peer-Reviewed Original ResearchConceptsAdaptive evolutionPrimary malaria vectorMalaria vectorsPatterns of selectionNon-vector speciesAnopheles gambiae complexMcDonald-KreitmanReplacement substitutionsPositive selectionGenetic variationMalaria vector AnLRIM1Immune genesSelection showGambiae complexGenesAdjacent codonsProtein differentiationLevel of resistanceAdaptive responsePlasmodium speciesCEC1Vector AnMaximum likelihood testSpecies
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 feverGenetic Divergence of Connecticut Melanoplus femurrubrum Populations
Lee J, Marshall J, Schmitz O, Caccone A. Genetic Divergence of Connecticut Melanoplus femurrubrum Populations. Journal Of Heredity 2006, 97: 290-293. PMID: 16598036, DOI: 10.1093/jhered/esj027.Peer-Reviewed Original ResearchConceptsGenetic diversityHigh mitochondrial diversityNuclear gene regionsAT-rich genesHigh sequence divergenceFixation index analysisMultiple genetic markersPhylogeographic patternsMitochondrial diversityMolecular varianceGenetic divergenceSequence divergenceEqual diversityGenetic variationLittle divergenceGene regionGenetic markersPopulation-level studiesITS1 geneGenesDiversityDivergenceSmall geographic areasND2Species
2004
Potential genetic consequences of a recent bottleneck in the Amur tiger of
Russello M, Gladyshev E, Miquelle D, Caccone A. Potential genetic consequences of a recent bottleneck in the Amur tiger of. Conservation Genetics 2004, 5: 707-713. DOI: 10.1007/s10592-004-1860-2.Peer-Reviewed Original ResearchWild populationsGenetic variationMitochondrial DNA control regionRemnant genetic diversityDNA control regionSingle widespread haplotypeMitochondrial DNA variationPotential genetic consequencesCaptive breeding programsAmur tigersRecent bottleneckPanthera tigris altaicaWidespread haplotypeGenetic consequencesDNA variationHaplotype diversityGenetic diversityControl regionScat samplesBreeding programsCaptive individualsSevere bottleneckPopulation sizeDemographic processesRussian Far EastVariation 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