2018
Temporal Mitogenomics of the Galapagos Giant Tortoise from Pinzón Reveals Potential Biases in Population Genetic Inference
Jensen E, Miller J, Edwards D, Garrick R, Tapia W, Caccone A, Russello M. Temporal Mitogenomics of the Galapagos Giant Tortoise from Pinzón Reveals Potential Biases in Population Genetic Inference. Journal Of Heredity 2018, 109: 631-640. PMID: 29659893, DOI: 10.1093/jhered/esy016.Peer-Reviewed Original Research
2017
Genetic 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
Asymmetric hybridization between non-native winter moth, Operophtera brumata (Lepidoptera: Geometridae), and native Bruce spanworm, Operophtera bruceata, in the Northeastern United States, assessed with novel microsatellites and SNPs
Havill N, Elkinton J, Andersen J, Hagen S, Broadley H, Boettner G, Caccone A. Asymmetric hybridization between non-native winter moth, Operophtera brumata (Lepidoptera: Geometridae), and native Bruce spanworm, Operophtera bruceata, in the Northeastern United States, assessed with novel microsatellites and SNPs. Bulletin Of Entomological Research 2016, 107: 241-250. PMID: 27876095, DOI: 10.1017/s0007485316000857.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsMicrosatellite lociBruce spanwormAsymmetric hybridizationWinter mothSpecies-diagnostic single nucleotide polymorphismsOperophtera brumataVariable microsatellite lociNon-native pestsTypes of markersBacterial symbiontsGenetic incompatibilitiesGenomic approachesLaboratory crossesNative speciesAsymmetrical hybridizationPopulation geneticsPutative hybridsHybrid backcrossesNovel microsatellitesForest treesOperophtera bruceataO. bruceataReciprocal crossesGenetic markersAncient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia
Havill N, Shiyake S, Lamb Galloway A, Foottit R, Yu G, Paradis A, Elkinton J, Montgomery M, Sano M, Caccone A. Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia. Molecular Ecology 2016, 25: 2065-2080. PMID: 26880353, DOI: 10.1111/mec.13589.Peer-Reviewed Original ResearchConceptsWestern North AmericaEastern North AmericaNorth AmericaAdelges tsugaeHost specializationExtreme genetic bottleneckWorldwide genetic structurePleistocene glacial periodsSouthern JapanMitochondrial COI sequencesGlacial periodSpecies traitsAdelgid invasionApproximate Bayesian computationInvasive insectsHemlock speciesContinental scaleInvasion pathwaysTsuga speciesGenetic bottleneckGenetic structureHost treesEndemic lineagesInvasive pestHemlock treesMultiple Paternity in the Norway Rat, Rattus norvegicus , from Urban Slums in Salvador, Brazil
Costa F, Richardson JL, Dion K, Mariani C, Pertile AC, Burak MK, Childs JE, Ko AI, Caccone A. Multiple Paternity in the Norway Rat, Rattus norvegicus , from Urban Slums in Salvador, Brazil. Journal Of Heredity 2016, 107: 181-186. PMID: 26733693, PMCID: PMC5893012, DOI: 10.1093/jhered/esv098.Peer-Reviewed Original Research
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 ResearchMeSH KeywordsAnimalsEcuadorGenetic SpeciationHybridization, GeneticIguanasMolecular Sequence DataPhylogenySequence Analysis, DNAConceptsGalápagos 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 islandsWhole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi
Carpi G, Walter KS, Bent SJ, Hoen AG, Diuk-Wasser M, Caccone A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics 2015, 16: 434. PMID: 26048573, PMCID: PMC4458057, DOI: 10.1186/s12864-015-1634-x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArthropod VectorsBorrelia burgdorferiGenome, BacterialHigh-Throughput Nucleotide SequencingHumansPolymorphism, Single NucleotideSequence Analysis, DNAConceptsWhole-genome captureGenome captureGenomic studiesPopulation genomic studiesArthropod vectorsPathogen DNABorrelia burgdorferi genomeNext-generation sequencing technologiesWhole genome sequencesMixed DNA templatesCulture-independent methodsGeneration sequencing technologyPathogen sequence dataFine-resolution studiesGenome sequenceVector-borne pathogensMixed DNA samplesSingle nucleotide polymorphismsComplete genomeEvolutionary dynamicsSequence dataSequencing technologiesDisease vectorsStudy systemDNA template
2014
Lineage fusion in Galápagos giant tortoises
Garrick R, Benavides E, Russello M, Hyseni C, Edwards D, Gibbs J, Tapia W, Ciofi C, Caccone A. Lineage fusion in Galápagos giant tortoises. Molecular Ecology 2014, 23: 5276-5290. PMID: 25223395, DOI: 10.1111/mec.12919.Peer-Reviewed Original ResearchConceptsLineage fusionGiant tortoise speciesGalápagos giant tortoisesWidespread introgressive hybridizationLong generation timesWolf VolcanoCryptic lineagesReticulate evolutionIntrogressive hybridizationLineage splittingMicrosatellite dataGalápagos tortoisesPopulation geneticsEvolutionary phenomenaMate selectivityTortoise speciesGiant tortoisesLineagesGeneration timeRapid extinctionTortoisesPurebred femalesFusionIslandsHistorical reconstructionAnalysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota
Aksoy E, Telleria EL, Echodu R, Wu Y, Okedi LM, Weiss BL, Aksoy S, Caccone A. Analysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota. Applied And Environmental Microbiology 2014, 80: 4301-4312. PMID: 24814785, PMCID: PMC4068677, DOI: 10.1128/aem.00079-14.Peer-Reviewed Original ResearchConceptsDifferent tsetse speciesRRNA gene clone librariesDifferent sympatric speciesGene clone librariesTsetse speciesLimited diversityQuantitative PCRV4 hypervariable regionGut microbiotaGut microbial abundanceSympatric speciesGut microbial diversityClone librariesMicrobial diversityMicrobial abundanceField fliesRRNA geneHost physiologyTsetse fly populationsDeep sequencingReduced diversityDifferent speciesFly populationsSpeciesWigglesworthia
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 periodTrypanosoma brucei gambiense Group 1 Is Distinguished by a Unique Amino Acid Substitution in the HpHb Receptor Implicated in Human Serum Resistance
Symula RE, Beadell JS, Sistrom M, Agbebakun K, Balmer O, Gibson W, Aksoy S, Caccone A. Trypanosoma brucei gambiense Group 1 Is Distinguished by a Unique Amino Acid Substitution in the HpHb Receptor Implicated in Human Serum Resistance. PLOS Neglected Tropical Diseases 2012, 6: e1728. PMID: 22802982, PMCID: PMC3393672, DOI: 10.1371/journal.pntd.0001728.Peer-Reviewed Original ResearchConceptsTrypanosome lytic factorHuman serum resistanceGroup 2Group 1Serum resistanceHaptoglobin-hemoglobin receptorHuman serumHuman African trypanosomiasisInnate immunityTrypanosoma brucei rhodesienseUnique amino acid substitutionsAltered activityLytic factorCausative agentLytic activityHemoglobin receptorTLF-1African trypanosomiasisBrucei rhodesienseSerumReceptorsAmino acid substitutionsFurther evidenceHpHbRTBR
2011
Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises
POULAKAKIS N, RUSSELLO M, GEIST D, CACCONE A. Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises. Molecular Ecology 2011, 21: 160-173. PMID: 22098061, DOI: 10.1111/j.1365-294x.2011.05370.x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionDNA, MitochondrialExtinction, BiologicalGenetic VariationMolecular Sequence DataPhylogenyPhylogeographySequence Analysis, DNATurtlesConceptsGiant Galápagos tortoisesHuman-mediated dispersal eventsVicariant eventsGalápagos tortoisesMainland South AmericaHuman activitiesIndependent evolutionary unitsAvailable geological dataSimple linear trendRecent human activitiesIsland lifeEvolutionary unitsEndangered taxaColonization eventsExtant speciesDispersal eventsEvolutionary historyGeological dataMultiple colonizationsExtinct speciesOcean islandsDNA dataOlder islandsYounger islandsOceanic islandsInfluence 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 variabilityPermanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2010–31 January 2011
Consortium M, AGATA K, ALASAAD S, ALMEIDA‐VAL V, ÁLVAREZ‐DIOS J, BARBISAN F, BEADELL JS, BELTRÁN JF, BENÍTEZ M, BINO G, BLEAY C, BLOOR P, BOHLMANN J, BOOTH W, BOSCARI E, CACCONE A, CAMPOS T, CARVALHO BM, CLIMACO GT, CLOBERT J, CONGIU L, COWGER C, DIAS G, DOADRIO I, FARIAS IP, FERRAND N, FREITAS PD, FUSCO G, GALETTI PM, GALLARDO‐ESCÁRATE C, GAUNT MW, OCAMPO ZG, GONÇALVES H, GONZALEZ EG, HAYE P, HONNAY O, HYSENI C, JACQUEMYN H, JOWERS MJ, KAKEZAWA A, KAWAGUCHI E, KEELING CI, KWAN Y, LA SPINA M, LEE W, LEŚNIEWSKA M, LI Y, LIU H, LIU X, LOPES S, MARTÍNEZ P, MEEUS S, MURRAY BW, NUNES AG, OKEDI LM, OUMA JO, PARDO BG, PARKS R, PAULA‐SILVA M, PEDRAZA‐LARA C, PERERA OP, PINO‐QUERIDO A, RICHARD M, ROSSINI BC, SAMARASEKERA NG, SÁNCHEZ A, SANCHEZ JA, dos ANJOS SANTOS C, SHINOHARA W, SORIGUER RC, SOUSA AC, da SILVA SOUSA C, STEVENS VM, TEJEDO M, VALENZUELA‐BUSTAMANTE M, VAN de VLIET MS, VANDEPITTE K, VERA M, WANDELER P, WANG W, WON Y, YAMASHIRO A, YAMASHIRO T, ZHU C. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2010–31 January 2011. Molecular Ecology Resources 2011, 11: 586-589. PMID: 21457476, DOI: 10.1111/j.1755-0998.2011.03004.x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDatabases, GeneticFungiMicrosatellite RepeatsMolecular Sequence DataPlantsSequence Analysis, DNAConceptsMolecular Ecology Resources DatabaseJaponica varPermanent Genetic ResourcesBlumeria graminis f.Microsatellite marker lociSalminus hilariiAustropotamobius italicusZootoca viviparaMicrotus cabreraeGraminis f.Salminus franciscanusGenetic resourcesKirengeshoma palmataPacifastacus leniusculusAlytes muletensisPulmonaria officinalisMarker lociDendroctonus ponderosaeChorus giganteusOrconectes virilisGlossina morsitans morsitansSalminus brasiliensisArapaima gigasProcambarus clarkiiMytilus galloprovincialisPhylogeography and Taxonomy of Trypanosoma brucei
Balmer O, Beadell J, Gibson W, Caccone A. Phylogeography and Taxonomy of Trypanosoma brucei. PLOS Neglected Tropical Diseases 2011, 5: e961. PMID: 21347445, PMCID: PMC3035665, DOI: 10.1371/journal.pntd.0000961.Peer-Reviewed Original Research
2009
Characterization and evolution of MHC class II B genes in Galápagos marine iguanas (Amblyrhynchus cristatus)
Glaberman S, Moreno M, Caccone A. Characterization and evolution of MHC class II B genes in Galápagos marine iguanas (Amblyrhynchus cristatus). Developmental & Comparative Immunology 2009, 33: 939-947. PMID: 19454336, DOI: 10.1016/j.dci.2009.03.003.Peer-Reviewed Original ResearchConceptsClass II B genesGalápagos marine iguanasB geneMarine iguanasMHC class II B genesAvian MHC evolutionInterlocus gene conversionAncestral locusEvolutionary forcesMHC evolutionBird speciesGene conversionGene groupsPositive selectionCDNA sequenceClass II genesLocus groupsVertebratesGenesMammalsShort tractsBeta 2 domainAdaptive immune systemMajor groupsSquamates
2008
Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise
Poulakakis N, Glaberman S, Russello M, Beheregaray LB, Ciofi C, Powell JR, Caccone A. Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 15464-15469. PMID: 18809928, PMCID: PMC2563078, DOI: 10.1073/pnas.0805340105.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDNA, MitochondrialEcuadorExtinction, BiologicalHumansMolecular Sequence DataPhylogenySequence Analysis, DNASpecies SpecificityTurtlesConceptsMuseum specimensHistorical DNA analysisDiversification of organismsCaptive breeding programsIsland of FloreanaModern DNA techniquesMicrosatellite dataGalápagos tortoisesConservation biologyMitochondrial DNANatural selectionExtinct speciesExtinct taxaBreeding programsGiant tortoisesIntense harvestingGenetic analysisGenetic dataGalápagos ArchipelagoTortoise populationsDNA techniquesHuman exploitationNearby islandsEnough individualsSpecies
2007
Independent evolutionary origins of landlocked alewife populations and rapid parallel evolution of phenotypic traits
PALKOVACS E, DION K, POST D, CACCONE A. Independent evolutionary origins of landlocked alewife populations and rapid parallel evolution of phenotypic traits. Molecular Ecology 2007, 17: 582-597. PMID: 18179439, DOI: 10.1111/j.1365-294x.2007.03593.x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsConnecticutDNA, MitochondrialEvolution, MolecularFishesGeographyMicrosatellite RepeatsMolecular Sequence DataSequence Analysis, DNAConceptsLandlocked populationsAnadromous populationsAlewife populationSmaller adult body sizeRapid parallel evolutionLife history divergenceFreshwater ancestorsIndependent evolutionary originsDivergence time estimatesLife-history variantsGill raker spacingMicrosatellite mutation ratesMtDNA control regionAdult body sizeRate of evolutionSmall prey itemsAnadromous ancestorsForaging traitsPopulation divergenceAllele frequency dataDivergence timesEvolutionary ratesMicrosatellite dataAnadromous formEvolutionary origin
2006
A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the Salamandridae with emphasis on Triturus newts
Steinfartz S, Vicario S, Arntzen J, Caccone A. A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the Salamandridae with emphasis on Triturus newts. Journal Of Experimental Zoology Part B Molecular And Developmental Evolution 2006, 308B: 139-162. PMID: 16969762, DOI: 10.1002/jez.b.21119.Peer-Reviewed Original ResearchConceptsCourtship traitsSpecies of TriturusDNA sequence dataLast common ancestorTrue salamandersSalamandrid speciesMitochondrial genesMolecular phylogenyTriturus newtsGenus TriturusSpecies assemblagesPhylogenetic positionCommon ancestorEuropean newtsFamily SalamandridaeEvolutionary patternsT. vittatusMorphological charactersSequence dataLife historySalamandridaeT. alpestrisTemporal divergenceNewtsTriturusAncient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids
Poulakakis N, Parmakelis A, Lymberakis P, Mylonas M, Zouros E, Reese D, Glaberman S, Caccone A. Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids. Biology Letters 2006, 2: 451-454. PMID: 17148428, PMCID: PMC1686204, DOI: 10.1098/rsbl.2006.0467.Peer-Reviewed Original ResearchConceptsEvolutionary historyDNA sequencesAncient DNA studiesDNA fragmentsMultiple displacement amplification (MDA) methodPygmy mammothsIndependent historyShort DNA sequencesB-DNA fragmentEastern MediterraneanMediterranean islandsPhylogenetic analysisMolecular dataMainland samplesCretan sampleDNA studiesHistoryElephantidsDiagnostic sitesElephasPrevailing viewIslandsMammothsMammuthusSequence