2021
Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises
Jensen E, Gaughran S, Garrick R, Russello M, Caccone A. Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises. Molecular Ecology 2021, 30: 6325-6339. PMID: 34510620, DOI: 10.1111/mec.16176.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsEvolution, MolecularGenetics, PopulationHumansPopulation DensityTurtlesWhole Genome SequencingConceptsGalapagos giant tortoisesPopulation genetics theoryGiant tortoisesWhole-genome sequencingMolecular evolutionWhole genomeGenetic theoryGenome sequencingPopulation genetic summary statisticsGiant tortoise speciesPopulation genetic predictionsLife-history traitsSignals of selectionPatterns of diversityMutation accumulation ratesGenetic summary statisticsEvolutionary distinctivenessRecent radiationExtant lineagesPhylogeographic studiesHistory traitsPopulation genomicsEvolutionary historyMutation accumulationDemographic historyFour times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America
Andersen J, Havill N, Caccone A, Elkinton J. Four times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America. Molecular Ecology 2021, 30: 3439-3452. PMID: 34033202, DOI: 10.1111/mec.15983.Peer-Reviewed Original ResearchConceptsWinter mothNortheastern United StatesNorth AmericaInvasive winter mothNon-native speciesPopulation genetic dataAmount of diversityInvasion successSerial invasionInvaded regionsWidespread defoliationGenetic bottleneckBayesian assignmentOperophtera brumataMicrosatellite lociApproximate Bayesian computation methodsIndependent introductionsNorthern FennoscandiaCentral EuropeGenetic dataHybridization eventsBritish ColumbiaGeographic originNova ScotiaAmericaA machine-learning approach to map landscape connectivity in Aedes aegypti with genetic and environmental data
Pless E, Saarman NP, Powell JR, Caccone A, Amatulli G. A machine-learning approach to map landscape connectivity in Aedes aegypti with genetic and environmental data. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2003201118. PMID: 33619083, PMCID: PMC7936321, DOI: 10.1073/pnas.2003201118.Peer-Reviewed Original Research
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
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 strategyDiversityGlobal population divergence and admixture of the brown rat (Rattus norvegicus)
Puckett EE, Park J, Combs M, Blum MJ, Bryant JE, Caccone A, Costa F, Deinum EE, Esther A, Himsworth CG, Keightley PD, Ko A, Lundkvist Å, McElhinney LM, Morand S, Robins J, Russell J, Strand TM, Suarez O, Yon L, Munshi-South J. Global population divergence and admixture of the brown rat (Rattus norvegicus). Proceedings Of The Royal Society B 2016, 283: 20161762. PMID: 27798305, PMCID: PMC5095384, DOI: 10.1098/rspb.2016.1762.Peer-Reviewed Original ResearchMeSH KeywordsAfricaAnimalsAustralasiaChinaEuropeEvolution, MolecularGenetics, PopulationHumansMongoliaNorth AmericaPolymorphism, Single NucleotideRatsRussiaConceptsEvolutionary clustersColonization of EuropeRat eradication programmeAgricultural settlementsWestward expansionEastward expansionSoutheast AsiaSouthward expansionAleutian ArchipelagoExpansion routesAstonishing degreeRecent migrantsGlobal population structureGlobal phylogeographyBlack ratsGlobal tradeCommensal rodentsEuropePatterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda
Gloria-Soria A, Dunn WA, Telleria EL, Evans BR, Okedi L, Echodu R, Warren WC, Montague MJ, Aksoy S, Caccone A. Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda. G3: Genes, Genomes, Genetics 2016, 6: 1573-1584. PMID: 27172181, PMCID: PMC4889654, DOI: 10.1534/g3.116.027235.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromosome MappingDNA, MitochondrialGene-Environment InteractionGenes, InsectGenetic LinkageGenetic VariationGenetics, PopulationGenome, InsectGenome-Wide Association StudyGenomicsGenotypeGeographyHigh-Throughput Nucleotide SequencingLinkage DisequilibriumMicrosatellite RepeatsPolymorphism, Single NucleotideSelection, GeneticTsetse FliesUgandaConceptsSingle nucleotide polymorphismsLinkage disequilibriumExtent of LDLocal environmental adaptationGenome-wide variationDetection of lociOverall linkage disequilibriumInsect vectorsDifferent environmental conditionsWhole-genome sequencingPopulation genomicsStrong selectionAssociation analysisEnvironmental adaptationGenomic patternsPopulation dynamicsSignificant genetic associationUninfected fliesDisease transmissionSequence technologyAssociation studiesEnvironmental conditionsTsetse fliesHuman African trypanosomiasisRelevant phenotypesAncient 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
Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island
Poulakakis N, Edwards D, Chiari Y, Garrick R, Russello M, Benavides E, Watkins-Colwell G, Glaberman S, Tapia W, Gibbs J, Cayot L, Caccone A. Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island. PLOS ONE 2015, 10: e0138779. PMID: 26488886, PMCID: PMC4619298, DOI: 10.1371/journal.pone.0138779.Peer-Reviewed Original ResearchConceptsMultiple independent evolutionary lineagesGiant tortoise speciesIndependent evolutionary lineagesCompelling genetic evidenceGalapagos tortoisesRank of speciesSanta Cruz IslandGenetic distinctivenessAnalysis of DNAEvolutionary lineagesEvolutionary relationshipsNatural populationsDNA charactersDistinct lineagesIsland of originTaxonomic revisionMorphological charactersMuseum specimensNew speciesGenetic evidenceTortoise speciesLineagesSpeciesTortoisesType specimen
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 reconstruction
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 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 outcomesGeneticsFuscipesDiversityPopulationWolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics
Symula RE, Alam U, Brelsfoard C, Wu Y, Echodu R, Okedi LM, Aksoy S, Caccone A. Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics. BMC Ecology And Evolution 2013, 13: 31. PMID: 23384159, PMCID: PMC3574847, DOI: 10.1186/1471-2148-13-31.Peer-Reviewed Original ResearchConceptsMtDNA haplotypesDifferent WolbachiaGenetic diversityHost haplotypesSequence diversityMultiple WolbachiaArthropod host reproductionPopulation genetic differentiationComplex evolutionary dynamicsMitochondrial DNA haplotypesAssociation of WolbachiaLow reproductive outputHost population geneticsHost genetic diversityTsetse fliesMulti-locus sequence typingMost WolbachiaHost genetic compositionGenetic differentiationWolbachia evolutionWolbachia associationsHost reproductionDNA haplotypesMtDNA groupsΑ-proteobacteria
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 periodGenetic rediscovery of an ‘extinct’ Galápagos giant tortoise species
Garrick R, Benavides E, Russello M, Gibbs J, Poulakakis N, Dion K, Hyseni C, Kajdacsi B, Márquez, Bahan S, Ciofi C, Tapia W, Caccone A. Genetic rediscovery of an ‘extinct’ Galápagos giant tortoise species. Current Biology 2012, 22: r10-r11. PMID: 22240469, DOI: 10.1016/j.cub.2011.12.004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChimeraEcuadorExtinction, BiologicalGenetic VariationGenetics, PopulationMicrosatellite RepeatsTurtlesConceptsFloreana IslandHybrid individualsGiant tortoise speciesUnique evolutionary lineagesGiant Galápagos tortoisesCaptive breeding programsEvolutionary lineagesGalápagos tortoisesHybrid offspringExtinct speciesGenetic footprintsTortoise speciesBreeding programsGalápagos IslandsGenetic signaturesExtant individualsIsabela IslandGenomeSpeciesMixed ancestryTortoisesAncestryIslandsLineagesLikely mechanism
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 barriers
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 ResearchMeSH KeywordsAnimalsCell NucleusDNA, MitochondrialEcuadorFemaleGene FlowGenetic VariationGenetics, PopulationIguanasLocus Control RegionMaleMicrosatellite RepeatsConceptsComplete 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 ResearchMeSH KeywordsAnimalsAnimals, ZooConservation of Natural ResourcesGene FlowGenetic VariationGenetics, PopulationGenotypePopulation DynamicsTigersConceptsGenetic 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
2008
High Levels of Genetic Differentiation between Ugandan Glossina fuscipes fuscipes Populations Separated by Lake Kyoga
Abila PP, Slotman MA, Parmakelis A, Dion KB, Robinson AS, Muwanika VB, Enyaru JC, Lokedi L, Aksoy S, Caccone A. High Levels of Genetic Differentiation between Ugandan Glossina fuscipes fuscipes Populations Separated by Lake Kyoga. PLOS Neglected Tropical Diseases 2008, 2: e242. PMID: 18509474, PMCID: PMC2386243, DOI: 10.1371/journal.pntd.0000242.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDNA, MitochondrialGenetic VariationGenetics, PopulationHumansInsect VectorsMicrosatellite RepeatsTrypanosomiasis, AfricanTsetse FliesUganda