2023
Galapagos giant tortoise trafficking case demonstrates the utility and applications of long‐term comprehensive genetic monitoring
Quinzin M, Bishop A, Miller J, Poulakakis N, Tapia W, Torres‐Rojo F, Sevilla C, Caccone A. Galapagos giant tortoise trafficking case demonstrates the utility and applications of long‐term comprehensive genetic monitoring. Animal Conservation 2023, 26: 826-838. DOI: 10.1111/acv.12870.Peer-Reviewed Original ResearchGalapagos giant tortoisesGiant tortoisesIllegal wildlife tradeGenetic analysisNuclear microsatellite markersGenetic repositoryBreeding CenterStandard genetic markersComprehensive genetic characterizationWild speciesIsland of originGenetic monitoringMicrosatellite markersGenetic markersGenetic characterizationSpecies protectionGalapagos IslandsLa conservaciónWildlife tradeSpeciesJuvenile tortoisesTortoisesSan CristobalJuvenilesFirst documentation
2022
The Galapagos giant tortoise Chelonoidis phantasticus is not extinct
Jensen E, Gaughran S, Fusco N, Poulakakis N, Tapia W, Sevilla C, Málaga J, Mariani C, Gibbs J, Caccone A. The Galapagos giant tortoise Chelonoidis phantasticus is not extinct. Communications Biology 2022, 5: 546. PMID: 35681083, PMCID: PMC9184544, DOI: 10.1038/s42003-022-03483-w.Peer-Reviewed Original ResearchConceptsGalapagos giant tortoisesGiant tortoisesMitochondrial DNA phylogenyDNA phylogenyMonophyletic groupCarapace morphologyPhylogeny GroupSame lineagePopulation sizeSpeciesTortoisesLineagesFemale tortoisesSingle specimenSingle individualPhylogenyCladeGenomeExtinctSaddlebackContinued existenceIslandsDiscovery
2021
Chapter 7 Evolution and phylogenetics
Caccone A. Chapter 7 Evolution and phylogenetics. 2021, 117-138. DOI: 10.1016/b978-0-12-817554-5.00019-8.Peer-Reviewed Original ResearchGalapagos giant tortoisesGiant tortoise populationChapter 7 EvolutionEvolutionary historyRepopulation programsCaptive breedingGenetic diversityGiant tortoisesTortoise populationsDifferent islandsConservation programsPhylogeneticsTortoisesPhylogeographyHuman activitiesPhylogenyBreedingData helpYears of researchSpeciesNatural eventsDiversityCurrent patternsGalapagosEvolution
2019
Widespread hybridization among native and invasive species of Operophtera moths (Lepidoptera: Geometridae) in Europe and North America
Andersen J, Havill N, Broadley H, Boettner G, Caccone A, Elkinton J. Widespread hybridization among native and invasive species of Operophtera moths (Lepidoptera: Geometridae) in Europe and North America. Biological Invasions 2019, 21: 3383-3394. DOI: 10.1007/s10530-019-02054-1.Peer-Reviewed Original ResearchWinter mothNorth AmericaBruce spanwormInvasive winter mothWsp gene fragmentsCytochrome oxidase I.Polymorphic microsatellite lociNortheastern United StatesNative congenerInvasive speciesWidespread hybridizationGeographic extentCrop systemsField-collected mothsPresence of WolbachiaMoth individualsMicrosatellite lociHybrid individualsPCR amplificationSpeciesAmericaGene fragmentsMothBritish ColumbiaNova Scotia
2018
Editing nature: Local roots of global governance
Kofler N, Collins JP, Kuzma J, Marris E, Esvelt K, Nelson MP, Newhouse A, Rothschild LJ, Vigliotti VS, Semenov M, Jacobsen R, Dahlman JE, Prince S, Caccone A, Brown T, Schmitz OJ. Editing nature: Local roots of global governance. Science 2018, 362: 527-529. PMID: 30385564, DOI: 10.1126/science.aat4612.Peer-Reviewed Original ResearchConceptsLocal communitiesGene-editing techniquesContext-dependent impactsMost policy discussionsEcological disturbancesIsland habitatsCollective oversightClimate changeEvolutionary resistanceWild speciesLocal inputGene editingTarget mutationsSpeciesCommunityCRISPREnvironmental applicationsEcosystemsHabitatsResponsible applicationExtinctionProfound benefitsInternational levelUnprecedented capacityPolicy discussionsUrban 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 analysisDispersalUncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes
Gloria-Soria A, Dunn WA, Yu X, Vigneron A, Lee KY, Li M, Weiss BL, Zhao H, Aksoy S, Caccone A. Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. G3: Genes, Genomes, Genetics 2018, 8: 887-897. PMID: 29343494, PMCID: PMC5844309, DOI: 10.1534/g3.117.300493.Peer-Reviewed Original ResearchConceptsGenomic resourcesRelated speciesCandidate genesNonmodel organismsTranscript librariesFunctional genomicsTranscriptome assemblyFunctional annotationWild populationsPhysiological traitsGenomic regionsDNA regulationMost speciesRNAseq experimentsGenetic basisLaboratory coloniesGenesFunctional studiesPolymorphic sitesSpeciesTrypanosome infection statusGenomeNew assemblyTrypanosoma infectionFlies
2017
Self-righting potential and the evolution of shell shape in Galápagos tortoises
Chiari Y, van der Meijden A, Caccone A, Claude J, Gilles B. Self-righting potential and the evolution of shell shape in Galápagos tortoises. Scientific Reports 2017, 7: 15828. PMID: 29192279, PMCID: PMC5709378, DOI: 10.1038/s41598-017-15787-7.Peer-Reviewed Original ResearchIdentification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provides Founders for Species Restoration Program
Miller J, Quinzin M, Poulakakis N, Gibbs J, Beheregaray L, Garrick R, Russello M, Ciofi C, Edwards D, Hunter E, Tapia W, Rueda D, Carrión J, Valdivieso A, Caccone A. Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provides Founders for Species Restoration Program. Scientific Reports 2017, 7: 11471. PMID: 28904401, PMCID: PMC5597637, DOI: 10.1038/s41598-017-11516-2.Peer-Reviewed Original ResearchConceptsGiant tortoisesGalápagos giant tortoisesHuman-driven environmental changesCaptive breeding programsCaptive breeding centerSpecies restoration programsHigh ancestryFloreana IslandSpecies todayIsland ecosystemsBreeding programsGalápagos IslandsGenetic analysisBreeding CenterEnvironmental changesRestoration programsTortoisesSpeciesEcosystemsDistinctive morphologyAncestryUnprecedented rateIslandsTranslocationUnique opportunity
2016
I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation
Jensen E, Mooers A, Caccone A, Russello M. I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation. PeerJ 2016, 4: e2350. PMID: 27635324, PMCID: PMC5012326, DOI: 10.7717/peerj.2350.Peer-Reviewed Original ResearchPhylogenetic diversityConservation prioritizationMitochondrial control region dataCurrent biodiversity crisisTotal phylogenetic diversityImportance of speciesGiant Galápagos tortoisesControl region dataSubset of taxaEvolutionary distinctivenessBiodiversity crisisConservation effortsEvolutionary isolationExtinction probabilityInordinate lossGalápagos tortoisesList of rankingsAccount complementarityExtinct speciesEvolutionary historyPhylogenetic networksDiversitySpeciesTaxaPrioritizationPotential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors
Guevara EE, Veilleux CC, Saltonstall K, Caccone A, Mundy NI, Bradley BJ. Potential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors. American Journal Of Biological Anthropology 2016, 161: 181-185. PMID: 27393125, DOI: 10.1002/ajpa.23046.Peer-Reviewed Original ResearchConceptsSweet proteinNew sequence dataAmino acid sitesSeed dispersersProtein evolutionAccelerated evolutionBiochemical mimicryPrimate lineageGorilla lineagePositive selectionSequence dataGorilla dietCaloric gainArms raceWestern gorillasBrazzeinAfrican primatesProteinLineagesCoevolutionPentadiplandra brazzeanaLocal plantsSpeciesSweet signalsMutations
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
Analysis 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
2013
HUMAN IMPACTS HAVE SHAPED HISTORICAL AND RECENT EVOLUTION IN AEDES AEGYPTI, THE DENGUE AND YELLOW FEVER MOSQUITO
Brown JE, Evans BR, Zheng W, Obas V, Barrera‐Martinez L, Egizi A, Zhao H, Caccone A, Powell JR. HUMAN IMPACTS HAVE SHAPED HISTORICAL AND RECENT EVOLUTION IN AEDES AEGYPTI, THE DENGUE AND YELLOW FEVER MOSQUITO. Evolution 2013, 68: 514-525. PMID: 24111703, PMCID: PMC3946797, DOI: 10.1111/evo.12281.Peer-Reviewed Original ResearchConceptsYellow fever mosquitoSingle nucleotide polymorphism (SNP) markersHuman trade routesPatterns of domesticationArthropod disease vectorsDomestic formsNuclear genesEcological overlapEvolutionary historyDomestic AePolymorphism markersNovel nichesDNA sequencesGenetic dataEvolutionary processesDisease vectorsGenetic studiesSuch speciesLater invasionDNA sequencingNew WorldSpeciesAnthropogenic impactsHuman impactAnthropogenic forcesGeographic 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
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 effortsGenetic 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 ResearchConceptsFloreana IslandHybrid individualsGiant tortoise speciesUnique evolutionary lineagesGiant Galápagos tortoisesCaptive breeding programsEvolutionary lineagesGalápagos tortoisesHybrid offspringExtinct speciesGenetic footprintsTortoise speciesBreeding programsGalápagos IslandsGenetic signaturesExtant individualsIsabela IslandGenomeSpeciesMixed ancestryTortoisesAncestryIslandsLineagesLikely mechanism
2011
DNA barcodes and molecular diagnostics to distinguish an introduced and native Laricobius (Coleoptera: Derodontidae) species in eastern North America
Davis G, Havill N, Adelman Z, Caccone A, Kok L, Salom S. DNA barcodes and molecular diagnostics to distinguish an introduced and native Laricobius (Coleoptera: Derodontidae) species in eastern North America. Biological Control 2011, 58: 53-59. DOI: 10.1016/j.biocontrol.2011.03.016.Peer-Reviewed Original ResearchBiological control agentsDNA barcodesL. nigrinusControl agentsDistinctive morphological charactersSpecies-specific assaysHemlock Woolly AdelgidPowerful identification toolEastern North AmericaMorphological charactersRestriction length polymorphismDNA sequencesLaricobius rubidusNucleotide differencesLaricobius speciesMolecular diagnosticsReal-time PCRWoolly AdelgidCoastal populationsLaricobius nigrinusNigrinusAvailable lab equipmentLength polymorphismSpeciesEastern United StatesPolyandry Is a Common Event in Wild Populations of the Tsetse Fly Glossina fuscipes fuscipes and May Impact Population Reduction Measures
Bonomi A, Bassetti F, Gabrieli P, Beadell J, Falchetto M, Scolari F, Gomulski LM, Regazzini E, Ouma JO, Caccone A, Okedi LM, Attardo GM, Guglielmino CR, Aksoy S, Malacrida AR. Polyandry Is a Common Event in Wild Populations of the Tsetse Fly Glossina fuscipes fuscipes and May Impact Population Reduction Measures. PLOS Neglected Tropical Diseases 2011, 5: e1190. PMID: 21666797, PMCID: PMC3110164, DOI: 10.1371/journal.pntd.0001190.Peer-Reviewed Original ResearchConceptsEffective population sizePopulation sizeInformative microsatellite lociNumber of matingsTsetse Fly GlossinaFemale rematingWild populationsReproductive biologyMicrosatellite lociFemale matesSterile malesDifferent matesFemale spermathecaeRematingReproductive potentialPolyandryDirect countsPopulation age structureFuscipesLake VictoriaSpermathecaeWildMatesDry seasonSpecies
2010
Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010–31 March 2010
Consortium M, AURELLE D, BAKER A, BOTTIN L, BROUAT C, CACCONE A, CHAIX A, DHAKAL P, DING Y, DUPLANTIER J, FIEDLER W, FIETZ J, FONG Y, FORCIOLI D, FREITAS T, GUNNARSSON G, HADDRATH O, HADZIABDIC D, HAUKSDOTTIR S, HAVILL N, HEINRICH M, HEINZ T, HJORLEIFSDOTTIR S, HONG Y, HREGGVIDSSON G, HUCHETTE S, HURST J, KANE M, KANE N, KAWAKAMI T, KE W, KEITH R, KLAUKE N, KLEIN J, KUN J, LI C, LI G, LI J, LOISEAU A, LU L, LUCAS M, MARTINS‐FERREIRA C, MOKHTAR‐JAMAÏ K, OLAFSSON K, PAMPOULIE C, PAN L, POOLER M, REN J, RINEHART T, ROUSSEL V, SANTOS M, SCHAEFER H, SCHEFFLER B, SCHMIDT A, SEGELBACHER G, SHEN J, SKIRNISDOTTIR S, SOMMER S, TAO Z, TAUBERT R, TIAN Y, TOMIUK J, TRIGIANO R, UNGERER M, Van WORMHOUDT A, WADL P, WANG D, WEIS‐DOOTZ T, XIA Q, YUAN Q. Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010–31 March 2010. Molecular Ecology Resources 2010, 10: 751-754. PMID: 21565086, DOI: 10.1111/j.1755-0998.2010.02871.x.Peer-Reviewed Original ResearchMolecular Ecology Resources DatabasePermanent Genetic ResourcesMicrosatellite marker lociParamuricea clavataGenetic resourcesHelianthus maximilianiCercis canadensisLaricobius rubidusMarker lociApodemus flavicollisLaricobius osakensisGlis glisHaliotis tuberculataApodemus sylvaticusLaricobius nigrinusAnser cygnoidesOenanthe javanicaLociSamanea samanSpeciesMaximilianiClavataFlavicollisCanadensisResource database