Adalgisa Caccone
Senior Research Scientist and Lecturer in Ecology and Evolutionary BiologyCards
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2025
Urban refuge? Squirrel pigmentation clines maintained by strong natural selection beyond city limits
Bonar M, Blumenfeld A, Fusco N, Campagna L, Timpson A, Thomas M, Cosentino B, Gibbs J, Caccone A. Urban refuge? Squirrel pigmentation clines maintained by strong natural selection beyond city limits. 2025 DOI: 10.21203/rs.3.rs-6967993/v1.Peer-Reviewed Original ResearchGenome sequenceDemographic modelsNatural selectionCoat colour polymorphismWhole-genome sequencingMelanocortin 1 receptor geneEastern gray squirrelsColour polymorphismTrait variationGenetic diversityGenomic backgroundGenomic dataPigmentation clineSelection landscapeMC1R allelesPhenotypic traitsModel of selectionVertebrate speciesClineMelanic morphsSciurus carolinensisSelection pressureCoat colorGrey squirrelsEvolutionary processPopulation Genetic Structure of Azara's Owl Monkey (Aotus azarae) From Northern Argentina: Insights Into Gene Flow and Dispersal Patterns in a Pair‐Living Primate
Corley M, Burchfield K, Fusco N, Fernandez‐Duque E, Caccone A. Population Genetic Structure of Azara's Owl Monkey (Aotus azarae) From Northern Argentina: Insights Into Gene Flow and Dispersal Patterns in a Pair‐Living Primate. American Journal Of Primatology 2025, 87: e70045. PMID: 40407255, DOI: 10.1002/ajp.70045.Peer-Reviewed Original ResearchConceptsPopulation genetic structureGene flowPair-living primatesAzara's owl monkeysGenetic structureGenetic differentiationGenetic diversityModerate level of genetic differentiationPattern of isolation-by-distanceGallery forestLevel of genetic differentiationPatterns of genetic diversityPatterns of gene flowEffects of habitat lossIsolation-by-distanceMitochondrial DNA sequencesAotus azaraeDispersal patternsNorthern ArgentinaSouth American Gran ChacoGran ChacoEvaluate dispersion patternsPatches of forestConservation management strategiesAssignment testsSynteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity
Jensen E, Marchisio C, Ochoa A, Gray R, Parra V, Miller J, Çilingir F, Caccone A. Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity. Ecology And Evolution 2025, 15: e71358. PMID: 40290375, PMCID: PMC12032190, DOI: 10.1002/ece3.71358.Peer-Reviewed Original ResearchContiguous genomeGiant tortoisesGenome assemblyGalapagos giant tortoisesChromosome-level genome assemblySynteny-based methodsGenome resequencing dataEstimates of inbreedingWhole-genome sequencingHigh-quality DNAAldabra giant tortoiseReference genomeResequencing dataComplete genomeImproved genomeSpecies groupsExtinct speciesGenomeTortoisesHomozygositySpeciesSequenceAssemblyImprove inferenceGalapagosConstraint Optimisation Approaches for Designing Group-Living Captive Breeding Programmes
Forshaw M, Gray R, VonHoldt B, Ochoa A, Miller J, Brzeski K, Caccone A, Jensen E. Constraint Optimisation Approaches for Designing Group-Living Captive Breeding Programmes. Proceedings Of The AAAI Conference On Artificial Intelligence 2025, 39: 27989-27997. DOI: 10.1609/aaai.v39i27.35016.Peer-Reviewed Original ResearchCaptive breeding programsBreeding program designsBreeding programsCaptive populationsEffective population sizeCaptive breeding programmesGalapagos giant tortoisesMultiple malesPrevent inbreedingCaptive breeding centresSpecies ecologyBreeding pairsReintroduction effortsGenetic healthBreeding programmesGiant tortoisesBreed groupsBreeding centresEndangered speciesBiodiversity crisisPopulation sizeBreedingRelatednessSpeciesComputational toolsPopulation Structure of the Invasive Asian Tiger Mosquito, Aedes albopictus, in Europe
Corley M, Cosme L, Armbruster P, Beebe N, Bega A, Boyer S, Caputo B, Chen C, Crawford J, della Torre A, Eritja R, Fontaine M, Gill R, Huynh T, Kadriaj P, Maringer K, Martins A, Maynard A, Mukherjee S, Munstermann L, Pichler V, Sharakhova M, Surendran S, Urbanelli S, Velo E, Wahid I, Akiner M, Balatsos G, Besnard G, Borg M, Bravo‐Barriga D, Marí R, Collantes F, Horvath C, Kavran M, Medialdea‐Carrera R, Melillo T, Michaelakis A, Mikov O, Puggioli A, Rogozi E, Schaffner F, Hackett K, Johnson T, Wu T, Pinto J, Valadas V, Caccone A. Population Structure of the Invasive Asian Tiger Mosquito, Aedes albopictus, in Europe. Ecology And Evolution 2025, 15: e71009. PMID: 40060725, PMCID: PMC11886418, DOI: 10.1002/ece3.71009.Peer-Reviewed Original ResearchGenetic structureMicrosatellite datasetNative rangePatterns of genetic differentiationPopulation genetic structureInvasive European populationsOrigin of invasionEuropean populationsAsian tiger mosquitoGenetic differentiationMicrosatellite lociSNP dataGenetic clustersSNP chipPopulation structureGenetic markersGenetic ancestryTiger mosquitoSampling effortSNPsInvasive mosquito speciesMicrosatelliteMosquito speciesAedes albopictusGenotypes
2024
Whole-genome sequencing confirms multiple species of Galapagos giant tortoises
Gaughran S, Gray R, Ochoa A, Jones M, Fusco N, Miller J, Poulakakis N, de Queiroz K, Caccone A, Jensen E. Whole-genome sequencing confirms multiple species of Galapagos giant tortoises. Evolution 2024, 79: 296-308. PMID: 39548869, DOI: 10.1093/evolut/qpae164.Peer-Reviewed Original ResearchInbreeding 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 conflictsMatingMammalsA 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
2023
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)
Fusco N, Cosentino B, Gibbs J, Allen M, Blumenfeld A, Boettner G, Carlen E, Collins M, Dennison C, DiGiacopo D, Picard A, Edmonson J, Fisher‐Reid M, Fyffe R, Gallo T, Grant A, Harbold W, Heard S, Lafferty D, Lehtinen R, Marino S, McDonald J, Mortelliti A, Murray M, Newman A, Oswald K, Ott‐Conn C, Richardson J, Rimbach R, Salaman P, Steele M, Stothart M, Urban M, Vandegrift K, Vanek J, Vanderluit S, Vezina L, Caccone A. Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis). Molecular Ecology 2023, 33: e17230. PMID: 38078558, DOI: 10.1111/mec.17230.Peer-Reviewed Original ResearchGalapagos 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
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