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 ResearchConceptsGalapagos 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 historyChapter 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
2017
Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study
Gaughran S, Quinzin M, Miller J, Garrick R, Edwards D, Russello M, Poulakakis N, Ciofi C, Beheregaray L, Caccone A. Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study. Evolutionary Applications 2017, 11: 1084-1093. PMID: 30026799, PMCID: PMC6050186, DOI: 10.1111/eva.12551.Peer-Reviewed Original ResearchGalápagos giant tortoisesSingle nucleotide polymorphismsGenetic differentiationPopulation structureGiant tortoisesRecent single nucleotide polymorphismGenomewide single nucleotide polymorphismsGenomic single nucleotide polymorphismsGiant tortoise speciesHigh-throughput DNA sequencingStructured natural populationsHundreds of SNPsThousands of SNPsPopulation genetics theoryTraditional genetic markersAge of genomicsMitochondrial DNA analysisNonmodel organismsNonmodel speciesEvolutionary historyNatural populationsGenetic theoryTortoise speciesUnnatural groupingGenomic dataGenomic insights into the ancient spread of Lyme disease across North America
Walter KS, Carpi G, Caccone A, Diuk-Wasser MA. Genomic insights into the ancient spread of Lyme disease across North America. Nature Ecology & Evolution 2017, 1: 1569-1576. PMID: 29185509, PMCID: PMC6431794, DOI: 10.1038/s41559-017-0282-8.Peer-Reviewed Original ResearchConceptsHistory of spreadEvolutionary historyNorth AmericaLyme disease epidemicLast Glacial MaximumAncient spreadLyme disease bacteriaComplex evolutionary historyPast centuryGlacial MaximumHistoryGenomic insightsEvolutionary changeAmericaUndocumented levelB. burgdorferi s.Large collectionSensu strictoBurgdorferi s.Vector-borne diseasesSouthern CanadaLand use changeBorrelia burgdorferi sensu strictoCenturyDisease bacteria
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 networksDiversitySpeciesTaxaPrioritizationEcological and evolutionary influences on body size and shape in the Galápagos marine iguana (Amblyrhynchus cristatus)
Chiari Y, Glaberman S, Tarroso P, Caccone A, Claude J. Ecological and evolutionary influences on body size and shape in the Galápagos marine iguana (Amblyrhynchus cristatus). Oecologia 2016, 181: 885-894. PMID: 27041683, DOI: 10.1007/s00442-016-3618-1.Peer-Reviewed Original ResearchConceptsGalápagos marine iguanasMarine iguanasEvolutionary historyBody sizeGenetic adaptationBody size variationSexual dimorphismHigh morphological diversityStrong sexual dimorphismContribution of plasticityShape variationPhylogeographic patternsMultiple colonizationsEndemic speciesLocal adaptationEvolutionary changeMorphological diversityEvolutionary influencesDistribution rangeOceanic islandsSource populationIguanasEnvironmental conditionsSize variationMorphological measurements
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 ResearchConceptsGalápagos 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 islands
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 forces
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 ResearchConceptsGiant 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 variability
2010
Anopheles Immune Genes and Amino Acid Sites Evolving Under the Effect of Positive Selection
Parmakelis A, Moustaka M, Poulakakis N, Louis C, Slotman MA, Marshall JC, Awono-Ambene PH, Antonio-Nkondjio C, Simard F, Caccone A, Powell JR. Anopheles Immune Genes and Amino Acid Sites Evolving Under the Effect of Positive Selection. PLOS ONE 2010, 5: e8885. PMID: 20126662, PMCID: PMC2811201, DOI: 10.1371/journal.pone.0008885.Peer-Reviewed Original ResearchConceptsPositive selectionImmune genesGambiae complexDN/dS ratiosLineage-specific evolutionPopulation genetics frameworkAmino acid sitesAnopheles gambiae complexSpecific amino acidsInnate immunity genesAncestral polymorphismComparative phylogeneticsGene diversityEvolutionary historyNatural populationsGenetic diversityGenetic frameworkNatural selectionImmunity genesVector biologyDS ratiosGenesAmino acidsDiversityGenetic knowledge
2008
Colonization and diversification of Galpagos terrestrial fauna: a phylogenetic and biogeographical synthesis
Parent C, Caccone A, Petren K. Colonization and diversification of Galpagos terrestrial fauna: a phylogenetic and biogeographical synthesis. Philosophical Transactions Of The Royal Society B Biological Sciences 2008, 363: 3347-3361. PMID: 18782729, PMCID: PMC2607378, DOI: 10.1098/rstb.2008.0118.Peer-Reviewed Original ResearchConceptsTerrestrial faunaPhylogenetic studiesDivergence of populationsSimilar geological historyDistinct evolutionary historiesMolecular phylogenetic studiesRemote oceanic islandsRange of organismsStudy of diversificationHabitat specializationBiogeographical synthesisGeological historyLow vagilityDiverse habitatsEvolutionary historyGeological formationsOceanic islandsGroup of islandsGalápagos IslandsRemarkable settingUnique assemblageComparable climateEvolutionary processesFaunaIslands
2006
Ancient 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 viewIslandsMammothsMammuthusSequenceMolecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area
Ketmaier V, Giusti F, Caccone A. Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area. Molecular Phylogenetics And Evolution 2006, 39: 439-451. PMID: 16442313, DOI: 10.1016/j.ympev.2005.12.008.Peer-Reviewed Original ResearchConceptsMolecular clock estimatesClock estimatesPeri-Tyrrhenian areaSardinia-Corsica microplateMain cladogenetic eventsNuclear genesVicariant processesCladogenetic eventsHistorical biogeographyMolecular phylogenyPhylogenetic resultsPhylogenetic relationshipsEvolutionary historyPhylogenetic hypothesisSister taxaInsular rangeGenetic relationshipsCalcareous substratesCorsica-Sardinia microplateMiddle–late PlioceneGenusSpeciesItalian peninsulaMiddle MioceneElba Island
2005
A rapid loss of stripes: the evolutionary history of the extinct quagga
Leonard J, Rohland N, Glaberman S, Fleischer R, Caccone A, Hofreiter M. A rapid loss of stripes: the evolutionary history of the extinct quagga. Biology Letters 2005, 1: 291-295. PMID: 17148190, PMCID: PMC1617154, DOI: 10.1098/rsbl.2005.0323.Peer-Reviewed Original ResearchConceptsEvolutionary historyDNA sequencesShort mitochondrial DNA sequencesMitochondrial DNA sequencesPlains zebraLittle genetic diversityPleistocene climate changePhylogeographic patternsGenetic diversityHolarctic faunaExtinct quaggaFirst extinct speciesAncient DNAExtinct speciesMuseum skinsGenetic informationQuaggaZebraDNARapid lossGlacial MaximumSequenceClimate changeFaunaSpecies
2002
Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises
Ciofi C, Milinkovitch M, Gibbs J, Caccone A, Powell J. Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises. Molecular Ecology 2002, 11: 2265-2283. PMID: 12406238, DOI: 10.1046/j.1365-294x.2002.01617.x.Peer-Reviewed Original ResearchConceptsGiant Galápagos tortoisesGenetic divergenceGalápagos tortoisesIsland populationsVolcan WolfIndividual island populationsIslands of IsabelaGene flowAdaptive differentiationGenetic structureMtDNA diversityExtant populationsColonization eventsEvolutionary historyMicrosatellite lociDifferent taxaAllelic similarityHeavy exploitationDNA workMicrosatellite analysisDeterministic threatsDistinct populationsTortoisesInteresting modelDivergence
1986
Genetic variability and divergence between cave dwelling populations of Typhlocirolana from majorca and sicily
Caccone A, Allegrucci G, Cesaroni D, Sbordoni M, de Matthaeis E, La Rosa G, Sbordoni V. Genetic variability and divergence between cave dwelling populations of Typhlocirolana from majorca and sicily. Biochemical Systematics And Ecology 1986, 14: 215-221. DOI: 10.1016/0305-1978(86)90066-9.Peer-Reviewed Original ResearchGenetic distance dataSicilian populationFreshwater systemsMarine ancestorsEvolutionary historyGenetic distanceTaxonomic statusSeparate speciesGenetic variabilityGene locusTyphlocirolanaPresent distributionSpeciesSouthern Mediterranean coastElectrophoretic analysisRecent discoveryBalearic IslandsHypogean crustaceansMediterranean coastThalassoidAncestorCrustaceansDistance dataUpper MioceneSicilian samples