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
2017
Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya
Okeyo WA, Saarman NP, Mengual M, Dion K, Bateta R, Mireji PO, Okoth S, Ouma JO, Ouma C, Ochieng J, Murilla G, Aksoy S, Caccone A. Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya. Parasites & Vectors 2017, 10: 471. PMID: 29017572, PMCID: PMC5635580, DOI: 10.1186/s13071-017-2415-y.Peer-Reviewed Original ResearchConceptsTemporal genetic differentiationGenetic diversityGenetic differentiationGenetic bottleneckGenetic variationNational ParkTemporal genetic variationExtensive control measuresAnimal African trypanosomiasisAllelic richnessPairwise FSTGenetic driftNe estimatesHabitat alterationPopulation geneticsTemporal differentiationMicrosatellite markersRuma National ParkClosest sampling sitesG. pallidipesMajor vectorTsetse fliesVector populationsDifferentiationDiversityMultiple evolutionary origins of Trypanosoma evansi in Kenya
Kamidi CM, Saarman NP, Dion K, Mireji PO, Ouma C, Murilla G, Aksoy S, Schnaufer A, Caccone A. Multiple evolutionary origins of Trypanosoma evansi in Kenya. PLOS Neglected Tropical Diseases 2017, 11: e0005895. PMID: 28880965, PMCID: PMC5605091, DOI: 10.1371/journal.pntd.0005895.Peer-Reviewed Original ResearchConceptsT. brucei strainsDifferent genetic backgroundsEvolutionary originGenetic diversityBrucei strainsMultiple evolutionary originsGenetic backgroundTsetse fly vectorT. evansiLethal human diseaseIndependent originsPolymorphic microsatellitesT. bruceiEvansi isolatesGenetic unitsHuman diseasesObligate linkBruceiEvansi strainsT. brucei bruceiTsetse fliesFly vectorsFliesDiversityBrucei brucei
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 strategyDiversityI-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 networksDiversitySpeciesTaxaPrioritizationVectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity
Walter KS, Carpi G, Evans BR, Caccone A, Diuk-Wasser MA. Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity. PLOS Pathogens 2016, 12: e1005759. PMID: 27414806, PMCID: PMC4944968, DOI: 10.1371/journal.ppat.1005759.Peer-Reviewed Original ResearchConceptsPathogen diversityPositive selectionVertebrate hostsHost pathogen diversityLyme disease bacteriaNatural transmission cycleNatural populationsPathogen evolutionGenomic variationHost diversityMajority of ticksHost processesDiverse inoculumUndocumented levelEvolutionary processesTick diversityDisease vectorsMixed strain infectionsImmune complementIndividual ticksDiversityEpidemiological sentinelsTick vectorTransmission cycleHost
2014
Cryptic structure and niche divergence within threatened Galápagos giant tortoises from southern Isabela Island
Edwards D, Garrick R, Tapia W, Caccone A. Cryptic structure and niche divergence within threatened Galápagos giant tortoises from southern Isabela Island. Conservation Genetics 2014, 15: 1357-1369. DOI: 10.1007/s10592-014-0622-z.Peer-Reviewed Original ResearchSouthern Isabela IslandGalápagos giant tortoisesGenetic clustersIsabela IslandGiant tortoisesMorphological diversityRecent gene flowBiodiversity lossConservation managementEcological divergenceSignificant unitsNiche divergenceFeral animalsEcological factorsGenetic differentiationEcological nichesGene flowCryptic structureMicrosatellite lociManagement successSpatial distributionCurrent taxonomyTortoisesManagement programDiversity
2013
Glossina 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 outcomesGeneticsFuscipesDiversityPopulation
2010
Genetic Differentiation between Marine Iguanas from Different Breeding Sites on the Island of Santa Fé (Galápagos Archipelago)
Lanterbecq D, Glaberman S, Vitousek M, Steinfartz S, Benavides E, Wikelski M, Caccone A. Genetic Differentiation between Marine Iguanas from Different Breeding Sites on the Island of Santa Fé (Galápagos Archipelago). Journal Of Heredity 2010, 101: 663-675. PMID: 20538757, DOI: 10.1093/jhered/esq067.Peer-Reviewed Original ResearchConceptsMarine iguanasGenetic diversitySex-biased dispersalMitochondrial control regionMitochondrial DNA markersGalápagos marine iguanasSanta FéDifferent breeding sitesSouthern sitesGenetic differentiationEvolutionary signalGenetic structureMicrosatellite lociDNA markersControl regionGenetic variationGenetic patternsBreeding sitesLittle differentiationBase pairsNeighboring islandsIguanasDiversitySampling sitesDifferentiationInference of Population History by Coupling Exploratory and Model-Driven Phylogeographic Analyses
Garrick R, Caccone A, Sunnucks P. Inference of Population History by Coupling Exploratory and Model-Driven Phylogeographic Analyses. International Journal Of Molecular Sciences 2010, 11: 1190-1227. PMID: 20480016, PMCID: PMC2871112, DOI: 10.3390/ijms11041190.Peer-Reviewed Original ResearchConceptsPhylogeographic analysisGene treesGenetic diversityConservation managementPopulation historyDNA sequencesGenetic datasetsGenetic dataCladistic analysisHistorical inferencesPopulation processesTemporal concordanceSynergistic interactionDiversitySpeciationSpatial distributionSequenceGeographic contextTreesAnopheles 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
2006
A set of highly discriminating microsatellite loci for the Galápagos marine iguana Amblyrhynchus cristatus
STEINFARTZ S, CACCONE A. A set of highly discriminating microsatellite loci for the Galápagos marine iguana Amblyrhynchus cristatus. Molecular Ecology Resources 2006, 6: 927-929. DOI: 10.1111/j.1471-8286.2006.01402.x.Peer-Reviewed Original ResearchGenetic Divergence of Connecticut Melanoplus femurrubrum Populations
Lee J, Marshall J, Schmitz O, Caccone A. Genetic Divergence of Connecticut Melanoplus femurrubrum Populations. Journal Of Heredity 2006, 97: 290-293. PMID: 16598036, DOI: 10.1093/jhered/esj027.Peer-Reviewed Original ResearchConceptsGenetic diversityHigh mitochondrial diversityNuclear gene regionsAT-rich genesHigh sequence divergenceFixation index analysisMultiple genetic markersPhylogeographic patternsMitochondrial diversityMolecular varianceGenetic divergenceSequence divergenceEqual diversityGenetic variationLittle divergenceGene regionGenetic markersPopulation-level studiesITS1 geneGenesDiversityDivergenceSmall geographic areasND2Species
2005
A cryptic taxon of Galpagos tortoise in conservation peril
Russello M, Glaberman S, Gibbs J, Marquez C, Powell J, Caccone A. A cryptic taxon of Galpagos tortoise in conservation peril. Biology Letters 2005, 1: 287-290. PMID: 17148189, PMCID: PMC1617146, DOI: 10.1098/rsbl.2005.0317.Peer-Reviewed Original ResearchConceptsBiological diversityFormal taxonomic designationGenetic divergenceGalápagos tortoisesAccurate taxonomyDistinct lineagesTaxonomic investigationGenetic divisionTaxonomic designationsSingle taxonGiant tortoisesBad taxonomyEvolutionary heritageNew taxonTaxaAccessible islandsTortoisesHuman intellectual historyDiversityConservationSanta CruzTaxonomyLineagesGalápagosOrganisms
1987
Intraspecific DNA divergence in Drosophila: a study on parthenogenetic D. mercatorum.
Caccone A, Amato G, Powell J. Intraspecific DNA divergence in Drosophila: a study on parthenogenetic D. mercatorum. Molecular Biology And Evolution 1987, 4: 343-350. PMID: 3447012, DOI: 10.1093/oxfordjournals.molbev.a040451.Peer-Reviewed Original ResearchConceptsDNA-DNA hybridizationIntraspecific genetic variationInsertion/deletion differencesIntraspecific DNA variationSpecies of invertebratesFurther genetic differencesDNA divergenceDNA diversityDNA variationD. mercatorumIndependent genomesIntraspecific variationDrosophila mercatorumGenetic variationDNA differencesParthenogenetic strainsBase pair mismatchesGenetic differencesInvertebratesGenomeSpeciesHybridizationDrosophilaStrainsDiversity