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
Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program
Gray R, Fusco N, Miller J, Tapia W, Mariani C, Caccone A, Jensen E. Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program. Integrative And Comparative Biology 2022, 62: 1864-1871. PMID: 35906184, DOI: 10.1093/icb/icac129.Peer-Reviewed Original ResearchConceptsCaptive breeding programsBreeding programsEffective population sizeGalapagos giant tortoisesCaptive breedingGenetic diversityGenetic trackingReproductive outputSpecies restorationGiant tortoisesConservation managersBreeding outcomesMicrosatellite markersGenetic analysisMore foundersBreeding cyclePopulation sizeBreeding facilitiesTortoisesValue of hybridsParentageOffspringGenomeHybridsBreedingThe 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 existenceIslandsDiscoveryA new lineage of Galapagos giant tortoises identified from museum samples
Jensen E, Quinzin M, Miller J, Russello M, Garrick R, Edwards D, Glaberman S, Chiari Y, Poulakakis N, Tapia W, Gibbs J, Caccone A. A new lineage of Galapagos giant tortoises identified from museum samples. Heredity 2022, 128: 261-270. PMID: 35217806, PMCID: PMC8987048, DOI: 10.1038/s41437-022-00510-8.Peer-Reviewed Original ResearchConceptsGalapagos giant tortoisesMitochondrial control regionGiant tortoisesSingle nucleotide polymorphismsControl regionMuseum samplesGenome-wide single nucleotide polymorphismsDivergent mitochondrial lineagesSingle mitochondrial haplotypeContemporary populationsIconic radiationMitochondrial lineagesAdditional lineagesMitochondrial haplotypesNuclear markersSan CristóbalSecond lineageMicrosatellite lociNew lineagePinta IslandSame cladeEvolutionary processesLineagesGalapagos ArchipelagoEarly evolution
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
2020
Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule
Poulakakis N, Miller J, Jensen E, Beheregaray L, Russello M, Glaberman S, Boore J, Caccone A. Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. Journal Of Zoological Systematics & Evolutionary Research 2020, 58: 1262-1275. DOI: 10.1111/jzs.12387.Peer-Reviewed Original ResearchGalapagos giant tortoisesGiant tortoisesPhylogeographic scenarioMitochondrial genomeProgression rulePhylogenetic relationshipsGalapagos IslandsExtinct speciesOlder islandsHuman-mediated dispersal eventsComplete mitochondrial genomeSouth American ancestorAncestral area reconstructionNon-native speciesMaximum likelihood analysisContribution of colonizationColonization historyDispersal eventsMultiple colonizationsAmerican ancestorsPhylogenetic treeAncestral formArea reconstructionSitu speciationBiogeographic approach
2019
Seeking compromise across competing goals in conservation translocations: The case of the ‘extinct’ Floreana Island Galapagos giant tortoise
Hunter E, Gibbs J, Cayot L, Tapia W, Quinzin M, Miller J, Caccone A, Shoemaker K. Seeking compromise across competing goals in conservation translocations: The case of the ‘extinct’ Floreana Island Galapagos giant tortoise. Journal Of Applied Ecology 2019, 57: 136-148. DOI: 10.1111/1365-2664.13516.Peer-Reviewed Original ResearchConservation translocationsSingle-objective solutionsDecision support toolGiant tortoisesIndividual-based simulation modelGalapagos giant tortoisesGeneralized Additive ModelsEcosystem servicesTranslocation projectsFloreana IslandIsland speciesManagement objectivesSevere declineSupport toolNumber of individualsModel-based decision support toolSource populationGalapagos IslandsStakeholder valuesManagement strategiesMulti-objective solutionsOptimal management strategyAdditive modelTortoisesCost constraints
2018
Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head‐starting in a Galapagos giant tortoise
Jensen E, Edwards D, Garrick R, Miller J, Gibbs J, Cayot L, Tapia W, Caccone A, Russello M. Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head‐starting in a Galapagos giant tortoise. Evolutionary Applications 2018, 11: 1811-1821. PMID: 30459831, PMCID: PMC6231475, DOI: 10.1111/eva.12682.Peer-Reviewed Original ResearchGiant tortoisesBottleneck eventsGenetic diversityGenetic variationPopulation declineTortoise populationsPopulation sizeCurrent genetic diversityEffective population sizePopulation genetics theoryWide single nucleotide polymorphism dataCaptive breeding programsRapid demographic recoveryRecent population declineSingle nucleotide polymorphism dataGalapagos giant tortoisesNucleotide polymorphism dataRapid population declineLarge population sizesPopulation genomicsSpecies restorationLong-term persistencePopulation structureGenetic patternsGenetic theoryGenome-Wide Assessment of Diversity and Divergence Among Extant Galapagos Giant Tortoise Species
Miller J, Quinzin M, Edwards D, Eaton D, Jensen E, Russello M, Gibbs J, Tapia W, Rueda D, Caccone A. Genome-Wide Assessment of Diversity and Divergence Among Extant Galapagos Giant Tortoise Species. Journal Of Heredity 2018, 109: 611-619. PMID: 29986032, DOI: 10.1093/jhered/esy031.Peer-Reviewed Original ResearchConceptsGiant tortoise speciesMitochondrial DNA sequencesSingle nucleotide polymorphismsTortoise speciesGenetic diversityMicrosatellite lociDNA sequencesGenotypic dataMicrosatellite genotypic dataNuclear microsatellite lociGenome-wide markersEstimates of diversityGenome-wide assessmentGalapagos giant tortoisesSpecies radiationEvolutionary geneticsSignificant unitsMitochondrial DNAPopulation structureSpecies conservationGenetic lineagesGiant tortoisesPopulation delineationTortoise populationsDNA sequencingGenetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island
Miller J, Quinzin M, Scheibe E, Ciofi C, Villalva F, Tapia W, Caccone A. Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island. Journal Of Heredity 2018, 109: 620-630. PMID: 29490038, DOI: 10.1093/jhered/esy010.Peer-Reviewed Original ResearchConceptsReproductive skewGalapagos giant tortoisesBreeding programsFloreana IslandGiant tortoisesAssortative matingSelf-sustaining wild populationsGenetic pedigree analysisMajority of progenyCaptive breeding programsSmall breeding groupsOrigin of individualsPedigree analysisLarge breeding programsFounding individualsWild populationsAllelic diversityGenetic diversityExtinct tortoisesGenetic variationGenetic analysisC. nigerPopulation sizeRelated individualsBreeding groups