Gary Bernardi, APRN, RN
Staff Affiliate in Emergency MedicineAbout
Research
Publications
2026
The origin of cichlids: The controversial phylogenomics of the convict fish, Pholidichthys leucotaenia
Witte E, Yamamoto S, Salazar-Sawkins A, Hinojosa N, Toy J, Chen C, Abdel-Raheem S, Johns J, Bernardi G. The origin of cichlids: The controversial phylogenomics of the convict fish, Pholidichthys leucotaenia. Molecular Phylogenetics And Evolution 2026, 219: 108581. PMID: 41740731, DOI: 10.1016/j.ympev.2026.108581.Peer-Reviewed Original ResearchConceptsDiverse group of freshwater fishesGroup of freshwater fishesUltra-conserved elementsNuclear phylogeniesBUSCO genesTaxon samplingGenome sizeMaximum parsimonyMitochondrial genomeSister taxaEvolutionary relationshipsSister relationshipPhylogenetic analysisCoral TriangleGenomic differencesMolecular dataDiverse groupFamily CichlidaeCichlidsEvolutionary biologyFreshwater fishMarine fishGenomeTaxaSister
2025
Composition and conservation status of rays sold in Baja California Sur, Mexico
Ossiander I, Bernardi G, Palacios M, Croll D, Zilliacus K, Trejo‐Ramirez A, Roberts M, Munguia‐Vega A, Perez‐Palafox X, Ahuja P, Gonzalez‐Armas R, Cronin M. Composition and conservation status of rays sold in Baja California Sur, Mexico. Conservation Science And Practice 2025, 7 DOI: 10.1111/csp2.70164.Peer-Reviewed Original ResearchBaja California SurSpecies compositionConservation statusPopulation declineSmall-scale fisheriesGlobal population declineIUCN Red ListIdentity of speciesLife history characteristicsBycatch fishFishing practicesDevil raysRed ListRay speciesAbstract SharksHarvested fishHypanus dipterurusGymnura marmorataHistory characteristicsIndividual speciesMexican PacificButterfly rayFish marketsSpecies identityDiamond stingrayPopulation Genomics, Local Adaptation and Cryptic Speciation in a Temperate Reef Fish, the Black Surfperch, Embiotoca jacksoni, Using Genome‐Wide Resequencing
Toy J, Oulès A, Longo G, Shaffer H, Bernardi G. Population Genomics, Local Adaptation and Cryptic Speciation in a Temperate Reef Fish, the Black Surfperch, Embiotoca jacksoni, Using Genome‐Wide Resequencing. Molecular Ecology 2025, 34: e70073. PMID: 40787783, DOI: 10.1111/mec.70073.Peer-Reviewed Original ResearchIsolation-by-distanceLocal adaptationCryptic speciationBlack surfperchEmbiotoca jacksoniWhole-genome resequencingProcess of speciationGenome-wide resequencingTemperate reef fishPelagic larval stageResponses to climate changeFST estimatesGenetic differentiationGenome resequencingGenetic structureCryptic speciesGene flowPopulation genomicsReproductive isolationGenome-wideGenetic divergenceGenetic driftReef fishesReproductive barriersSperm-eggA new species of Anemonefish from French Polynesia, Amphiprion maohiensis, (Pomacentridae, Amphiprioninae), the Polynesian anemonefish
O’Donnell J, Beldade R, Johns J, Bernardi G. A new species of Anemonefish from French Polynesia, Amphiprion maohiensis, (Pomacentridae, Amphiprioninae), the Polynesian anemonefish. ZooKeys 2025, 1244: 225-237. PMID: 40687518, PMCID: PMC12272074, DOI: 10.3897/zookeys.1244.141409.Peer-Reviewed Original ResearchFrench PolynesiaSpecies of anemonefishSpecies of damselfishCryptic speciesColour morphsGenome sequenceMitochondrial markersAnemonefishDistribution rangeSea anemonesGenetic resultsIndo-PacificWhite-tailedMorphsSpeciesPolynesiaIsolated islandsDamselfishGenomeAmphiprionAnemonesIslandsSequencePotential presenceMarshall Islands
2024
Coalition-building for labor actions in life sciences departments: lessons from the largest academic strike in history
Ellis A, Beck J, Howard E, Rabearisoa A, Alissa L, Barasi S, Beltran R, Bernardi G, Bernier K, Cronin M, Cruz N, Flores I, Gerraty F, Goetz L, Harenčár J, Kroeker K, Kurle C, Lai E, Lederman-Beach R, Malakooti N, Mason S, McElfish M, McNelis M, Molinari M, Munro C, Nazario E, Payne A, Poudel S, Rivera M, Slimp M, Sridhar N, Tershy B, Third G, Uckele K, Vilches F, Walker B, Wishingrad V, Witte E, Yeager M, Young J, Zilliacus K, Croll D. Coalition-building for labor actions in life sciences departments: lessons from the largest academic strike in history. BioScience 2024, 75: 152-162. DOI: 10.1093/biosci/biae123.Peer-Reviewed Original ResearchGraduate student unionizationLabor strikesImproved payLabor actionsWorkplace challengesSimultaneously workersLow wagesDepartmental levelCommunication strategiesInadequate benefitsGraduate workersCoalition buildingWorking conditionsWorkersStudent unionsDiverse concernsPayEquityCoalition-buildingLaborAcademic environmentA Genomic Contribution to the Classification of the Blennioid Fishes of the Family Clinidae
Wright D, Bernardi G. A Genomic Contribution to the Classification of the Blennioid Fishes of the Family Clinidae. Ichthyology & Herpetology 2024, 112: 544-551. DOI: 10.1643/i2023043.Peer-Reviewed Original ResearchThe genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile
Bernardi G, Kavembe G, Bergman H, Bucciarelli G, Wood C. The genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile. Journal Of Great Lakes Research 2024, 50: 102326. DOI: 10.1016/j.jglr.2024.102326.Peer-Reviewed Original ResearchGC-rich isochoresGC-rich regionBase compositionLake Magadi tilapiaGC-poorRepetitive elementsGC-rich genomic regionsGC-poor genomeRepetitive element analysisProtein coding genesGenomes of vertebratesMagadi tilapiaNile tilapiaGenome organizationGenome sequenceGC-richGenomic regionsCoding genesGenomeHot-waterNatural selectionAlcolapia grahamiFish speciesTilapiaCichlidsWhole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific
Gatins R, Arias C, Sánchez C, Bernardi G, De León L. Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific. Gigabyte 2024, 2024: 1-18. PMID: 38550358, PMCID: PMC10973836, DOI: 10.46471/gigabyte.115.Peer-Reviewed Original ResearchBenchmarking Universal Single-Copy OrthologsTropical eastern PacificGenome assemblyPopulation expansionMarine fishUniversal Single-Copy OrthologsAnnotated genome assemblyGenome assembly sizeSingle-copy orthologsWhole-genome assemblyProtein-coding genesIsthmus of PanamaContig N50Illumina readsNuclear genomeGenomic resourcesDemographic historyRepetitive elementsMolecular resourcesHolacanthus passerLocal adaptationEastern PacificGenomeAngelfishMarine organismsGenomics of a novel ecological phase shift: the case of a ‘weedy’ Montipora coral in Ulithi, Micronesia
Bernardi G, Gatins R, Paddack M, Nelson P, Rulmal J, Crane N. Genomics of a novel ecological phase shift: the case of a ‘weedy’ Montipora coral in Ulithi, Micronesia. Coral Reefs 2024, 43: 601-611. DOI: 10.1007/s00338-024-02486-9.Peer-Reviewed Original ResearchStony coralsMontipora coralsUlithi AtollSpecies of stony coralsHuman-mediated spreadEvidence of natural selectionRAD-seq dataFederated States of MicronesiaCoral resilienceCoral assemblagesCoral diversityCoral reefsFish diversityFocal speciesRestoration effortsEcological integrityFish biomassEcosystem functionEcological stressorsMontipora sp.ReefsCoralsDominant speciesSpread successHuman activitiesInvasion genomics of lionfish in the Mediterranean Sea
Bernardi G, Azzurro E, Bariche M, Jimenez C, Kalogirou S, Kleitou P. Invasion genomics of lionfish in the Mediterranean Sea. Ecology And Evolution 2024, 14: e11087. PMID: 38450316, PMCID: PMC10915480, DOI: 10.1002/ece3.11087.Peer-Reviewed Original ResearchLionfish invasionEvidence of population structureMediterranean SeaEffects of lionfishRate of biological invasionsRed SeaInvasion genomicsInvasion successGenetic diversityGenomic approachesPopulation structureInvasive rangeGenomic markersBiological invasionsEvolutionary patternsFuture invasionsLionfishFish speciesPopulation dynamicsCaribbean SeaSuez CanalCentral MediterraneanMediterraneanInvasionSea