Gary Bernardi, APRN, RN
Staff Affiliate in Emergency MedicineAbout
Research
Publications
2026
How Garibaldi Got Its Red Coat: The Genome of Hypsypops rubicundus, a Conspicuous Fish of the Northeastern Pacific Kelp Forests
Bernardi G. How Garibaldi Got Its Red Coat: The Genome of Hypsypops rubicundus, a Conspicuous Fish of the Northeastern Pacific Kelp Forests. Marine Ecology 2026, 47 DOI: 10.1111/maec.70107.Peer-Reviewed Original ResearchH. rubicundusHypsypops rubicundusOxford Nanopore long readsHigh-quality genomesCarotenoid-based colorationNanopore long readsKinesin-1 motor proteinsAmino acid substitutionsBUSCO completenessMitochondrial genomeLong readsGenomic resourcesSexual selectionPhylogenetic analysisColor genesSpecialized pigment cellsAcid substitutionsMotor proteinsKinesin-1GenomePolar residuesDamselfishKelp forestsKIF5BProtein conformationOn the occurrence of the Pennant Coralfish Heniochus acuminatus (Linnaeus, 1758) and the Red Sea Bannerfish Heniochus intermedius Steindachner, 1893 in the Mediterranean Sea: New records and a regional review
AZZURRO E, KLEITOU P, BERNARDI G, BARICHE M. On the occurrence of the Pennant Coralfish Heniochus acuminatus (Linnaeus, 1758) and the Red Sea Bannerfish Heniochus intermedius Steindachner, 1893 in the Mediterranean Sea: New records and a regional review. Mediterranean Marine Science 2026, 27: 248-256. DOI: 10.12681/mms.41007.Peer-Reviewed Original ResearchMultiple introduction eventsMediterranean SeaHeniochus acuminatusIntroduction eventsNew recordsOpportunistic observationsH. intermediusContribution of citizen scienceMediterranean recordsTropical fishUnderwater videoHeniochusAcuminatusSteindachnerMediterraneanSpatio-temporal patternsCitizen scienceChaetodontidaeButterflyfishSpatial clusteringRegional reviewPennantSppEstablished PopulationsSeaThe 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 organisms