2025
Applying multilevel selection to understand cancer evolution and progression
Laplane L, Lamoureux A, Richker H, Alcaraz G, Fortunato A, Shaffer Z, Aktipis A, Mischel P, Plutynski A, Townsend J, Maley C. Applying multilevel selection to understand cancer evolution and progression. PLOS Biology 2025, 23: e3003290. PMID: 40680084, PMCID: PMC12303392, DOI: 10.1371/journal.pbio.3003290.Peer-Reviewed Original ResearchUrban refuge? Squirrel pigmentation clines maintained by strong natural selection beyond city limits
Bonar M, Blumenfeld A, Fusco N, Campagna L, Timpson A, Thomas M, Cosentino B, Gibbs J, Caccone A. Urban refuge? Squirrel pigmentation clines maintained by strong natural selection beyond city limits. 2025 DOI: 10.21203/rs.3.rs-6967993/v1.Peer-Reviewed Original ResearchGenome sequenceDemographic modelsNatural selectionCoat colour polymorphismWhole-genome sequencingMelanocortin 1 receptor geneEastern gray squirrelsColour polymorphismTrait variationGenetic diversityGenomic backgroundGenomic dataPigmentation clineSelection landscapeMC1R allelesPhenotypic traitsModel of selectionVertebrate speciesClineMelanic morphsSciurus carolinensisSelection pressureCoat colorGrey squirrelsEvolutionary process
2024
A substitution at the cytoplasmic tail of the spike protein enhances SARS-CoV-2 infectivity and immunogenicity
Li Y, Zhang X, Tai W, Zhuang X, Shi H, Liao S, Yu X, Mei R, Chen X, Huang Y, Liu Y, Liu J, Liu Y, Zhu Y, Wang P, Tian M, Yu G, Li L, Cheng G. A substitution at the cytoplasmic tail of the spike protein enhances SARS-CoV-2 infectivity and immunogenicity. EBioMedicine 2024, 110: 105437. PMID: 39531918, PMCID: PMC11603013, DOI: 10.1016/j.ebiom.2024.105437.Peer-Reviewed Original ResearchS proteinCytoplasmic tailFERM-binding motifTrans-complementation systemSpike proteinAmino acid substitutionsProline-to-leucine substitutionSystematic bioinformatics analysisHigh-frequency mutationsSARS-CoV-2 virionsBinding motifAcid substitutionsSARS-CoV-2Natural selectionBioinformatics analysisEzrin/radixin/moesin proteinsMolecular mechanismsMutationsOmicron variantProteinVaccine developmentMRNA vaccinesGlobal disseminationSARS-CoV-2 Omicron sublineagesSublineagesReproductive endocrinology and aging in human males: An evolutionary perspective
Bribiescas R. Reproductive endocrinology and aging in human males: An evolutionary perspective. Neuroscience & Biobehavioral Reviews 2024, 167: 105898. PMID: 39293503, DOI: 10.1016/j.neubiorev.2024.105898.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 speciesTilapiaCichlidsWeakened tanning ability is an important mechanism for evolutionary skin lightening in East Asians
Pu Y, Pu S, Chen Y, Kong Q, Liu X, Zhao Q, Xu K, Liu J, Li M, Xu X, Qiao X, Su B, Chen J, Yang Z. Weakened tanning ability is an important mechanism for evolutionary skin lightening in East Asians. Journal Of Genetics And Genomics 2024, 51: 703-713. PMID: 38461943, DOI: 10.1016/j.jgg.2024.03.001.Peer-Reviewed Original ResearchBinding activity of transcription factorsActivation of transcription factorsEast AsiansTranscription factor binding assaysBinding to Smad2Zebrafish embryosHan Chinese individualsEnhanced activityAdaptive allelesAssociated with skin colorAncestral alleleHigh-latitude environmentsHan Chinese malesPigment genesIntronic mutationTanning abilityTranscription factorsGenetic mechanismsSelection signalsT alleleUltraviolet radiation responsesNatural selectionLight skin pigmentationMelanin productionBinding activity
2023
Establishment genomics of the Indo-Pacific damselfish Neopomacentrus cyanomos, in the Greater Caribbean
Bernardi G, Cohn F, Dominguez-Dominguez O, Kingon K, Tornabene L, Robertson D. Establishment genomics of the Indo-Pacific damselfish Neopomacentrus cyanomos, in the Greater Caribbean. Biological Invasions 2023, 26: 1017-1031. DOI: 10.1007/s10530-023-03226-w.Peer-Reviewed Original ResearchNon-native speciesNon-native populationsGreater CaribbeanReef fishesNative rangeNatural selectionTrinidad populationIndo-Pacific reef fishMitochondrial DNA lineagesProtein coding genesSeparate genetic clustersDNA lineagesGenetic differentiationCoding genesAtlantic individualsRocky reefsGenetic clustersGenetic diversityEstablishment successRAD sequencesPopulation structureIsolated populationCoral reefsAdaptable speciesNearby reefsBTG1 mutation yields supercompetitive B cells primed for malignant transformation
Mlynarczyk C, Teater M, Pae J, Chin C, Wang L, Arulraj T, Barisic D, Papin A, Hoehn K, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh H, Evans C, Chadburn A, Chen Z, Shen H, Isles H, Pelzer B, Tsialta I, Doane A, Geng H, Rehman M, Melnick J, Morgan W, Nguyen D, Elemento O, Kharas M, Jaffrey S, Scott D, Khelashvili G, Meyer-Hermann M, Victora G, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science 2023, 379: eabj7412. PMID: 36656933, PMCID: PMC10515739, DOI: 10.1126/science.abj7412.Peer-Reviewed Original ResearchConceptsGerminal center B cellsPositive selection signalsB-cell fitnessCell fitnessUnicellular organismsB cellsMulticellular lifeNatural selectionSelection signalsInduction kineticsGatekeeper mechanismAdaptive immune systemAltruistic cooperationNew mouse modelNormal counterpartsHuman lymphomasAntibody affinity maturationCellsInvasive lymphomaClinical outcomesMouse modelImmune systemMalignant transformationSupercompetitorsAffinity maturation
2020
Characterizing the effect of background selection on the polygenicity of brain-related traits
Wendt FR, Pathak GA, Overstreet C, Tylee DS, Gelernter J, Atkinson EG, Polimanti R. Characterizing the effect of background selection on the polygenicity of brain-related traits. Genomics 2020, 113: 111-119. PMID: 33278486, PMCID: PMC7855394, DOI: 10.1016/j.ygeno.2020.11.032.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesBrain-related traitsGWAS of schizophreniaTrait-associated lociLocus effect sizesSubset of traitsGenotype networksGenetic architectureIntolerant regionsBrain-related phenotypesBackground selectionNatural selectionEvolutionary pressurePositive selectionSNP heritabilityLocal ancestryAssociation studiesTraitsFunctional significanceLociPolygenicityBinary annotationPhenotypeRisk allelesSize varianceUnmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi
Merényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi. Molecular Biology And Evolution 2020, 37: 2228-2240. PMID: 32191325, PMCID: PMC7403615, DOI: 10.1093/molbev/msaa077.Peer-Reviewed Original ResearchConceptsComplex multicellularityGene familyMulticellular fruiting bodiesGene family levelLarge phylogenetic distancesSimilar selection pressuresRecent common ancestorFungal ancestorsFungal genomesGenomic repertoireMolecular convergenceMulticellular fungiPhylogenetic distanceConvergent evolutionEvolutionary convergenceLarge cladeEvolutionary trajectoriesCommon ancestorIndependent evolutionNatural selectionSelection pressureEvolutionary predispositionMulticellularityCladeFruiting bodies
2017
Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana
Park B, Rutter MT, Fenster CB, Symonds VV, Ungerer MC, Townsend JP. Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics 2017, 206: 2105-2117. PMID: 28550014, PMCID: PMC5560809, DOI: 10.1534/genetics.116.199190.Peer-Reviewed Original ResearchConceptsMutation accumulation dataDirectional selectionNatural selectionMutational effectsPhenotypic traitsDirectional natural selectionQuantitative trait lociDivergent lineagesRosette diameterTrait lociHistorical selectionQuantitative traitsLineagesArabidopsisTraitsDensity traitsAccumulation dataDivergenceKey roleUltimate sourceLociSelectionOrganismsKey componentMutationsPerceptive costs of reproduction drive ageing and physiology in male Drosophila
Harvanek ZM, Lyu Y, Gendron CM, Johnson JC, Kondo S, Promislow DEL, Pletcher SD. Perceptive costs of reproduction drive ageing and physiology in male Drosophila. Nature Ecology & Evolution 2017, 1: 0152. PMID: 28812624, PMCID: PMC5657004, DOI: 10.1038/s41559-017-0152.Peer-Reviewed Original ResearchLife-history traitsReproductive costsBenefits of matingPopulation genetic studiesCost of reproductionAct of matingMale Drosophila melanogasterOrganismal fitnessDrosophila melanogasterReproductive effortMale DrosophilaNatural selectionStress resistancePheromone perceptionPhysiological constraintsGenetic studiesMechanistic basisKey survivalPhysiological costsReproductionFat storageMolecular frameworkMatingTraitsImportant insights
2016
Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India
Lewnard JA, Townsend JP. Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 14601-14608. PMID: 27791071, PMCID: PMC5187705, DOI: 10.1073/pnas.1604985113.Peer-Reviewed Original ResearchConceptsPlague resistanceEnvironmental driversIntense natural selectionWild host populationsIntense selective pressureEvolutionary driversPossible evolutionary basisHost evolutionNatural selectionDisease resistanceEvolutionary selectionFlea population dynamicsEvolutionary basisSelective pressureEvolutionary processesPopulation dynamicsHost populationsWildlife hostsLocal persistencePlague dynamicsCommensal ratsDisease agentsPowerful insightsDisease transmissionEcologyEvidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits
Polimanti R, Yang BZ, Zhao H, Gelernter J. Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits. PLOS ONE 2016, 11: e0160654. PMID: 27537407, PMCID: PMC4990182, DOI: 10.1371/journal.pone.0160654.Peer-Reviewed Original ResearchConceptsPolygenic adaptationNatural selectionSystems geneticsProtein interaction networksWide association studyPolygenic mechanismsEuropean populationsPolygenic selectionAnthropometric traitsGene networksHuman genomeEpistatic interactionsInteraction networksEnrichment analysisGenetic signaturesSystems biologyAssociation studiesLipid transportMolecular processesAdaptation signalsLocomotory behaviorTraitsSelective mechanismGeneticsInfection resistanceThe Transcriptomic Evolution of Mammalian Pregnancy: Gene Expression Innovations in Endometrial Stromal Fibroblasts
Kin K, Maziarz J, Chavan AR, Kamat M, Vasudevan S, Birt A, Emera D, Lynch VJ, Ott TL, Pavlicev M, Wagner GP. The Transcriptomic Evolution of Mammalian Pregnancy: Gene Expression Innovations in Endometrial Stromal Fibroblasts. Genome Biology And Evolution 2016, 8: 2459-2473. PMID: 27401177, PMCID: PMC5010902, DOI: 10.1093/gbe/evw168.Peer-Reviewed Original ResearchConceptsEndometrial stromal fibroblastsGene expression changesTherian speciesEutherian lineagesTranscriptome compositionBovine lineageStem lineageNatural selectionStromal fibroblastsTherian mammalsEutherian mammalsKey genesLoss of expressionTranscriptomic evolutionGene expressionExpression changesLatter cell typeGenesLineagesCell typesCell type presentMammalsMammalian pregnancyExpressionTissue invasionUpstream ORFs are prevalent translational repressors in vertebrates
Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. The EMBO Journal 2016, 35: 706-723. PMID: 26896445, PMCID: PMC4818764, DOI: 10.15252/embj.201592759.Peer-Reviewed Original ResearchConceptsUpstream open reading framesUntranslated mRNA regionsPost-transcriptional regulationOpen reading frameMRNA leader sequenceClear repressionVertebrate transcriptomesRibosome footprintingCellular diversityTranslational repressorIndividual genesNatural selectionUpstream ORFsReading frameLeader sequenceRegulatory potentialActive translationRegulatory codeInitiation contextGene expressionMRNA regionsUnknown functionReporter experimentsVertebratesIntercistronic distance
2015
Inferring the Origin of Metastases from Cancer Phylogenies
Hong WS, Shpak M, Townsend JP. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Research 2015, 75: 4021-4025. PMID: 26260528, PMCID: PMC4833389, DOI: 10.1158/0008-5472.can-15-1889.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsComplete phylogenyEvolutionary historyPhylogeny-based testsFuture phylogenetic studiesMolecular evolutionary modelsMetastatic subclonesMonophyletic cladePhylogenetic reconstructionCancer lineagesPhylogenetic studiesNatural selectionPhylogenyCancer phylogeniesOrigin of metastasesCancer biologyMetastatic cascadeSubclonesTargeted sequencingEvolutionary modelsDriver mutationsUltra-deep sequencingSequencingRecent studiesMonophylyCladeExperimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness
Grubaugh ND, Smith DR, Brackney DE, Bosco-Lauth AM, Fauver JR, Campbell CL, Felix TA, Romo H, Duggal NK, Dietrich EA, Eike T, Beane JE, Bowen RA, Black WC, Brault AC, Ebel GD. Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness. PLOS Pathogens 2015, 11: e1004874. PMID: 25993022, PMCID: PMC4439088, DOI: 10.1371/journal.ppat.1004874.Peer-Reviewed Original ResearchConceptsRNA virus populationsWNV populationsBird speciesRNA virusesNatural selectionFitness gainsVirus populationsStrength of selectionWest Nile virusSpecies-specific mannerDistinct phenotypic consequencesAverage mutation frequencyExperimental evolutionMutational toleranceError-prone replicationCompetitive fitnessPopulation structureNext-generation sequencingPhenotypic consequencesGenetic compositionWild birdsSelective pressureSequencing dataDefective genomesDifferent hostsMaking Sense of Transcription Networks
Sorrells T, Johnson A. Making Sense of Transcription Networks. Cell 2015, 161: 714-723. PMID: 25957680, PMCID: PMC4531093, DOI: 10.1016/j.cell.2015.04.014.Peer-Reviewed Original ResearchGene Expression Evolves under a House-of-Cards Model of Stabilizing Selection
Hodgins-Davis A, Rice DP, Townsend JP. Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection. Molecular Biology And Evolution 2015, 32: 2130-2140. PMID: 25901014, PMCID: PMC4592357, DOI: 10.1093/molbev/msv094.Peer-Reviewed Original ResearchConceptsGene expression evolvesGene expressionPhenotypic evolutionGenetic architectureExpression evolvesEvolutionary quantitative genetic modelsMutation accumulation linesNatural genetic variationStrength of selectionGenomic mutation rateQuantitative genetic modelGenomic data setsGene expression levelsEffects of selectionEvolutionary timeRegulatory evolutionStabilizing selectionAccumulation linesGene regulationMost genesNatural selectionGenetic variationMutational effectsFruit flyPhenotype space
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