Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer.docVIP

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Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer.doc

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Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer

BayesianAnalysisofCongruenceofCoreGenesin ProchlorococcusandSynechococcusandImplicationson HorizontalGeneTransfer NicholasJ.Matzke1¤.,PatrickM.Shih2.,CherylA.Kerfeld2,3 * 1DepartmentofIntegrativeBiology,UniversityofCalifornia,Berkeley,California,UnitedStatesofAmerica, 2DepartmentofPlantandMicrobialBiology,Universityof California,Berkeley,California,UnitedStatesofAmerica,3USDepartmentofEnergy-JointGenomeInstitute,WalnutCreek,California,UnitedStatesofAmerica Abstract It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the patternof vertical inheritance is oversimplified or even positively misleading. ‘‘Universal proteins’’ have beenusedtoinfertheorganismalphylogeny,buthavebeencriticizedasbeingonlythe‘‘treeofonepercent.’’Currently, fewoptionsexistforthosewishingtorigorouslyassesshowwellauniversalproteinphylogeny,basedonarelativehandful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees – a‘‘treecloud’’ –for each,aswellasforaconcatenateddatasetbasedonputative‘‘universalproteins.’’Wethencalculatetheaveragedistance betweentreeswithinandbetweenalltreecloudsonvariousmetricsandvisualizethishigh-dimensionalspacewithnon- metricmultidimensionalscaling(NMMDS).Weshowthatthetreespaceisstronglyclusteredandthattheuniversalprotein treecloudisstatisticallysignificantlyclosertothecenterofthistreespacethananyindividualgenetreecloud.Weapply severalcommonly-usedtestsforincongruence/HGTandshowthattheyagreeHGTisrareinthisdataset,butmakedifferent choicesaboutwhichgenesweresubjecttoHGT.Ourresultsshowthatthequestionof