Genomes are clearly suited for inferring common ancestry and for understanding ancestorâdescendent relationships and interspecies gene transfer. Genomic evolutionary models can tell us a great deal about the processes that drive genome evolution, the mutational and selective pressures that lead to the genesis of biochemical pathways and operons, and the nature and extent of lateral gene transfer (LGT). Simultaneously, a robust phylogeny can be constructed that depicts the evolutionary relationships of the organisms in which the genomes are found.

Several approaches have been employed to infer species phylogenies at the genome level. In general terms, these can be divided into ad hoc summary statistics based on genome content, the use of concatenated alignments and the use of consensus methods (i.e. phylogenetic supertrees [1]

McInerney, James

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LettersOn the desirability of models for inferring genomephylogeniesJames O. McInerneyDepartment of Biology, National University of Ireland, Maynooth, County Kildare, IrelandGenomes are clearly suited for inferring commonancestry and for understanding ancestor–descendentrelationships and interspecies gene transfer. Genomicevolutionary models can tell us a great deal about theprocesses that drive genome evolution, the mutationaland selective pressures that lead to the genesis ofbiochemical pathways and operons, and the nature andextent of lateral gene transfer (LGT). Simultaneously, arobust phylogeny can be constructed that depicts theevolutionary relationships of the organisms in which thegenomes are found.Several approaches have been employed to infer speciesphylogenies at the genome level. In general terms, thesecan be divided into ad hoc summary statistics based ongenome content, the use of concatenated alignmentsand the use of consensus methods (i.e. phylogeneticsupertrees [1]).The basic premise of methods based on summarystatistics is that genomes are compared and a genecontent matrix is compiled. Then, either a distance isestimated between all pairs of taxa and entered into adistance matrix that is summarized using a clusteringalgorithm, or a dendrogram is inferred using maximumparsimony. This is usually referred to as the speciesphylogeny. The principal difference between thisapproach and the approaches that use concatenatedalignments or supertrees is that information concerninghomolog interrelationships is not used. Presence orabsence of homologs is the only information that isscored, and this approach can be considered ad hoc in thesense that the methods are applied uniformly to alldatasets and, therefore, the assumptions are notinformed by the data themselves.Unsurprisingly, the results of using summary statisticshave been variable. Although many methods haverecovered groups that seem sensible and have supportfrom external biochemical or morphological data, therehave been cases in which the inferred trees areunusual [2].For example, the haloarchaea are a group ofhalophilic Archaea, long taken to be members of theEuryarchaeota. Wolf et al. [2] and Korbel et al. [3] placedthis taxon at the base of the Archaea. In the figures ofHenz et al. [4], this taxon was placed among the Bacteriain one instance, within the Euryarchaeota in a secondexample and as the deepest-branching Archaeon in athird example. Dutilh et al. [5] point out that the correctplacement of the haloarchaea is within the Eury-archaeota and that previous methods placed this taxonerroneously as a deep-branching Archaeon. Thiserroneous placement is likely to be due to the largenumber of bacterial genes present in the haloarchaea [6].The haloarchaea are, therefore, pulled to a position thatis intermediate between the two groups from which thehaloarchaea genes came. The data violate the ad hocassumptions of the methods. Problems of this natureargue for the development of explicit genomeevolutionary models.Evolutionary models are statements concerning how itis thought that evolution has occurred [7]. If a model werecorrect, the inferred distances between two genomeswould be accurate and would provide consistent estimatesof the topology of the resulting phylogeny. The mostdesirable properties of these models are explicitness whendescribing the evolutionary process, realism or plausi-bility of the assumptions contained in the models andclarity in the interpretation of the output [8]. Usually,models are derived in amaximum likelihood framework inwhich the model consists of the phylogenetic tree of thegenomes and the process underlying their evolution [9].However, even when alternative models are not tested orlengthy computational optimization is not performed, anexplicit model of evolution can still be assumed incalculations [10].A realistic model of genome evolution must, as aminimum, deal with gene duplication and loss, in additionto acquisition of genes by LGT. This is not to say that allparameters are necessary for all analyses. When modelsdiffer in their numbers of free parameters and are nested,a likelihood ratio test can be used to choose the mostappropriate parameter.Gu and Zhang [11] describe a model called the extendedgenome content distance. This model uses the number ofhomologs (0, 1 orO1) to derive the genome distance. Themodel does not take account of horizontal gene transferand, as a result, the authors report a position for thehaloarchaea that is the same as the much simpler methodof Korbel et al. [3]. A model has also been developed thatdeals with LGT, albeit in a slightly different setting [12].Nonetheless, the development of explicit model-basedapproaches is to be welcomed as a useful step towardsthe understanding of genome evolution.When the genomic age began, it was assumed that thehuge increase in the amount of available data would resultin more-accurate phylogenies. Instead, the extent ofapparent genome plasticity has fueled a passionate debateCorresponding author: McInerney, J.O. (james.o.mcinerney@nuim.ie).Available online 3 November 2005Update TRENDS in Microbiology Vol.14 No.1 January 2006www.sciencedirect.comconcerning prokaryotic evolution. Sensible genomemodels that provide information about phylogeny andthe process of evolution should be a goal for genomicsand systematics.References1 Creevey, C.J. and McInerney, J.O. (2005) Clann: investigatingphylogenetic information through supertree analyses. Bioinformatics21, 390–3922 Wolf, Y.I. et al. (2001) Genome trees constructed using five differentapproaches suggest new major bacterial clades. BMC Evol. Biol. 1, 83 Korbel, J.O. et al. (2002) SHOT: a web server for the construction ofgenome phylogenies. Trends Genet. 18, 158–1624 Henz, S.R. et al. (2005) Whole-genome prokaryotic phylogeny.Bioinformatics 21, 2329–23355 Dutilh, B.E. et al. (2004) The consistent phylogenetic signal ingenome trees revealed by reducing the impact of noise. J. Mol. Evol.58, 527–5396 Kennedy, S.P. et al. (2001) Understanding the adaptation ofHalobacterium species NRC-1 to its extreme environment throughcomputational analysis of its genome sequence. Genome Res. 11,1641–16507 Felsenstein, J. (1988) Phylogenies from molecular sequences:inference and reliability. Annu. Rev. Genet. 22, 521–5658 Huelsenbeck, J.P. and Crandall, K.A. (1997) Phylogeny estimationand hypothesis testing using maximum likelihood. Annu. Rev. Ecol.Syst. 28, 437–4669 Edwards, A.W.F. (1972) Likelihood, 2nd edn, Johns Hopkins Univer-sity Press10 Lake, J.A. and Rivera, M.C. (2004) Deriving the genomic tree of life inthe presence of horizontal gene transfer: conditioned reconstruction.Mol. Biol. Evol. 21, 681–69011 Gu, X. and Zhang, H. (2004) Genome phylogenetic analysis based onextended gene contents. Mol. Biol. Evol. 21, 1401–140812 Novozhilov, A.S. et al. (2005) Mathematical modeling ofevolution of horizontally transferred genes. Mol. Biol. Evol.22, 1721–17320966-842X/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved.doi:10.1016/j.tim.2005.10.006Bifunctional TatA subunits in minimal Tat proteintranslocasesJan D.H. Jongbloed1,2, Rene´ van der Ploeg3 and Jan Maarten van Dijl31Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Kerklaan 30, 9751 NN Haren,The Netherlands2Present address: Department of Clinical Genetics, University Medical Centre Groningen, A. Deusinglaan 4, 9713 AW Groningen,The Netherlands3Laboratory of Molecular Bacteriology, Department of Medical Microbiology, University Medical Centre Groningen and Universityof Groningen, P.O. Box 30001, 9700 RB Groningen, The NetherlandsBacteria export numerous proteins across the cytoplasmicmembrane into the periplasmic space and outer mem-brane (Gram-negative species) or the extracellular milieu(Gram-positive species). In most bacteria, the bulk of thisprotein traffic is mediated by the general secretory(Sec) pathway, which requires ‘threading’ of transportedproteins through a membrane-bound Sec translocon in anunfolded state. Upon membrane translocation, exportedproteins fold into their final conformation. Recently, asecond pathway for protein export has been identified: thetwin-arginine translocation (Tat) system, which derivesits name from the twin-arginine (RR) motif that is anessential determinant in the signal peptide of Tat-systemsubstrates. This pathway is conserved in Bacteria,Archaea and chloroplast thylakoids. In marked contrastto the Sec system, the Tat system translocates globularproteins in a folded state. This striking characteristic ofTat systems has attracted wide interest and is discussed inexcellent reviews by Palmer et al. [1], and Robinson andBolhuis [2].In Escherichia coli and chloroplast thylakoids, anactive Tat system canonically requires the presence ofthree membrane-bound subunits: TatA, TatB and TatC.Absence of one of these subunits results in impairedfunction of the Tat machinery, at least with respect to theexport of known authentic substrates. The currentlyaccepted view is that, in complex, TatB and TatC servein RR-signal-peptide reception, whereas, in complex withmultiple TatA subunits, they form protein-conductingchannels [3,4]. Association of TatA with complexed TatBand TatC subunits requires a functional precursor and theDpH component of the proton-motive force [3,4]. TatAsubunits are likely to be recruited by TatB [1]. Here, wehighlight the novel finding that TatA has the intrinsiccapability to complement for the essential TatB subunit.Phylogenetic analyses have shown that many bacteriaand archaea contain genes that encode multiple TatA-,TatB-, and TatC-like proteins. Known TatA and TatBproteins show limited amino acid sequence similarity(Figure 1). Much clearer similarities between TatAand TatB proteins are, however, observed at the levelof their predicted membrane topologies and structures(Figure 2a). A distinctive feature of these proteins is thepresence of a conserved motif at the hinge betweenthe transmembrane segment and the amphipathiccytoplasmic helix: Phe-Gly (FG) in TatA and Gly-ProCorresponding author: van Dijl, J.M. (j.m.van.dijl@med.umcg.nl).Available online 21 November 2005Update TRENDS in Microbiology Vol.14 No.1 January 20062www.sciencedirect.com

On the desirability of models for inferring genome phylogenies

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On the desirability of models for inferring genome phylogenies

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