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dc.contributor.CRUESPUniversidade Estadual de Campinaspt_BR
dc.typeArtigo de periódicopt_BR
dc.titleGene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partnerspt_BR
dc.contributor.authorCampos, PRApt_BR
dc.contributor.authorde Oliveira, VMpt_BR
dc.contributor.authorWagner, GPpt_BR
dc.contributor.authorStadler, PFpt_BR
unicamp.authorUniv Leipzig, Inst Informat, Lehrstuhl Bioinformat, Bioinformat Grp,Dept Comp Sci, D-04103 Leipzig, Germany Univ Leipzig, Interdisciplinary Ctr Bioinformat, D-04103 Leipzig, Germany Univ Vienna, Inst Theoret Chem & Mol Strukt Biol, A-1090 Vienna, Austria Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06405 USA Univ Federal Rural Pernambuco, Dept Fis & Matemat, BR-52171900 Recife, PE, Brazil Univ Estadual Campinas, Inst Fis Gleb Wataghin, BR-13083070 Campinas, SP, Brazilpt_BR
dc.subjectgene phylogenypt_BR
dc.subjecttree reconstructionpt_BR
dc.subjectcorrelated substitutionspt_BR
dc.subject.wosComparative Sequence-analysispt_BR
dc.subject.wosHox Proteinspt_BR
dc.subject.wosHomeodomain Proteinspt_BR
dc.subject.wosCorrelated Mutationspt_BR
dc.subject.wosSecondary Structurept_BR
dc.subject.wosHomeobox Genespt_BR
dc.description.abstractThe study of gene families critically depends on the correct reconstruction of gene genealogies, as for instance in the case of transcription factor genes like Hox genes and Dlx gene families. Proteins belonging to the same family are likely to share some of the same protein interaction partners and may thus face a similar selective environment. This common selective environment can induce co-evolutionary pressures and thus can give rise to correlated rates and patterns of evolution among members of a gene family. In this study, we simulate the evolution of a family of sequences which share a set of interaction partners. Depending on the amount of sequence dedicated to protein-protein interaction and the relative rate parameters of sequence evolution three outcomes are possible: if the fraction of the sequence dedicated to interaction with common co-factors is low and the time since divergence is small, the trees based on sequence information tend to be correct. If the time since gene duplication is long two possible outcomes are observed in our simulations. If the rate of evolution of the interaction partner is small compared to the rate of evolution of the focal protein family, the reconstructed trees tend towards star phylogenies. As the rate of evolution of the interaction partner approaches that of the focal protein family the reconstructed phylogenies tend to be incorrectly resolved. We conclude that the genealogies of gene families can be hard to estimate, in particular if the proteins interact with a conserved set of binding partners, as is likely the case for transcription factors. (C) 2004 Elsevier Ltd. All rights
dc.relation.ispartofJournal Of Theoretical Biologypt_BR
dc.relation.ispartofabbreviationJ. Theor. Biol.pt_BR
dc.publisherAcademic Press Ltd Elsevier Science Ltdpt_BR
dc.identifier.citationJournal Of Theoretical Biology. Academic Press Ltd Elsevier Science Ltd, v. 231, n. 2, n. 197, n. 202, 2004.pt_BR
dc.sourceWeb of Sciencept_BR
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