{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T11:56:24Z","timestamp":1773662184893,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: We compare phylogenetic approaches for inferring functional gene links. The approaches detect independent instances of the correlated gain and loss of pairs of genes from species' genomes. We investigate the effect on results of basing evidence of correlations on two phylogenetic approaches, Dollo parsminony and maximum likelihood (ML). We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data.<\/jats:p><jats:p>Results: We detect correlated evolution among a test set of pairs of yeast (Saccharomyces cerevisiae) genes, with a case study of 21 eukaryotic genomes and test data derived from known yeast protein complexes. If the rate at which genes are gained is constrained to be low, ML achieves by far the best results at detecting known functional links. The model then has fewer parameters but it is more realistic by preventing genes from being gained more than once.<\/jats:p><jats:p>Availability: BayesTraits by M. Pagel and A. Meade, and a script to configure and repeatedly launch it by D. Barker and M. Pagel, are available at<\/jats:p><jats:p>Contact: \u00a0m.pagel@rdg.ac.uk<\/jats:p><jats:p>Supplementary information: Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl558","type":"journal-article","created":{"date-parts":[[2006,11,8]],"date-time":"2006-11-08T03:38:43Z","timestamp":1162957123000},"page":"14-20","source":"Crossref","is-referenced-by-count":84,"title":["Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes"],"prefix":"10.1093","volume":"23","author":[{"given":"Daniel","family":"Barker","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Meade","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Reading 1 \u00a0 1 \u00a0 \u00a0 Whiteknights, Reading, RG6 6AJ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Pagel","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Reading 1 \u00a0 1 \u00a0 \u00a0 Whiteknights, Reading, RG6 6AJ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,11,7]]},"reference":[{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/387489a0","article-title":"Evidence for a clade of nematodes, arthropods and other moulting animals","volume":"387","author":"Aguinaldo","year":"1997","journal-title":"Nature"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1093\/bioinformatics\/16.6.501","article-title":"Phylogenetically enhanced statistical tools for RNA structure prediction","volume":"16","author":"Akmaev","year":"2000","journal-title":"Bioinformatics"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"11319","DOI":"10.1073\/pnas.200346997","article-title":"Lineage-specific loss and divergence of functionally linked genes in eukaryotes","volume":"97","author":"Aravind","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"e3","DOI":"10.1371\/journal.pcbi.0010003","article-title":"Predicting functional gene links from phylogenetic-statistical analyses of whole genomes","volume":"1","author":"Barker","year":"2005","journal-title":"PLoS Comput. Biol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1126\/science.1098119","article-title":"Ultraconserved elements in the human genome","volume":"304","author":"Bejerano","year":"2004","journal-title":"Science"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1111\/j.2517-6161.1962.tb00468.x","article-title":"Further results on tests of separate families of hypotheses","volume":"24","author":"Cox","year":"1962","journal-title":"J. R Stat. Soc. Series B (Methodological)"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/S0968-0004(98)01274-2","article-title":"Conservation of gene order: a fingerprint of proteins that physically interact","volume":"23","author":"Dandekar","year":"1998","journal-title":"Trends Biochem. Sci."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/47056","article-title":"Protein interaction maps for complete genomes based on gene fusion events","volume":"402","author":"Enright","year":"1999","journal-title":"Nature"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/S0168-9525(01)02384-8","article-title":"Modularity in the gain and loss of genes: applications for function prediction","volume":"17","author":"Ettema","year":"2001","journal-title":"Trends Genet."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"77","DOI":"10.2307\/2412867","article-title":"Phylogenetic analysis under Dollo's Law","volume":"26","author":"Farris","year":"1977","journal-title":"Syst. Zoology"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"Felsenstein","year":"1981","journal-title":"J. Mol. Evol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/284325","article-title":"Phylogenies and the comparative method","volume":"125","author":"Felsenstein","year":"1985","journal-title":"Am. Nat."},{"key":"2023041105102266500_","volume-title":"Inferring Phylogenies","author":"Felsenstein","year":"2004"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"D322","DOI":"10.1093\/nar\/gkj021","article-title":"The Gene Ontology (GO) project in 2006","volume":"34","author":"Gene Ontology Consortium","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1007\/BF00166252","article-title":"Statistical tests of models of DNA substitution","volume":"36","author":"Goldman","year":"1993","journal-title":"J. Mol. Evol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"D364","DOI":"10.1093\/nar\/gki053","article-title":"CYGD: the Comprehensive Yeast Genome Database","volume":"33","author":"G\u00fcldener","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1128\/EC.4.6.1102-1115.2005","article-title":"Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae","volume":"4","author":"Hall","year":"2005","journal-title":"Eukaryot. Cell"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198546412.001.0001","volume-title":"The Comparative Method in Evolutionary Biology","author":"Harvey","year":"1991"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1002\/yea.706","article-title":"Assessment of prediction accuracy of protein function from protein\u2013protein interaction data","volume":"18","author":"Hishigaki","year":"2001","journal-title":"Yeast"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1126\/science.1087361","article-title":"A Bayesian networks approach for predicting protein\u2013protein interactions from genomic data","volume":"302","author":"Jansen","year":"2003","journal-title":"Science"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2004-5-2-r7","article-title":"A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes","volume":"5","author":"Koonin","year":"2004","journal-title":"Genome Biol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1038\/nbt988","article-title":"Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs","volume":"22","author":"Korbel","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1101\/gr.1589103","article-title":"Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution","volume":"13","author":"Krylov","year":"2003","journal-title":"Genome Res."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/1471-2105-5-154","article-title":"Information assessment on predicting protein-protein interactions","volume":"5","author":"Lin","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1101\/gr.1145203","article-title":"Multimeric threading-based prediction of protein\u2013protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome","volume":"13","author":"Lu","year":"2003","journal-title":"Genome Res."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1126\/science.285.5428.751","article-title":"Detecting protein function and protein\u2013protein interactions from genome sequences","volume":"285","author":"Marcotte","year":"1999","journal-title":"Science"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/47048","article-title":"A combined algorithm for genome-wide prediction of protein function","volume":"402","author":"Marcotte","year":"1999","journal-title":"Nature"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"15655","DOI":"10.1073\/pnas.2136653100","article-title":"Extensive gene gain associated with adaptive evolution of poxviruses","volume":"26","author":"McLysaght","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nature750","article-title":"Comparative assessment of large-scale data sets of protein\u2013protein interactions","volume":"417","author":"von Mering","year":"2002","journal-title":"Nature"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"15428","DOI":"10.1073\/pnas.2136809100","article-title":"Genome evolution reveals biochemical networks and functional modules","volume":"100","author":"von Mering","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/nbt834","article-title":"Systematic discovery of analogous enzymes in thiamin biosynthesis","volume":"21","author":"Morett","year":"2003","journal-title":"Nat. Biotechnol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","article-title":"The use of gene clusters to infer functional coupling","volume":"96","author":"Overbeek","year":"1999","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1098\/rspb.1994.0006","article-title":"Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters","volume":"255","author":"Pagel","year":"1994","journal-title":"Proc. R Soc. Lon. B Biol. Sci."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1111\/j.1463-6409.1997.tb00423.x","article-title":"Inferring evolutionary processes from phylogenies","volume":"26","author":"Pagel","year":"1997","journal-title":"Zool. Scr."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1080\/106351599260184","article-title":"The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies","volume":"48","author":"Pagel","year":"1999","journal-title":"Syst. Biol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1080\/10635150490522232","article-title":"Bayesian estimation of ancestral character states on phylogenies","volume":"53","author":"Pagel","year":"2004","journal-title":"Syst. Biol."},{"key":"2023041105102266500_","first-page":"235","article-title":"Bayesian estimation of correlated evolution across cultures: a case study of marriage systems and wealth transfer at marriage","volume-title":"The Evolution of Cultural Diversity: A Phylogenetic Approach","author":"Pagel","year":"2005"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1086\/503444","article-title":"Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo","volume":"167","author":"Pagel","year":"2006","journal-title":"Am. Nat."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1016\/j.jmb.2004.10.019","article-title":"A domain interaction map based on phylogenetic profiling","volume":"344","author":"Pagel","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1016\/j.jmb.2005.07.005","article-title":"Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome","volume":"352","author":"Pazos","year":"2005","journal-title":"J. Mol. Biol."},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","article-title":"Assigning protein functions by comparative genome analysis: protein phylogenetic profiles","volume":"96","author":"Pellegrini","year":"1999","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041105102266500_","volume-title":"The Explanation of Organic Diversity: The Comparative Method and Adaptations for Mating","author":"Ridley","year":"1983"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-5-75","article-title":"Extreme conservation of noncoding DNA near HoxD complex of vertebrates","volume":"5","author":"Sabarinadh","year":"2004","journal-title":"BMC Genomics"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"3409","DOI":"10.1093\/bioinformatics\/bti532","article-title":"Refined phylogenetic profiles method for predicting protein\u2013protein interactions","volume":"21","author":"Sun","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"S276","DOI":"10.1093\/bioinformatics\/18.suppl_1.S276","article-title":"A tree kernel to analyse phylogenetic profiles","volume":"18","author":"Vert","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1101\/gr.1347404","article-title":"Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis","volume":"14","author":"Wolf","year":"2004","journal-title":"Genome Res."},{"key":"2023041105102266500_","volume-title":"Biostatistical Analysis","author":"Zar","year":"1996","edition":"3rd edn"},{"key":"2023041105102266500_","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1016\/j.jmb.2006.04.011","article-title":"Inferring functional linkages between proteins from evolutionary scenarios","volume":"359","author":"Zhou","year":"2006","journal-title":"J. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/1\/14\/49816324\/bioinformatics_23_1_14.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/1\/14\/49816324\/bioinformatics_23_1_14.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,11]],"date-time":"2025-01-11T22:17:01Z","timestamp":1736633821000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/1\/14\/189792"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,11,7]]},"references-count":48,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl558","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,1,1]]},"published":{"date-parts":[[2006,11,7]]}}}