title: On surrogate methods for detecting lateral gene transfer.
abstract: Surrogate methods for detecting lateral gene transfer are those that do not require inference of phylogenetic trees. Herein I apply four such methods to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer. Only two of these methods detect the same ORFs more frequently than expected by chance, whereas several intersections contain many fewer ORFs than expected. Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees.
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia. m.ragan@imb.uq.edu.au
authors.forename: M A
authors.initials: MA
authors.lastname: Ragan
mesh_terms: D001482:Base Composition; D003198:Computer Simulation; D003596:Cytosine / Q000032:analysis; D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D006147:Guanine / Q000032:analysis; D008390:Markov Chains; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny
chemical_list: D006147:Guanine; D003596:Cytosine