A Bayesian Method for Analyzing Lateral Gene Transfer
2014 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 3, 409-420 p.Article in journal (Refereed) Published
Lateral gene transfer (LGT)uwhich transfers DNA between two non-vertically related individuals belonging to the same or different speciesuis recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications (GDs). Consequently, proposed LGT among specific gene families, and the rate of LGT in general, remain debated. We present a Bayesian Markov-chain Monte Carlo-based method that integrates GD, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close-species LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events. [Bayesian; gene duplication; gene loss; horizontal gene transfer; lateral gene transfer; MCMC; phylogenetics.].
Place, publisher, year, edition, pages
2014. Vol. 63, no 3, 409-420 p.
Bayesian, gene duplication, gene loss, horizontal gene transfer, lateral gene transfer, MCMC, phylogenetics
IdentifiersURN: urn:nbn:se:kth:diva-145578DOI: 10.1093/sysbio/syu007ISI: 000334752600010ScopusID: 2-s2.0-84899026794OAI: oai:DiVA.org:kth-145578DiVA: diva2:722995
FunderSwedish Research Council, 2010-4757 2010-4634Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
QC 201406102014-06-102014-05-232014-06-10Bibliographically approved