Original Research ARTICLE
Evaluating the evolutionary origins of unexpected character distributions within the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae superphylum
- European Molecular Biology Laboratory, Heidelberg, Germany
Recently, several characters that are absent from most bacteria, but which are found in many eukaryotes or archaea, have been identified within the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum. Hypotheses of the evolutionary history of such characters are commonly based on the inference of phylogenies of gene or protein families associated with the traits, estimated from multiple sequence alignments (MSAs). So far, studies of this kind have focused on the distribution of (i) two genes involved in the synthesis of sterol, (ii) tubulin genes, and (iii) c1 transfer genes. In many cases, these analyses have concluded that horizontal gene transfer (HGT) is likely to have played a role in shaping the taxonomic distribution of these gene families. In this article, we describe several issues with the inference of HGT from such analyses, in particular concerning the considerable uncertainty associated with our estimation of both gene family phylogenies (especially those containing ancient lineage divergences) and the Tree of Life (ToL), and the need for wider use and further development of explicit probabilistic models to compare hypotheses of vertical and horizontal genetic transmission. We suggest that data which is often taken as evidence for the occurrence of ancient HGT events may not be as convincing as is commonly described, and consideration of alternative theories is recommended. While focusing on analyses including PVCs, this discussion is also relevant for inferences of HGT involving other groups of organisms.
Keywords: PVC superphylum, lateral gene transfer, LGT, gene loss, gene duplication, phylogenetic estimation errors
Citation: Budd A and Devos DP (2012) Evaluating the evolutionary origins of unexpected character distributions within the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. Front. Microbio. 3:401. doi: 10.3389/fmicb.2012.00401
Received: 15 June 2012; Accepted: 31 October 2012;
Published online: 23 November 2012.
Edited by:Naomi L. Ward, University of Wyoming, USA
Reviewed by:Jan Mrazek, University of Georgia, USA
William C. Nelson, University of Southern California, USA
Copyright: © 2012 Budd and Devos. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
*Correspondence: D. P. Devos, Centre for Organismal Studies, Ruprecht-Karls-Universitat, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany. e-mail: firstname.lastname@example.org
†Present address: D. P. Devos, Centre for Organismal Studies, Ruprecht-Karls-Universitat, Heidelberg, Germany.