Journal article
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
BMC Biology, Vol.7, 78
2009
Abstract
Background: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion: We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer. © 2009 Pearson et al; licensee BioMed Central Ltd.
Details
- Title
- Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
- Authors
- T Pearson (Author) - Northern Arizona University, United StatesP Giffard (Author) - Queensland University of TechnologyS Beckstrom-Sternberg (Author) - Northern Arizona University, United StatesR Auerbach (Author) - Northern Arizona University, United StatesH Hornstra (Author) - Northern Arizona University, United StatesA Tuanyok (Author) - Northern Arizona University, United StatesErin P Price (Author) - Northern Arizona University, United StatesM B Glass (Author) - National Center for Zoonotic, Vector-Borne, and Enteric Diseases, United StatesB Leadem (Author) - Northern Arizona University, United StatesJ S Beckstrom-Sternberg (Author) - Translational Genomics Research Institute, United StatesG J Allan (Author) - Northern Arizona University, United StatesJ T Foster (Author) - Northern Arizona University, United StatesD M Wagner (Author) - Northern Arizona University, United StatesR T Okinaka (Author) - Northern Arizona University, United StatesS H Sim (Author) - Defense Medical and Environmental Research Institute, SingaporeO Pearson (Author) - Denver Federal Center, United StatesZ Wu (Author) - University of Washington, United StatesJ Chang (Author) - University of Washington Genome Center and Division of Medical Genetics, United StatesR Kaul (Author) - University of Washington Genome Center and Division of Medical Genetics, United StatesA R Hoffmaster (Author) - National Center for Zoonotic, Vector-Borne, and Enteric Diseases, United StatesT S Brettin (Author) - DOE Joint Genome Institute, United StatesR A Robison (Author) - Brigham Young University, United StatesM Mayo (Author) - Queensland University of TechnologyJ E Gee (Author) - National Center for Zoonotic, Vector-Borne, and Enteric Diseases, United StatesP Tan (Author) - Defense Medical and Environmental Research Institute, SingaporeB J Currie (Author) - Queensland University of TechnologyP Keim (Author) - Northern Arizona University, United States
- Publication details
- BMC Biology, Vol.7, 78; 14
- Publisher
- BioMed Central Ltd.
- Date published
- 2009
- DOI
- 10.1186/1741-7007-7-78
- ISSN
- 1741-7007
- Copyright note
- Copyright © 2009 Pearson et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- Organisation Unit
- University of the Sunshine Coast, Queensland; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99451135902621
- Output Type
- Journal article
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