Open Access Research article

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Talima Pearson1, Philip Giffard23, Stephen Beckstrom-Sternberg14, Raymond Auerbach115, Heidie Hornstra1, Apichai Tuanyok1, Erin P Price14, Mindy B Glass5, Benjamin Leadem1, James S Beckstrom-Sternberg4, Gerard J Allan6, Jeffrey T Foster1, David M Wagner1, Richard T Okinaka17, Siew Hoon Sim8, Ofori Pearson9, Zaining Wu10, Jean Chang10, Rajinder Kaul10, Alex R Hoffmaster5, Thomas S Brettin11, Richard A Robison12, Mark Mayo2, Jay E Gee5, Patrick Tan138, Bart J Currie142 and Paul Keim14*

Author affiliations

1 Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA

2 Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia

3 Menzies School of Health Research, Charles Darwin University, Darwin, Australia

4 Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA

5 Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-Borne, and Enteric Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA

6 Northern Arizona University, Department of Biological Sciences, Environmental Genetics & Genomics Facility, Flagstaff, Arizona, USA

7 Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico, USA

8 Defense Medical and Environmental Research Institute, Singapore, Republic of Singapore

9 US Geological Survey, Denver Federal Center, MS 939 Denver, Colorado, USA

10 University of Washington Genome Center and Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA

11 DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA

12 Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UT, USA

13 Genome Institute of Singapore, Singapore, Republic of Singapore

14 Northern Territory Clinical School, Royal Darwin Hospital, Darwin, Australia

15 Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA

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Citation and License

BMC Biology 2009, 7:78  doi:10.1186/1741-7007-7-78

Published: 18 November 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.