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

Pearson, Tamila , Giffard, Philip, Beckstrom-Sternberg, Stephen , Auerbach, Raymond , Hornstra, Heidie , Tuanyok, Apichai , Price, Erin , Glass, Mindy , Leadem, Benjamin , Beckstrom-Sternberg, James , Allan, Gerard , Foster, Jeffrey , Wagner, David , Okinaka, Richard , Sim, Siew Hoon , Pearson, Ofori , Wu, Zaining , Chang, Jean , Kaul, Raginder , Hoffmaster, Alex , Brettin, Thomas , Robison, Richard , Mayo, Mark , Gee, Jay , Tan, Patrick , Currie, Bart , & Keim, Paul (2009) Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biology, 7(78), pp. 1-14.

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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.

Impact and interest:

45 citations in Scopus
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36 citations in Web of Science®

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ID Code: 42856
Item Type: Journal Article
Keywords: Phylogeographic Reconstruction, Lateral Gene Transfer, Burkholderia pseudomallei,
DOI: 10.1186/1741-7007-7-78
ISSN: 1741-7007
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > EVOLUTIONARY BIOLOGY (060300) > Biogeography and Phylogeography (060302)
Divisions: Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Deposited On: 13 Jul 2011 23:07
Last Modified: 03 Dec 2012 12:08

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