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

Pearson, Talima, Giffard, Philip M., Beckstrom-Sternberg, Stephen, Auerbach, Raymond, Hornstra, Heidie, Tuanyok, Apichai, Price, Erin P., Glass, Mindy B., Leadem, Benjamin R., Beckstrom-Sternberg, James S., Allan, Gerard J., Foster, Jeffrey T., Wagner, David M., Okinaka, Richard T., Sim, Siew Hoon, Pearson, Ofori, Wu, Zaining, Robison, Richard A., Mayo, Mark J., Currie, Bart J. and et al. (2009). Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biology,7:78-91.

Document type: Journal Article
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Title Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
Author Pearson, Talima
Giffard, Philip M.
Beckstrom-Sternberg, Stephen
Auerbach, Raymond
Hornstra, Heidie
Tuanyok, Apichai
Price, Erin P.
Glass, Mindy B.
Leadem, Benjamin R.
Beckstrom-Sternberg, James S.
Allan, Gerard J.
Foster, Jeffrey T.
Wagner, David M.
Okinaka, Richard T.
Sim, Siew Hoon
Pearson, Ofori
Wu, Zaining
Robison, Richard A.
Mayo, Mark J.
Currie, Bart J.
et al.
Journal Name BMC Biology
Publication Date 2009
Volume Number 7
ISSN 1741-7007   (check CDU catalogue open catalogue search in new window)
Start Page 78
End Page 91
Total Pages 14
Place of Publication United Kingdom
Publisher BioMed Central Ltd.
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.
Keywords phylogeographic reconstruction
lateral gene transfer
bacterial populations
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