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


CONCLUSIONS
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.
Pearson
Talima
T
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA. Talima.Pearson@NAU.edu
Giffard
Philip
P
Beckstrom-Sternberg
Stephen
S
Auerbach
Raymond
R
Hornstra
Heidie
H
Tuanyok
Apichai
A
Price
Erin P
EP
Glass
Mindy B
MB
Leadem
Benjamin
B
Beckstrom-Sternberg
James S
JS
Allan
Gerard J
GJ
Foster
Jeffrey T
JT
Wagner
David M
DM
Okinaka
Richard T
RT
Sim
Siew Hoon
SH
Pearson
Ofori
O
Wu
Zaining
Z
Chang
Jean
J
Kaul
Rajinder
R
Hoffmaster
Alex R
AR
Brettin
Thomas S
TS
Robison
Richard A
RA
Mayo
Mark
M
Gee
Jay E
JE
Tan
Patrick
P
Currie
Bart J
BJ
Keim
Paul
P
D001315:Australia; D016957:Burkholderia pseudomallei / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000502:physiology*; D005798:Genes, Bacterial; D005828:Genetics, Population; D016680:Genome, Bacterial; D006801:Humans; D017720:Molecular Epidemiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
D004269:DNA, Bacterial