title: Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.
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.
  
  
  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.
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA. Talima.Pearson@NAU.edu
authors.forename: Talima
authors.initials: T
authors.lastname: Pearson
authors.forename: Philip
authors.initials: P
authors.lastname: Giffard
authors.forename: Stephen
authors.initials: S
authors.lastname: Beckstrom-Sternberg
authors.forename: Raymond
authors.initials: R
authors.lastname: Auerbach
authors.forename: Heidie
authors.initials: H
authors.lastname: Hornstra
authors.forename: Apichai
authors.initials: A
authors.lastname: Tuanyok
authors.forename: Erin P
authors.initials: EP
authors.lastname: Price
authors.forename: Mindy B
authors.initials: MB
authors.lastname: Glass
authors.forename: Benjamin
authors.initials: B
authors.lastname: Leadem
authors.forename: James S
authors.initials: JS
authors.lastname: Beckstrom-Sternberg
authors.forename: Gerard J
authors.initials: GJ
authors.lastname: Allan
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Foster
authors.forename: David M
authors.initials: DM
authors.lastname: Wagner
authors.forename: Richard T
authors.initials: RT
authors.lastname: Okinaka
authors.forename: Siew Hoon
authors.initials: SH
authors.lastname: Sim
authors.forename: Ofori
authors.initials: O
authors.lastname: Pearson
authors.forename: Zaining
authors.initials: Z
authors.lastname: Wu
authors.forename: Jean
authors.initials: J
authors.lastname: Chang
authors.forename: Rajinder
authors.initials: R
authors.lastname: Kaul
authors.forename: Alex R
authors.initials: AR
authors.lastname: Hoffmaster
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Brettin
authors.forename: Richard A
authors.initials: RA
authors.lastname: Robison
authors.forename: Mark
authors.initials: M
authors.lastname: Mayo
authors.forename: Jay E
authors.initials: JE
authors.lastname: Gee
authors.forename: Patrick
authors.initials: P
authors.lastname: Tan
authors.forename: Bart J
authors.initials: BJ
authors.lastname: Currie
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
mesh_terms: 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
chemical_list: D004269:DNA, Bacterial