Figure 5

Use case 4. Identify recombination. Recombination among bacterial genomes leaves genomic footprints that are identifiable by tests of homoplasy (i.e., phylogenetic inconsistency). (A) The “four-gametes” test. Two SNP sites within the b18-b19 IGS region are shown. All four possible haplotypes (labeled “1” through “4” and highlighted in yellow) are present in this region among the 14 B. burgdorferi sensu stricto genomes, suggesting at least one recombination event between these two SNP sites. (B) Cross-species gene conversion. A codon alignment of a region of b22 is shown. The B. burgdorferi sensu stricto strain BOL26 has a haplotype in this region that closely resembles its homologs in two B. afzelii strains (PKo and ACA-1), caused apparently by a replacement of the allele in BOL26 by an allele originated from a B. afzelii strain. (C) The “sister-group” test. Two SNP sites in a18 segregating between 156a and 297, two phylogenetic sister-group strains, are shown. The “C” at the first SNP site is a singleton while both alleles at the second SNP site have multiple copies. Since sister-group genomes are most closely related to each other, the first SNP suggests a recent point mutation (non-synonymous in this case) while the second SNP is likely to be introduced by recombination. The latter two analyses require a phylogenetic framework.