Rapid Evolution of Mycoplasma gallisepticum Figure 1. Overview of the genome of the House Finch strain of Mycoplasma gallisepticum summarizing variation among 12 House Finch MG isolates and comparing these to a poultry reference (0.99 Mb). Blue ticks indicate SNPs fixed within the House Finch isolates and differing from the chicken MG reference. Red ticks indicate polymorphisms among the House Finch isolates. Yellow regions are unassembled repetitive regions including VlhA and AprE genes. Grey regions indicate 4.8% of the aligned genome that is deleted in the House Finch isolates; numbers correspond to deletions detailed in Table S12. Green and light blue ticks indicate IS elements (family IS1634) in the reference genome and novel sites in the House Finch strains, respectively; letters next to novel sites correspond to insertions detailed in Table S9. doi:10.1371/journal.pgen.1002511.g001 totaling 9,275 bp were shared among all strains except the reference. In addition, we detected six novel IS element insertions in the House Finch MG lineage (Text S3, Table S8) and three of the genomic deletions were likely mediated by illegitimate recombination between flanking IS elements (Table S7). In addition to the 34 genes deleted as part of genomic deletions, we found evidence for pseudogenization of 19 genes relative to the chicken MG reference (Text S3, Table S9). Two genes appear to have been disrupted by transposon insertions and 17 genes were pseudogenized by frameshift or nonsense mutations (Table S9). The substantial gene losses we detected, a total of 52 genes (,8.6%) fixed in the House Finch MG lineage, presumably as a result of the bottleneck during host switch. By contrast, we failed to find a single novel gene in House Finch MG that was not also found in the poultry MG strains (Text S5). Comparative analysis with other Mycoplasma genomes showed that 15% of these lost genes also lacked a homologue in the other genomes surveyed whereas 13% had a homologue in every genome (Table S9). Recombination and lateral gene flow Despite the small amount of genetic variation segregating among our House Finch Mycoplasma samples (only 412 SNPs), it is not possible to construct a phylogenetic tree for these strains that is free of homoplasies. Although the four 2007 strains and all 2001 PLoS Genetics | www.plosgenetics.org 3 February 2012 | Volume 8 | Issue 2 | e1002511