Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum
a) Comparison of nucleotide diversity between historical chicken MG strains and serially sampled House Finch MG isolates for a 1.3 kb region . b) Expansion of House Finch nucleotide diversity measured across the whole-genome alignment (approximately 738 kb when considering only the 12 House Finch isolates). c) Patterns of synonymous and nonsynonymous substitution for all MG isolates sequenced in this study as well as the reference. The values in this histogram reflect estimates of ω = dn/ds across a tree including all House Finch isolates and the poultry Rlow reference. For a full list of patterns of substitution for each gene, see Data S1 (Estimates of omega.xls). d) Bayesian skyline plot estimated from the alignment of 12 of house finch Mycoplasma strains. Although the upper and lower 95% confidence limits (gray lines) on the skyline plot are substantial, the overall trend (black line) is indicative of population growth approximately 17 years before 2007, or 1990, placing the spread of MG somewhat earlier than the first field observations in 1994. Note that time is reversed so that time proceeds from left (past) to right (most recent time of sampling).