Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum
The basic topology and branch lengths of the tree come from the output for the BEAST analysis made while estimating evolutionary rates. From this tree we collapsed branches with less than 0.6 posterior probability or if there were no phylogenetically informative SNPs supporting that branch. Several strains are shown as polytomies because their genomic histories are shaped by recombination. Within the House Finch MG clade, branch lengths are proportional to time. Major genomic events are indicated on appropriate branches. The numbers of diagnostic SNPs indicated on various branches are minima. The numbers of CRISPR changes shown are only those that can be constructed with reasonable support (Figure 5); one possible reconstruction is presented.