polymorphic to conserved sites is equivalent across all three datasets. (EPS) Figure S3 Illustration of the recursive method used to assign segments of the genome to phylogenetically concordant blocks. At the initialization of the algorithm the phylogenetically informative SNPs in the genome (x’s in the diagram) are used to determine continuous segments that are in agreement with all possible trees. Sections of a genome in agreement with a particular tree are shown as solid colored lines over that genome segment. Note that any one SNP can be in agreement with multiple trees. If only one of two adjacent SNPs are in agreement with a tree, then half of the distance between the two SNPs is assigned to the concordant segment. (EPS) Figure S4 Distribution of the number of phylogenetically concordant segments in the genome and in a dataset obtained by a single random permutation of the SNPs. Block sizes are in bp. (EPS) Figure S5 Distribution of the size of phylogenetically concor- dant segments in the genome and in a dataset obtained by repeatedly creating permutations of the SNPs. (EPS) Figure S6 95% HPD intervals of the rate estimated in BEAST using our actual dataset, as well as 20 permutations of the data where the dates on the tips are randomly reassigned. The interval for the true dataset is shown in red, and the randomized datasets are shown in blue. (EPS) Characteristics of MG isolates used in this study. SNP counts in the alignments. SNPs validated by PCR amplification and Sanger Cross validation of 454 and Illumina data. Estimates of genetic diversity based on the LS-MSA. Patterns of synonymous and nonsynonymous substi- Table S1 (PDF) Table S2 (PDF) Table S3 sequencing. (PDF) Table S4 (PDF) Table S5 (PDF) Table S6 tutions. (PDF) Table S8 (PDF) References Table S7 Regions of the reference genome that had been lost in House Finch MG isolates. (PDF) Descriptions of six novel insertion sites of IS elements. Table S9 Comparative evaluation of genes pseudogenized or deleted in the House Finch MG isolates. (PDF) Mutations in the UvrB gene and possible effects. Table S11 Instances of polymorphic adjacent SNPs among the house finch MG strains. (PDF) Table S12 Counts of unique and total (due to duplication) CRISPR spacers from each strain. (PDF) Sequencing, alignment, and SNP calls. Text S2 Inference of mutation rate, recombination, times to common ancestry, and population dynamics. (PDF) Evaluating the effect of frameshift and nonsense Transposon (IS) Movements. Searching for Novel Genes in the House Finch MG Table S10 (PDF) Text S1 (PDF) Text S3 mutations. (PDF) Text S4 (PDF) Text S5 isolates. (PDF) Text S6 (PDF) Text S8 (PDF) Rapid Evolution of Mycoplasma gallisepticum Detecting recombination. CRISPR Analysis Text S7 Effect of recombination on the estimated substitution rate and demonstration of true temporal signal. (PDF) Acknowledgments We thank J. Jones at the University of South Carolina Environmental Genomics Core Faciltiy for conducting the 454 sequencing; the University of Utah Huntsman Cancer Institute for Illumina sequencing; J. Banfield, C. Dale, D. Jeruzalmi, W. Smith, and members of the Marx lab for helpful dicussion; and R. Kofler for sharing programming code libraries. T. Modak and I. Soltero conducted manual SNP verification. S. Bensch, C. Anderson, and three anonymous reviewers provided helpful comments on the manuscript. Sequence data and BEAST xml files for this project were deposited in the Dryad Repository: doi:10.5061/dryad.353tj334. Author Contributions Conceived and designed the experiments: SVE GEH NFD. Performed the experiments: NFD CB SB. Analyzed the data: NFD SVE PT AR. Contributed reagents/materials/analysis tools: NFD CJM NF-N. Wrote the paper: NFD SVE GEH AR CJM. 1. Fischer J, Stallknecht D, Luttrell P, Dhondt A, Converse K (1997) Mycoplasmal conjunctivitis in wild songbirds: the spread of a new contagious disease in a mobile host population. Emerg Infect Diseases 3: 69. 2. Nolan P, Hill G, Stoehr A (1998) Sex, size, and plumage redness predict house finch survival in an epidemic. Proceedings of the Royal Society B-Biological Sciences 265: 961. 3. Dhondt AA, Dhondt KV, Hawley DM, Jennelle CS (2007) Experimental evidence for transmission of Mycoplasma gallisepticum in house finches by fomites. Avian Pathol 36: 205–208. 4. Dhondt AA, Tessglia DL, Slothower RL (1998) Epidemic mycoplasmal conjunctivitis in House Finches from eastern North America. J Wildlife Dis 34: 265–280. 5. Faustino C, Jennelle C, Connolly V, Davis A, Swarthout E, et al. (2004) Mycoplasma gallisepticum infection dynamics in a house finch population: seasonal variation in survival, encounter and transmission rate. Ecology 73: 651–669. 6. Hochachka WM, Dhondt AA (2000) Density-dependent decline of host abundance resulting from a new infectious disease. Proc Natl Acad Sci (USA) 97: 5303–5306. PLoS Genetics | www.plosgenetics.org 10 February 2012 | Volume 8 | Issue 2 | e1002511