Additional file 1 of Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus

Additional file 1: Fig. S1. Principal component analysis (PCA) reveals four defined groups. Fig. S2. Relation between genetic groups and sample mating type. Fig. S3. The unfolded Site Frequency Spectrum (SFS). Fig. S4. Recent increase of population size in clonal lineages of Magnaporthe oryzae. Fig. S5. Effect of recombination on the Magnaporthe oryzae phylogeny construction. Fig. S6. Estimated Time to Most Recent Common Ancestor (TMRCA) for clonal lineages with / without invariant sites. Fig. S7. Effect of sample size on the topology of the tree and on the estimation of divergence times. Fig. S8. Phylogenetic inference using Single Nucleotide Polymorphisms using SNAPP. Fig. S9. Phylogenetic inference using SVDquartets. Fig. S10. Two Chinese individuals display consistent introgression with the clonal lineage II. Fig. S11. Ancestry-based genomic segmentation of Chinese individuals CH1016 and HB-LTH18 reveals a 4 Mb putative introgressed region on chromosome 3. Fig. S12. Effector loadings reveal major effector loss in clonal lineage III.