Figure 4: Comparative genomics and population structure of T. gondii.

(a) Population genetic structure of T. gondii. Neighbour-net analysis based on genome-wide SNPs (802,764 common data points) from 62 isolates of T. gondii. Colour wheel indicates major clades of T. gondii. Haplogroup numbers are indicated within parenthesis based on previous designation. Pink names denote the representative strains. Scale bar, number of SNPs per site. (b) Pairwise comparison of SNPs between indicated strains to ME49 shown across 14 chromosomes. y axis=number of SNPs/10 kb window. (c) Chromosome painting of 62 T. gondii strains. Local admixture analyses were conducted on SNP blocks of size 1,000 on each of the 14 chromosomes. For each SNP block, local admixture was used to assign strains to a particular ancestral population. The shared inheritance of blocks across members reveals colour patterns that extend vertically in the plot. For example, several pink regions show strong vertical patterns bifurcating across multiple clades, although the dominant colour is not meant to imply origin. (d) Network of chromosome Ia (ChrIa) showing high conservation within most haplogroups (number) and clades. Monomorphic forms (Mono, 3′ Chimeric, 5′ Chimeric) are shared by most lineages, while a few strains are highly divergent. Scale bar, total number of changes. (e) Heatmap clustering of co-inheritance of shared blocks. The percentage of shared blocks between two strains was determined for all 62 × 62 pairwise strain comparisons (1,953 non-redundant comparisons): Scale bar, % shared blocks. Hierarchical clustering on percent shared blocks independently grouped the strains by clade.