Figure 3. Modified eBURST analysis output.

Default eBURST settings were used to analyze Sarcocystis neurona sequence types based on MS markers Sn2–Sn5 and Sn7–Sn11. MS types identified are represented as small circles and designated by lowercase letters. Lines connect MS types that are identical at 8 out of 9 MS loci and are therefore considered part of a clonal complex (CC). eBURST identified 8 clonal complexes (designated CC1–CC8) and 8 singletons. Large colored ovals are overlain to indicate the Ag type (Ag types I–XII) that characterizes each MS type identified by eBURST. MS and Ag type color schemes refer to those described in Table S1. Results support an intermediate population structure with both clonal propagation and sexual recombination. All members of CC1 possess an identical Ag type (Ag type I). MS types x and bb were found in samples with different Ag types (VII and VIII). Ag types VII and VIII differ by a single di-nucleotide indel at Ag marker SnSAG3, likely representative of drift rather than recombination as a mechanism to account for allele differences in this case. In contrast, MS type k has a markedly different Ag type (III) compared to other members of the CC2, which all possess Ag type II. Ag types II and III have different alleles at all Ag loci examined, making a recombination event the most parsimonious explanation for the difference between MS type k and other members of CC2 rather than genetic drift.