Genetic analyses of atypical Toxoplasma gondii strains reveal a fourth clonal lineage in North America

► Guidelines are provided for analyzing new genotypes of Toxoplasma gondii and categorizing those using population genetic tools. ► Analysis of strains of T. gondii previously designated as “atypical” reveals a new clonal lineage in North America referred to as group 12. ► Group 12 has a strongly clonal population structure. ► The abundant type 2 lineage has been the parental strain for at least three examples of natural recombinations that led to clonal expansion.