Toxoplasma gondii, an obligate intracellular protozoan of the phylum Apicomplexa, is estimated to infect over a billion people worldwide as well as a great many other mammalian and avian hosts. Despite this ubiquity, the vast majority of human infections in Europe and North America are thought to be due to only three genotypes. Using a genome-wide analysis of single-nucleotide polymorphisms, we have constructed a genealogy for these three lines. The data indicate that types I and III are second-and first-generation offspring, respectively, of a cross between a type II strain and one of two ancestral strains. An extant T. gondii strain (P89) appears to be the modern descendant of the non-type II parent of type III, making the full genealogy of the type III clonotype known. The simplicity of this family tree demonstrates that even a single cross can lead to the emergence and dominance of a new clonal genotype that completely alters the population biology of a sexual pathogen.clonal population structure ͉ genetic recombination ͉ virulence A central question in understanding the biology of parasitic protozoa is the role of sexual reproduction in shaping their population structure (1). In Toxoplasma gondii, the sexual cycle occurs exclusively within felines, but this species is an unusual coccidian parasite in that transmission can also occur between intermediate hosts (e.g., an infected mouse eaten by a hawk) and so propagation does not depend on sexual reproduction (2). When the parasite does enter the sexual cycle in a cat, an individual parasite can give rise to an infection that includes both micro-and macrogametes (3); therefore, self-mating will be the rule unless the cat ingests multiple strains simultaneously or in rapid succession (4).These properties have led to an unusual population structure for Toxoplasma: in North America and Europe, at least, a majority of the isolates obtained from humans and livestock appear to fall into just three clonal lineages (5-7). Remarkably, these three clonotypes, as well as many of the less common strains, appear to represent the recent merging of two distinct gene pools (8, 9), because among these strains there are just two major allelic types for each locus (9, 10). The success of Toxoplasma as a parasite belies this genetic simplicity: it can infect almost any warm-blooded vertebrate, and it maintains a high prevalence in many host species, including humans. It appears, then, that much of the ''success'' of Toxoplasma in certain geographical locales is due to the emergence of only a few lines that have dramatically enhanced fitness when compared to other genotypes (8,9). Similar clonal population structures have been described in other parasitic protozoa (1), and although the mechanisms that led to clonal propagation may differ between species (and the clonal line), identifying the genetic basis for their emergence and eventual dominance in a large geographical area has the potential to shed considerable light on the evolution of eukaryotic pathogens. To do this, a gene...