Minot S$, Melo MB$, Li F, Lu D*, Niedelman W*, Levine SS, Saeij JP. PNAS. 14;109(33):13458-63; 2012. PDF
Not so long ago people thought that Toxoplasma population structure was largely clonal and consisted of only a couple of strains that propagated mainly asexually. This was partially due because most Toxoplasma isolates were from Europe and North America and often only a couple of genetic markers were used to genotype strains. Sampling from other continents, especially South America, and the use of many more genetic markers subsequently showed that in South America a large variety of strains exist without the predominance of any specific strain.
We were interested in determining what the influence of sexual recombination was on the current Toxoplasma population structure. To do this we identified a genome-wide SNP set from 26 different strains, representing global diversity, to show that most current isolates are recent recombinants and cannot be easily grouped into a limited number of haplogroups. A complex picture emerges in which some genomic regions have not been recently exchanged between any strains, and others recently spread from one strain to many others. Particularly, three haploblocks, on chrIa, XI, and XII, have recent common ancestry across multiple diverse lineages, perhaps suggesting that these regions may contain fitness loci. Our approach improves upon current methods because it analyzes recombination-defined haploblocks, building a more precise and comprehensive genealogy of Toxoplasma. We also put forward the hypothesis that the limited Toxoplasma diversity in North America might be a result of the late Pleistocene extinction (∼11,500 y ago), which eliminated ∼80% of large vertebrates in North America, including most Felidae members, causing a severe bottleneck and the demise of most North American Toxoplasma strains.