Résumé
Toxoplasma gondii, a cyst-forming apicomplexan parasite of virtually all warm-blooded species, is the etiologic agent of toxoplasmosis, a disease causing substantial public health burden worldwide. Its wide range of host species and its global occurrence probably complicate the study of its evolutionary history, and conflicting scenarios have been proposed to explain its global spread. By analysis a global set of 156 genomes and by providing the first direct estimate of T. gondii mutation rate, we show that major Old World domestic clonal lineages have spread from Europe and Africa to the Americas in the last few centuries and hybridized with New World specific clades. These events coincide with the recent expansion in the New World of the domestic cat and of a number of rodent species, the main hosts of T. gondii in the domestic environment. By combining environmental and functional data to selection inference tools, we identify the top candidate genes under selection in these hybrid populations of North and South America. We show that a unique domestic allele inherited from the recently introduced Old World lineages has been selected in these emergent domestic populations in the New World. The selection of this domestic allele is most parsimoniously explained by local adaptation to the domestic ecotype and to transmission by domestic cats.