Extraordinary Trypanosoma cruzi diversity within single mammalian reservoir hosts implies a mechanism of diversifying selection

► We report extraordinary genetic diversity within single reservoir hosts of Trypanosoma cruzi. ► Two hundred and thirty-three biological clones were taken from eight mammals. ► Nine polymorphic microsatellite markers were amplified. ► Forty-nine distinct multilocus genotypes were defined. ► Widespread multiclonality contrasts with the precarious nature of T. cruzi vectorial transmission. ► We propose that non-neutral processes could account for the diversity observed.