Natural and emergent Trypanosoma cruzi I genotypes revealed by mitochondrial (Cytb) and nuclear (SSU rDNA) genetic markers

► Trypanosoma cruzi I subdivided in two genotypes related to transmission cycles. ► T. cruzi I sylvatic clones phylogenetically related to hybrids TcIII/TcIV. ► Reticulation events were detected among T. cruzi I Cytb and SSU rDNA sequences.