Maximum likelihood tree of COII-ND1 sequences (unique haplotypes).
Clades and subclades are indicated according to corresponding major T. cruzi lineage (see text). Black circles indicate TcIII haplotypes and black triangles indicate TcIV haplotypes, clearly showing paraphyly of TcIV and TcIII sequences and sharing of identical haplotypes between subsets of TcIII and TcIV samples. Where clear geographic associations were evident these are indicated using standard two letter country codes; TcIV(SA) are TcIV samples from South America. Bootstrap support values for branches (if >50%) are shown and were calculated for the equivalent nodes of the bootstrap consensus NJ/MP trees (1000 replicates). Scale units are substitutions/site.