To further investigate the phylogeny of protozoa from the order Kineto
plastida we have sequenced the small subunit (SSU) and a portion of th
e large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences we
re determined from a lizard trypanosome, Trypanosoma scelopori and a b
odonid, Rhynchobodo sp., and the LSU sequences were determined from an
insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigel
la trypaniformis. Contrary to previous results, in which trypanosomes
were found to be paraphyletic, with Trypanosoma brucei representing th
e earliest-diverging lineage, we have now found evidence for the monop
hyly of trypanosomes. Addition of new taxa which subdivide long branch
es (such as that of T. brucei) have helped to identify homoplasies res
ponsible for the paraphyletic trees in previous studies. Although the
monophyly of the trypanosome clade is supported in the bootstrap analy
ses for maximum likelihood at 97% and maximum parsimony at 92%, there
is only a small difference in In-likelihood value or tree length betwe
en the most optimal monophyletic tree and the best suboptimal paraphyl
etic tree. Within the trypanosomatid subtree, the clade of trypanosome
s is a sister group to the monophyletic clade of the nontrypanosome ge
nera. Different groups of trypanosomes group on the tree according to
their mode of transmission. This suggests that the adaptation to inver
tebrate vectors plays a more important role in the trypanosome evoluti
on than the adaptation to vertebrate hosts.