Molecular taxonomy of trypanosomatids: some problems and pitfalls

Trypanosomids appear to have attracted the particular attention of taxonomists, and a wealth of data from studies using a variety of techniques are available. There are, however, some potential pitfalls in such studies. A general problem in the taxonomy of Trypanosomatids resides in that only a small amount of its true diversity is reflected in the reduced number of isolates identified and studied from this family. An associated problem is that of confusion over the identity of the organisms. Other concerns include the problems of long branch attractions and mutational saturation, the loss of phylogenetic signal from the accumulation of overlapping mutations, and the fact that gene phylogeny cannot be equated with organism phylogeny and that organisms are more than just the sum of their genes. Additional complications can occur due to numerous cases of horizontal gene transfer between organisms. The use of a large sample of recent isolates from the field is also important so that the true diversity of these organisms is reflected in these studies, and bias due to selection, contamination, and misidentification when isolates have been maintained for long periods in culture is eliminated.