The potential value of indels as phylogenetic markers: position of trichomonads as a case study.

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Abstract
The phylogeny of eukaryotes is in a state of flux (Philippe, Germot, and Moreira 2000 ). The tree based on the small subunit ribosomal RNA, for long taken as a reference, has been challenged by the discovery of serious tree reconstruction artifacts, especially the long-branch attraction (LBA) (Felsenstein 1978 ). To eschew these methodological issues, one can improve tree reconstruction methods, especially through the implementation of more realistic models of sequence evolution, which we have called the statistical approach (Philippe and Laurent 1998 ). However, it is also possible to use the hennigian approach, i.e., the maximum parsimony method applied to less noisy characters, which are a priori not prone to convergence and reversion and thus less homoplastic. As recently reviewed (Rokas and Holland 2000 ), rare genomic changes (RGCs), like intron positions, retrotransposon insertions, insertions-deletions (known as indels), mitochondrial and nuclear DNA genetic code variants, chloroplastic and mitochondrial DNA gene orders gave several interesting results.