Peterís Notes and Links on Giardia
Pictures at MBL microscope
How to build trees:† Parsimony, ml, distance (see here)
Logdet: distances that work well when the composition of sequences varies, but the measure is very sensitive to among site rate variation.†
Long Branch Attraction (LBA) tendency to long branches to group together in phylogenetic reconstructions.† (See Olgaís online poster)
Giardia:† ATPase subunit phylogenies (as well as most other protein families) have Giardia as deepest eukaryotic branch (however Giardia shares only 5 signature residues with the outgroup, (Trichomonas share 25) (Microsporidia go with the fungi));† however, the V-ATPase is a typical eukaryotic V-ATPase.† There are no indications whatsoever that this ATPase might function in ATP synthesis (similar to the archaeal type ATP synthases (here).
Bottomline:† Giardia and other diplomonads, while possibly representing a deep branching eukaryotic lineage, do not appear to be a missing link between the prokaryotic and the eukaryotic cell organization.†