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mito carriers and evol. split

Andrew J. Roger aroger at is.dal.ca
Tue Aug 6 05:04:56 EST 1996

David R. Nelson wrote:
>         In looking at an alignment of about 130 mitochondrial carriers
> (http://drnelson.utmem.edu/nelsonhomepage.html) I have found one conserved
> motif that is repeated in these proteins that is relevant to the divergence
> of lower eukaryotes, plants and animals.  This is a position within the
> mitochondrial carrier signature motif P(hydrophobic)(D,E)XX(K,R).  This
> motif occurs 3 times in each carrier, reflecting an early gene triplication
> to form the common ancestor of these proteins.  Pro is seen in 95% of 352
> occurrences of this motif, however, it is replaced by S in 15 sequences in
> the second domain.  It seems logical to assume that P was the ancestral
> condition and S occured later.
> All 15 sequences are either plant sequences or lower eukaryotes like yeast,
> Chlamydomonas, Neurospora and one trypanosome.  The remainder of the
> sequences are animal, with two Plasmodium sequences and one Chlorella
> sequence.
>         This seems to suggest that S appeared in the second domain of these
> carriers, only in a lineage that gave rise to plants and lower eukaryotes.
> Animals appear to have retained the P at this position.
>                      S  |------ plants
>               P   |-----|
>          ---------|     |------ lower eukaryotes
>                   |------------ animals
>                      p
> This does not fit with the tree of life homepage that puts plants splitting
> first before animals and fungi diverged.
> http://phylogeny.arizona.edu/tree/eukaryotes/crown_eukaryotes.html
> I would be interested in your comments on this discrepancy.  Just how
> firmly is this divergence established?  If it is well established, how can
> I explain this observation?

The branching order (plants,(animals,fungi)) is relatively well supported 
(unlike many aspects of the tree of eukaryotes). Three relatively recent
papers report this:

Baldauf et al., Proc. Natl. Acad. Sci. USA, 90:11558-11562 (1993)
Wainright et al., Science 260:340-342 (1993)
Nikoh et al., Mol. Biol. Evol. 11:762-768 (1994)

It is also supported by ultrastructural characters--
both animals and fungi have flattened mitochondrial cristae, 
the flagellated members of both kingdoms have a single
posterior flagellum (both relatively weak characters).

Nevertheless the molecular data appears pretty solid. Explaining the
S in fungi, plants and trypanosomes involves letting
parsimony slip just a little

    *   |---trypanosomes (S)
        |   |--plants (S)
            |   |--fungi (S)
                |--animals (P)
* means transition between states

So instead of one change (transition) there are two:
1) once occurring prior to the divergence of all of the euks you mention  (P-->S)
2) once occurring prior to the animal radiation (S-->P)

Such a proposition can be tested by looking at deep branching
animals (Cnidarians, Sponges, Ctenophores and Placozoa), as
well as protist groups known to be close relatives of animals
like the myxosporidia and the choanoflagellates. If they show
S and not P, then it is pretty clear that this is the ancestral
state for the animal lineage.

Andrew Roger
aroger at is.dal.ca
Dept. of Biochemistry
Dalhousie University
Halifax, N.S.
B3H 4H7

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