Australopithecus and orangutans

[Jason de Koning]

> The question is not whether one accepts gene or protein sequence data,
> but
> how one interprets that data and the possibility of congruence with
> other
> data.

I agree, this should be the question.

> Most tree modelling systems assume bifurcation - I don't think we can
> assume that this holds true in nature. Such a system also assumes that
> a)

Again, I agree and this may be problematic, particularly in prokaryotes
and plants without strict sexual reproduction.  We occasionally see
unresolved multifurcations even in strictly sexually reproducing
mammalian groups, where some very rapid speciation events probably
occurred.  Is this a "failure" of tree building methods due to
insufficient data to resolve the proper series of bifurcating splits,
or does it imply that the true history was a radiation?  I think that
answer is unknown, and perhaps unknowable in any general way.

> Such a system also assumes that a)
> the ancestors always become extinct and that b) we can always identify
> the
> terminal taxa. If you were to analyse the genes of children, their
> parents
> and the grand parents unless you knew in advance which were the
> "ancestors"
> you would not get a "true reflection" of the "real phylogeny". In the
> case
> of organisms with a known fossil record this may not be so much of a
> problem, but the problem has become acute in the absence of a fossil
> record
> i.e. in the case of prokaryotes.

I do disagree here.  Strictly speaking, any taxon which remains extant
is a terminal taxon.  Reconstructing the genealogy of individuals of
the same species isn't a fair analogy, in my opinion.  In the case of
the experiment described in the paper, there is no natural analogous
situation to sequencing genes from the simulated ancestors.  You'd have
to travel back in time; but what were then the ancestral taxa, are
today either something else (terminal taxa), or are extinct.   I do
believe that in that study, however, they did sample ancestral
sequences, and they were nearly identical to the statistically
reconstructed ancestral states (using the same model as estimated for
phylogenetic reconstruction).  That means that if they included the
ancestral sequences in their phylogenetic analysis (which is impossible
to do in systematics, excepting ancient DNA), they would have appeared
as near-zero length branches at the appropriate internal nodes.

> The point is not whether one uses the sequence data, but what that
> data is
> telling us. As a microbiologist I am fully aware of the contribution
> which
> the sequence data has made to our understanding of prokaryote
> systematics,
> but I am also aware of some of the problems which are there and are
> simply
> ignored. The message is caution, as with most data sets.
> Best wishes
> Brian

That sounds imminently reasonable to me.

All the best,
- Jason