Bacterial phylogeny, was Australopithecus and orangutans

[Jason de Koning]

> evidence of isolating bacteria from amber, salt deposits and glaciers
> which range in age from
> 10,000 years to 250 million years - the assumption being that they were
> enclosed in their "geological strata" at the time it was formed. The
> problem is that all these "ancient" bugs end up at the end of branches
> (terminal taxa) and certainly do not "oblige" by taking up a position
> close
> to a node. The reason why you may get this with DNA from, say fossil
> bones,

That is quite fascinating.  If that work were based on the rejuvenation
of truly ancient spores, it would be a remarkable test.  (It would, of
course, necessarily have to deal with strains that were not simply
'anciently isolated', but were in fact frozen somehow in time and
precisely dated).  In those cases, however, if the ancient specimens
fell along long branches, not close to nodes, that could simply
indicate the possible contingency that they are not direct ancestors of
extant (sequenced) strains.  Especially if we're talking about mostly
asexual lineages, the true evolutionary history must be so 'bushy', and
the 'species' sampling of persisting lineages so great, that many
ancient specimens may have no extant 'close relatives' (or perhaps they
may not have been sampled).  But then again, if the rooting is correct,
and the evolutionary model is unsaturated, they should still branch
more basally than recently derived groups.  I'm just speculating, but
this result is not unexplainable.  I think the problem is with
phylogeny of asexuals in general--what is our expectation with current
phylogenetic methods?  I imagine this was your original point...

> in most trees other than as a terminal taxon, because most prgrammes
> could
> only handle it as an extant taxon - there are exceptions. If you

As far as I know, all programs for molecular analysis (particularly for
maximum likelihood analysis and parsimony) are capable of yielding a
tree with short (close to 0 length) branches.  It is true, I imagine,
that no programs will actually collapse a terminal taxon into an
internal node, but a branch length of zero is in consequence the same
as this.

> but take a look at the
> papers on "ancient" bacteria and you will see that this is not what
> they
> have done!

I will indeed, they sound very interesting.

Thanks,
- Jason

> Best wishes
> Brian
>
> At 11:00 16.5.2003 -0400, Jason de Koning wrote:
>>
>>> 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.
>>
>>
>> All the best,
>> - Jason
>>
>
>
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