Australopithecus and orangutans

[B.J.Tindall]

I appreciate your comments, but your objections to using individuals is no
different to the methods used in the paper you quote. If you use a
bacterial strain, you are almost certainly dealing with an "indivdual -
strictly speaking a population of cells" - it's certainly not a "species".
Secondly there would appear to be some (questionable) 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,
is that "naked DNA" seems to have a limited survival in the environment - I
recall figures of no more than 100,000 years (I could be wrong), in which
case in slower evolving genes there would also be relatively few changes
compared to the modern descendants. If you really could get hold of DNA
which was 500 million years old I have my doubts about it taking up a place
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
extrapolate the ancestoral sequence and then compare it with what you have
as you have suggested, that is a different matter, but take a look at the
papers on "ancient" bacteria and you will see that this is not what they
have done!

Again I fully accept the role of sequences (protein or DNA) in helping
solve evolutionary and systematic problems, but I do not always believe
what I read!!
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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