More on the 'cladistics' of sequences

[pierre deleporte]

A 16:54 07/06/2004 +0200, vous avez écrit :
>pierre (quoting Swofford and Farris - correctly I believe :-):
>
>..given that one can always make a mistake in choosing "the" outgroup (i.e.
>choose a taxon that is in fact a member of the ingroup at stake), it's
>preferable to take into account several putative outgroups in the analysis,
>in order to try and minimize the risk.
>If they all fall into the same place on the optimal topology, there is no
>ambiguity in rooting. ...
>--------------------
>
>True, but note an interesting point: in searching for an outgroup we are 
>doing so in an phenetic way (=overall similarity, no polarization).

Thanks Zdenek, I do like your way of pitilessly tracking possible phenetic 
steps in phylogenetic approaches. Remember the thread about "not naming all 
clades"...

But in the present case, things are not necessarily so. Some notion of a 
phylogeny at a larger scale often guides the analysis.

>  This is perhaps unavoidable (no cladogram topology is known a priori)

Not the internal topology of the group under analysis, but possibly some 
notion at a larger scale. You can have an a priori notion that primates are 
among mammals, which are among tetrapods, based on the analysis of some 
characters. And then, decide to try and decipher the internal phylogeny of 
primates, while accepting that primates are a putative monophyletic group 
on the basis of prior knowledge.
Please note that by "outgroup", one needs not mean "the closest outgroup" 
(= "the" sister-group). Outgroup(s) means "standing outside the group", not 
obligatorily "the closest", which could effectively require a phenetic 
criterion as you suggest.
Please also note that well conceived programs and practice, accepting 
several outgroups, will not represent these outgroups as a resolved 
phylogenetic arrangement, but as a "bush" at the bottom of the rooted tree. 
This in order to make clear that these taxa are just used for rooting, and 
are not properly part of the putatively monophyletic ingroup under 
phylogenetic analysis.

>  but still a thing that is a bit discrediting the cladistic way of 
> thinking. If there is no limitation for phenetic selection of outgroup, 
> why not to use it more widely in the whole tree construction, somebody 
> could say. One could start with 2 taxa, add 1 as "outgroup", then add 
> next one etc. etc. ending with a "cladogram" constructed by successive 
> phenetic addition of taxa.

I think I get your point, but as stated above, the outgroup criterion is 
classically based on a decision as for some resolution of the phylogeny at 
a larger scale, and not on a phenetic criterion. As far as I know and as I 
practice...

The real objection in my view is that cladistic analysis can have no 
outgroup criterion for the basal branching of the tree of life, and this 
basal branching requires some external argument, I think some polarized 
model of the evolution of the characters at stake in the considered taxa.
But this is, and was, another thread, which you can check years ago on 
Taxacom, including the immediate jumping of Ken in the arena for tempeting 
against what he thinks is a basal misrooting of the tree of life (I mention 
this, expecting to dispense Ken with the pain of repeating himself this 
time ;-).
The point at stake in my view is that life has no relevant outgroup 
(non-life is still hard to sequence and align, or to dissect and describe 
morphologically...), and thus one has to make decisions another way before 
engaging in the procedure of outgroup rooting for detailed resolution of 
internal clades.

And to try and prevent your possible counter-argument: maybe also one can 
be tempted to make phenetic clusters inside "life" and call them putative 
clades before engaging into a classic cladistic analysis of their 
relationships... if this is done, overtly or implicitly, I think it just 
means that we still lack computing power for putting "Life" into a single 
data matrix of "all known taxa  x  all known characters" and perform the 
phylogenetic analysis under the diverse relevant evolutionary models... and 
face the abyss: now I have just one rooting decision to take, but how the 
h... will I root this one?...

Best,
Pierre



Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 66
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