More on the 'cladistics' of sequences
skala at INCOMA.CZ
Tue Jun 8 16:41:49 CDT 2004
I do not want to reinvent the weels but still - there is one side fact that seems to be often overlooked:
Outgroup(s) is(are) used for character matrix polarization in an "absolute way", i.e. the character states found in outgroup(s) are believed to represent plesiomorphic states for the group in question. Consequently, all the "homoplasy burden" is placed on the group studied. This seems to be unbalanced approach - the character states found in outgroup should be given some probability of being homoplastic too; there is no reason why the homoplasies should arise only in the group under question while outgroup would be homoplasy-free. (perhaps even contrary is true - outgroup is by definition longer branch than any of the internal branches of the group studied, so the probability of homoplasies (provided being a function of the evolutionary time) is higher in the outgroup than in the internal branches).
This will of course further obscure the outgroup-ingroup relations, especially when taking into account that the clade structure of the multiple outgroups is unknown.
From: pierre deleporte [mailto:pierre.deleporte at UNIV-RENNES1.FR]
Sent: Tuesday, June 08, 2004 2:19 PM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: More on the 'cladistics' of sequences
A 13:37 07/06/2004 -0400, Herb wrote:
>It does bring up the point touch on by Zdenek Skala: If taxa are not in the
>outgroup are they then in the ingroup, or is there a limbo out there? For
>example if I find that taxa A,B,&C used as outgroups each changes the ingroup
>topology but find that C,D,&E produce the same ingroup topology, does that
>that A,B&C are really part of the ingroup?
I fear you simply can't get the answer by counting this way. It's a
topological question: maybe A, or B, or C+D+E is the true outgroup to the
remaining of the taxa. The mere fact that (C,D,E) are three terminal taxa
rooting in the same place changes nothing at all to the conclusion that
"there is some error somewhere", but we still don't know where.
The recommendable solution is to enlarge the phylogenetic scope of the
analysis, putting all these taxa together in the analysis as the putative
ingroup, and picking putative outgroups outside (had I said "farther away",
Zdenek would certainly have suggested: "phenetic criterion"!).
> Whether building a tree this way is
>phenetic or not is an idea that I will have to think about.
I think this "counting" argument has something to do with, for instance,
the majority rule consensus. When you have several optimal topologies for a
data set, some researchers suggest to count the number of times one clade
is supported and use this criterion in order to try and reduce the range of
acceptable topologies. I think this is no argument, because each and every
topology is as plausible as other ones. The same way, the trio "C,D,E"
provides just a different rooting compared to that implied by "A" or "B",
and each rooting is both as plausible and as puzzling than the two other ones.
Note that you can, and even should, put all five putative outgroups
A,B,C,D,E together in the analysis. Outgroups can displace the relative
position of taxa in the ingroup, but there is little argument against
putting more relevant data in the analysis, and no argument in favor of one
against another putative outgroup. Everything being equal otherwise, i.e.
that you have no a priroi strong argument for discarding one or another of
these putative outgroups as likely misleading (very doubtful alignment for
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