[Taxacom] cladistics (was: clique analysis in textbooks)
jgrehan at sciencebuff.org
Wed Aug 17 07:41:30 CDT 2011
Pierre speaks, of course, authoritatively on such matters, so it was interesting to find myself in some agreement even though I am pretty much an amateur when it comes to the theory of clustering algorithms.
> it seems to me that the discussions could be clarified by restricting
> the use of "cladist" to name the nomenclatural procedure while using
> "parsimony" for phylogenetic analysis, the more when "cladistics" as a
> method covers a range of diverse procedures (unweighted or weighted
> parsimony with possibly different weighting schemes, compatibility
> "clique" analysis with possibly different thresholds of selection...)
> e.g. the debate about Grehanian methods would be formulated in terms
> dispensing with the use of the rather vague term "cladistics" -
> grehanistic algorithm =
> 1) perform prior character selection by applying a strict compatibility
> criterion: characters homoplastic in outgroups play no role in the
> ingroup analysis, only the clique of compatible characters are retained
> prior to ingroup detailed analysis [except for e.g. thick enamel because
> it's just so]
'Compatible' here is defined as those character states that are compatible with the criterion of being uniquely shared within the ingroup?????
Please explain the 'just so' rejection of thick enamel.
> 2) perform ingroup analysis by applying unweighted parsimony [not
> compatibility analysis] so that now homoplastic characters can play
> their role in defining subclades inside the ingroup, while this is
> denied for outgroups [according to the goose / gander principle].
What homoplastic characters?
I am not tied to any particular analysis. I've used parsimony because it's widely accepted readily accessible and presents a straightforward clustering procedure (with caveats). In principle I would be happy to use three-item analysis, although right now I do not have access to a program to do that.
> in summary: grehanistics = compatibility analysis for character
> selection outside the ingroup [with exceptions] and unweighted parsimony
> analysis inside the ingroup with the immediate consequence that the
> retained data set, hence possibly the topology of the ingroup, will
> mechanically change without biological reasons according to the scope of
> the analysis (larger or narrower ingroup)
Don't understand what is meant about how the retained data set will mechanically change without biological reasons with respect to larger or narrower ingroup.
> as already noted by John Grehan himself in a recent post
> this logical incoherence can easily be corrected by applying unweighted
> parsimony throughout, or possibly compatibility analysis throughout (for
> amateurs only)
Where this is done to include all characters, whether or not they are restricted to the ingroup, to my mind results in an analysis of overall similarity rather than cladistic derivation. I'm ok with everything being analyzed as a supermatrix of all life, although one would still end up 'selecting' character states found in 'life' rather than 'non life', or on reflection maybe according to Pierre's perspective one could include 'non life' features as well (e.g. various structural arrangements).
> grehanistics is an original method, exposed in no "cladist" textbook,
> John Grehan's claim to be "cladist" is obviously not informative in
> itself, and the question "is grehanistics cladist or not cladist" has
> little interest (what is at stake, after all?)
Some say I am a cladist, others say I am not. No sleep lost.
Le 17/08/2011 04:49, Kenneth Kinman wrote:
> Dear All,
> Gee, I am a fan of cladistic analysis (if done correctly), but I
> never thought that ANY form of cladistics was "necessarily" correct (but
> a lot that seemed better than John's, although admittedly I have seen
> some that were worse, even at higher taxonomic levels, and thus more
> detrimental and regretably sometimes accepted by far too many).
> As for some people having used "refuted" as a synonym of
> "rejected", whoever they might be, I really doubt that they are
> restricted to users of US language (as opposed to English language as a
> whole or even other languages). In any case, I predict an exclusive
> orangutan-hominid clade will continue to be both refuted and rejected.
> It has very clearly been "rejected" by the vast majority, but a small
> minority still insists that it has not been "refuted". Anyway, I'm not
> going to lose any sleep over that one, but I am admittedly still
> bothered by the question of whether chimps clade exclusively with
> gorillas or with hominids. Hopefully we will see some more informative
> papers on that subject in the near future.
> ------a user of "US language",
> Ken Kinman
> John Grehan wrote:
> Yes I am asserting that 'my' form of cladistics is necessarily
> correct - or at least more correct or better than some others. And I
> realize that I am sticking my neck out on that and perhaps setting
> myself up for a fall - in which case the orangutan evidence will not
> doubt be refuted (and I am not using that term as a synonym of rejected
> as often occurs in US language).
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