[Taxacom] cladistics (was: clique analysis in textbooks)

Wed Aug 17 05:39:49 CDT 2011

Hi Ken,

do you know if "cladist" originally qualified a nomenclatural procedure 
(naming only holophyletic-monophyletic clades: your pet topic on this 
list) rather than a phylogenetic analysis method? (now widely called 
"parsimony analysis" or "maximum parsimony analysis" by contrast with 
"maximum likelihood analysis").
e.g. the program "PAUP" means "Phylogeny analysis using parsimony" (not 
"cladistics")
and the scope of the journal "Cladistics" is not restricted to parsimony 
analysis only

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]
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].

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), 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)

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?)

discussing the logical coherence, and further the implicit models of 
evolutionary processes (as already hinted by Richard Zander and 
attempted by Barry Roth) could help turning the debate into a 
contemporaneous discussion (be it just to please Peter)
of course reading textbooks and the relevant literature is highly 
recommended (to begin with the 2 volumes of "Advances in cladistics" and 
the following complete collection of the journal "Cladistics" as 
starters - at least it's what I did when I got interested in 
"cladistics" in the eighties)

best,
Pierre

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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-- 
Pierre DELEPORTE
UMR 6552 EthoS
Université Rennes 1, CNRS
Station Biologique
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