[Taxacom] clique analysis in texbooks (was: Evolution of human-ape relationships...)

Pierre Deleporte pierre.deleporte at univ-rennes1.fr
Thu Aug 11 11:30:24 CDT 2011 

I also consider that this discussion is becoming interesting for the 
little history of "cladistics"

John, you said that you can demonstrate a synapomorphy the way it is 
explained in "all textbooks";
can you please tell me what textbooks you currently use?
at least what is your favorite textbook, where I could find exposed both 
your particular method and your particular vocabulary?

what you call "cladistics" seems to me very close to what is universally 
known among cladists as "clique analysis" (compatibility analysis), a 
method largely debated (and rejected) by cladists in the seventies and 
eighties, as already underlined by Peter;
I can remember of no textbook recommending clique analysis 
(compatibility) as the best parsimony method for phylogeny inference;
I can remember of no textbook recommending to implement clique analysis 
by hand through a priori rejecting characters (a procedure also known as 
"character assassination" among cladists) followed by standard parsimony 
optimisation, rather than using a dedicated computer program - e.g. the 
"CLIQUE" program in Felsenstein's phylogeny inference package PHYLIP, 
finding the largest clique of compatible characters (and it's free);

the fact that you don't call your own approach by its proper name 
(clique/compatibility analysis) is for me strongly suggesting that you 
don't make reference to any classic texbook or any classic literature
so I am quite certain that your method is not "in all textbooks" (or 
demonstrate me wrong), which does not exclude the marginal possibility 
that it would be exposed and recommended in some texbook I ignore;
I would like to know what is this particular textbook, and maybe what 
you do not explain on this list is explained in this textbook...

Pierre




Le 11/08/2011 15:13, John Grehan wrote:
> Yes, that is correct - or at least that it is not cladistic analysis.
> Transformation 'series' in the sense of restricting the data set to
> putatively shared derived features - putatively since it requires some
> king of analysis to corroborate the best supported arrangements of taxa
> within the ingroup, and those not supporting that arrangement being
> homoplasious and attributed to origin other than from a unique common
> ancestor.
>
>
>
> I often see (in the study of hominid relationships at least) the
> assertion that homoplasy is a problem for analysis. I do not since
> homoplasy can only be identified after a particular relationship is
> selected.
>
>
>
> As a subset, I am not very comfortable with multistate characters as I
> do not know with any confidence how clustering algorithms treat the
> transitions. For a multi state character with states 1, 2, 3, 4 where
> the outgroup is 4 - whether the program groups 1 with 2, and then (1+2)
> with 3, and how the presence of intermediate states may affect the
> grouping of taxa where the same intermediate character state codes are
> present in more than one taxon. I have heard, but not seen any
> publication on this that I recall, that the presence of intermediate
> states in multiple ingroup taxa can affect the analysis. I would be
> interested in any comment on that as I am not an algorithm theorist.
>
>
>
> John Grehan
>
>
>
>
>
>
>
> ________________________________
>
> From: P.H. HOVENKAMP [mailto:phovenkamp at casema.nl]
> Sent: Wednesday, August 10, 2011 4:19 AM
> To: John Grehan
> Subject: Antw:Re: [Taxacom] Evolution of human-ape relationships
> remainsopenforinvestigation
>
>
>
> John,
>
> It was my distinct impression that you do not accept that cladistic
> analysis is possible without first assessing the direction of the
> transformation series. Maybe I'm right, maybe not.
>
> By the way, I seem to have problems getting my messages to the taxacom
> list - are we off-list now?
>
> Best,
>
> Peter Hovenkamp
>
> Op 09/08/11, John Grehan<jgrehan at sciencebuff.org>  schreef:
>
> And the methods that I refuse to accept are?
>
>
>
> ________________________________
>
> From: P.H. HOVENKAMP [mailto:phovenkamp at casema.nl]
> <phovenkamp at casema.nl]>
> Sent: Tuesday, August 09, 2011 3:56 PM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Evolution of human-ape relationships
> remainsopenforinvestigation
>
>
>
> This discussion is becoming interesting -- if only from a historical
> point of view.
>
> I remember that Don Colless engaged in a discussion of exactly the same
> topics in the late sixties - and was answered by Ghiselin, who, other
> than Brundin, did have an answer available. There's no mention of wodka,
> though.
> The topic was then picked up by Lundberg and others, among whom Peter
> Stevens, the oft-cited Watrous and Wheeler (QD, not WC) and Steve
> Farris. Yes, and Dick Jensen too contributed his bit. But most of this
> was played out in the 70ties and early 80ies, and as a result, cladists
> settled for the methods that John Grehan now refuses to accept. The
> papers can easily be retrieved through WOS and still make good reading.
> May I suggest that we all read these papers and come back to the
> discussion when we have digested them properly?
>
> Peter Hovenkamp
>
>
>
> Op 09/08/11, John Grehan<jgrehan at sciencebuff.org>  schreef:
>
> Don knows full well the answer if he has read the orangutan paper. The
> point of his asking the question is not the answer, but that he already
> disputes that answer (with respect to the question in general) as
> demonstrated by his reference to his inability to agree over the answer
> with Brundin. If Don would present what he sees as problematic I might
> be happy to address it.
> John Grehan
>
> -----Original Message-----
> From: Don.Colless at csiro.au [mailto:Don.Colless at csiro.au]
> <Don.Colless at csiro.au]>
> <Don.Colless at csiro.au]>
> Sent: Tuesday, August 09, 2011 1:49 AM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] Evolution of human-ape relationships
> remainsopenforinvestigation
>
> John: How do you "demonstrate"  that a character state is "derived"?
>
> Donald H. Colless
> CSIRO Ecosystem Sciences
> GPO Box 1700
> Canberra 2601
> don.colless at csiro.au
> tuz li munz est miens envirun
> ________________________________________
> From: John Grehan [jgrehan at sciencebuff.org]
> Sent: 08 August 2011 20:27
> To: Colless, Donald (CES, Black Mountain)
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] Evolution of human-ape relationships
> remainsopenforinvestigation
>
> Please explain what you see as the problem first.
>
> John Grehan
>
> -----Original Message-----
> From: Don.Colless at csiro.au [mailto:Don.Colless at csiro.au]
> <Don.Colless at csiro.au]>
> <Don.Colless at csiro.au]>
> Sent: Monday, August 08, 2011 12:56 AM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] Evolution of human-ape relationships
> remainsopenforinvestigation
>
> John: Please answer the question.
>
> Donald H. Colless
> CSIRO Ecosystem Sciences
> GPO Box 1700
> Canberra 2601
> don.colless at csiro.au
> tuz li munz est miens envirun
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu
> [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
> [jgrehan at sciencebuff.org]
> Sent: 07 August 2011 00:06
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Evolution of human-ape relationships remains
> openforinvestigation
>
>   Hey, if it could not be done with Brundin, then perhaps it cannot be
> done at all and systematics is just a delusion. It seems that for the
> most part, systematists (including molecular) aspire to something called
> cladistics. All we did was follow what we understand as necessary
> protocols to show that the preponderance of mrophogenetic evidence
> supports the orangutan relationship, and that so far this evidence is
> 'better' than the critics have come up with. Of course that is just our
> opinion, but our 'legal brief' is there for anyone to argue for or
> against. At least the theory has now transitioned from the level of
> being totally ignored to being attacked. Progress of sorts perhaps.
>
> John Grehan
>
> -----Original Message-----
> From: Don.Colless at csiro.au [mailto:Don.Colless at csiro.au]
> <Don.Colless at csiro.au]>
> <Don.Colless at csiro.au]>
> Sent: Saturday, August 06, 2011 2:27 AM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] Evolution of human-ape relationships remains
> openforinvestigation
>
> I do wish John would show us how to "demonstrate" that a character state
> is "derived" and its sharing therefore a synapomorphy. I once tried this
> on Lars Brundin, but all we could finally agree on was that the vodka
> botle was empty.
>
> Donald H. Colless
> CSIRO Ecosystem Sciences
> GPO Box 1700
> Canberra 2601
> don.colless at csiro.au
> tuz li munz est miens envirun
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu
> [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
> [jgrehan at sciencebuff.org]
> Sent: 05 August 2011 21:35
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Evolution of human-ape relationships remains open
> forinvestigation
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu]
> <taxacom-bounces at mailman.nhm.ku.edu]>
> <taxacom-bounces at mailman.nhm.ku.edu]>  On Behalf Of Kenneth Kinman
> Sent: Thursday, August 04, 2011 10:54 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Evolution of human-ape relationships remains open
> forinvestigation
>
> Interesting:
>>        The last sentence in the abstract refers to "the fact that
>> identification of shared similarity does not translate into
>> demonstration of synapomorphy."
>>        Ironically, that has actually been my biggest criticism of the
>> theory that orangutans and hominids form an exclusive clade---that the
>> identification of shared similarities between orangutans and hominids
>> does not translate into a demonstration of synapomorphies (but that
>> they are actually most likely symplesiomorphies).
> If one reads the paper one will see that similarity alone is does not
> translate into a demonstration of synapomorphy, whereas  shared derived
> similarities (which is what we use) does. That is the difference. Quite
> simple really.
>
>
>>       So I certainly agree with the subject line that the "Evolution of
>> human-ape relationships remains open", although a third theory (that
>> chimps and gorillas form an exclusive clade) is sadly not getting the
>> attention that it probably deserves.
> We do, if one reads the 2009 paper.
>
>> Meanwhile, those championing exclusive chimp-hominid or orangutan-
>> hominid clades are probably BOTH labelling symplesiomorphies as
>> synapomorphies.  So I don't sympathesize with either side of that
>> debate, and that both are probably throwing rocks from glass houses.
>                 -------Ken Kinman
>
> One is entitled to take any view one prefers, but in this case the above
> opinion is noting more than an opinion, and one that has no empirical
> grounding.
>
> John Grehan
>
> --------------------------------------------------------
>
> Last sentence in the abstract reads:
>         In brief, DOM fails both to test theories of relatedness and to
> take into account the fact that identification of shared similarity does
> not translate into demonstration of synapomorphy.
>
>
>
>
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-- 
Pierre DELEPORTE
UMR6552 EthoS
Université Rennes 1
CNRS
Station Biologique
35380 PAIMPONT
tél (+33) 02 99 61 81 63
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