[Taxacom] SINES, LINES and chromosomal rearrangements

John Grehan jgrehan at sciencebuff.org
Mon May 9 09:51:36 CDT 2011


-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Pierre Deleporte
Sent: Monday, May 09, 2011 10:09 AM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] SINES, LINES and chromosomal rearrangements


> OK, my statement wa a shortcoming

> the fact is that your ingroup is so small that your approach _nearly 
> boils down to_ a priori clique analysis
> because you reject from the analysis characters showing some homoplasy 
> in ougroups

You mean I reject from the analysis of the ingroup relationships those characters that show the same character state in the outgroup (in this case gibbons and OW monkeys)?

> if you included more species in your ingroup, some characters you reject 
> a priori because you already observed their homoplasy would be included 
> in the analysis,
> would you use your usual standard parsimony analysis with PAUP (and, OK, 
> not a clique analysis)

But I included all species that are known to exist. What else can one do?

> now your position did not change:
> you will not analyse molecular data
> although you could perfectly analyse them "your own pet way"-
> this may be a comfortable psychological protection (refusing to see what 
> happens),
> but it has no logical justification

To the contrary - there is a logical justification, but of course one over which we differ.

> so you go on saying that molecularists analyse their data the wrong way 
> = "phenetically",
> even when they analyse them cladistically (e.g. parsimony with PAUP, 
> just like you...)

Yes they use clustering algorithms used by cladists, but it is my contention hat this does not make their analysis cladistic because they cannot (or have not so far) restrict the character data to shared derived states.

> and alternatively / complementarily you qualify molecular data of being 
> "phenetic" in themselves,
> which make no sense at all under any definition of "phenetics" since the 
> beginnings of phenetics

In phenetic analysis there is no restriction of character states to those that are shared derived.

> now 3-item analysis pops up in your last post below, really at no 
> surprise for me

> a must reading about this bizarre approach is Farris 2010, "Systematic 
> foundering", Cladistics 27 p.207-220
> ( = a criticism of the recent book by Williams and Ebach "Foundations of 
> systematics and biogeography")
> 3-item analysis is not the standard parsimony analysis (neither 
> classical "cladistics", nor clique analysis)
> it simply does not optimize character state contiguity on the cladogram
> this approach has never been the object of any attempt at a biological 
> (or biogeographical) justification,
> particularly not at any evolutionary justification

Well, each to their own as far as what is bizarre or not. I liked the idea of each character being represented as a definitive relationship.

> among other bizarre statements, the authors consider that molecular data 
> have no hierarchical structure,
> which sounds much like your own position that molecular data are 
> "phenetic" in themselves

Well, whether it is bizarre or not remains to be seen. No more bizarre than the contention that morphology is unreliable and cannot provide the foundation for the tree of life while at the other side of the mouth they say that fossils can be definitively recognized in their relationship to the living and are so definitive that they can be used to calibrate molecular clocks.

> now the authors also consider that standard "cladistic" parsimony analysis
> (like you performed with PAUP) _is "phenetic"_
> more generally, it appears that any non-3-itemic approach is "phenetic"
> (according to an odd, esoteric concept of "pheneticism" of course,
> distorted from a comment by Nelson in the eighties...
> but it is a too long and boring story of nonsense to tell)

I can see that PAUP of itself is just a similarity method for clustering data and there have been enough papers out there that draw attention to those constraints. But as I said, I use it because everyone else does and it suits me to do so for that reason.

> good luck John if you try and understand this one...

And good luck to you Pierre in your efforts to understand different perspectives.

> but it's just a variation on the (ana-)thema "other methods and data are 
> phenetic" (= they are bad),
> and in this respect it sounds very much like your own position,
> so I understand the attractiveness of such 3-itemism for you... at first 
> glance

For the future then.

> by the way, Farris for one should know what phenetics is all about,
> being himself trained in (real) phenetics some times ago,
> and quite good at it for that...

Perhaps so.

John Grehan

Pierre


Le 09/05/2011 14:46, John Grehan wrote:
> "You say that I select a priori a set of non-homoplastic
> characters like Dick Jensen just explained it" but that would mean there would be nothing to analyze. I do not understand your assertion since my approach is to include all characters with derived character states for the ingroup that may be shared by any two or more taxa belonging to that ingroup, not just a non-homplastic set. My understanding is that using characters that have derived states within the in-group is the basis of cladistics (am I wrong?). After that the method of analysis used for picking the best set does not matter so much to me - whether it is parsimony analysis or any other clustering analysis. I've used PAUP because it is widely used and so does not become a red herring with respect to the result. From what I understand of it, 3-item analysis might be a lot more suitable.
>
> As for molecular data - there are plenty of others who have analyzed that data so I don't need to repeat what I consider their misunderstandings.
>
> John Grehan
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Pierre Deleporte
> Sent: Monday, May 09, 2011 8:35 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] SINES, LINES and chromosomal rearrangements
>
>
> With permission, John,
>
> may I recall you that I explained you on this list (some years ago now)
> that what you call "cladistic" analysis IS clique analysis properly
> (=finding the largest set of mutually compatible characters =
> "compatibility" analysis, = you select a priori a set of non-homoplastic
> characters like Dick Jensen just explained it) -
>
> so I invited your readers to understand "clique analysis" every time you
> had written "cladistic";
> I also invited you to write "clique analysis" any time you mean it, to
> be understood by your readers -
> without such a correction, many of your statements concerning
> "cladistics" are not (logically) understandable
>
> I observe that you have persisted in using "cladistics" instead of
> compatibility-clique analysis
>
> I otherwise suggested that you should use the clique analysis algorithm
> to analyse your morphological data,
> so that you can realise that this algorithm does exactly what you do by
> hand;
>
> and also that you should analyse some molecular data the same way,
> finally demonstrating by yourself that molecular data are not "phenetic"
> in themselves,
> for the very good reason that you would have yourself analysed these
> data your proper "cladistic" way (=clique analysis).
>
> last time I exposed this to you, you concluded that you would'nt analyse
> molecular data yourself anyway -
> now, clique analysis being practically no more in use in contemporaneous
> phylogenetics since decades, there is little chance that you ever find a
> molecular analysis (or even a morphological analysis) fitting your taste
> in the contemporaneous literature
>
> let's see what happens this time... will you perform a molecular clique
> analysis and have the sudden revelation that molecular data are not
> "phenetic" in themselves?... who bets?
>
> Pierre
>
>
>    Le 06/05/2011 15:28, John Grehan a écrit :
>> Perhaps it's my ignorance, but picking the largest set of mutually
>> congruent characters seems like it's effectively the same thing as a
>> 'tree'. But then I admit my ignorance of the clique analysis algorithm
>> and accept I could be wrong in that assertion.
>>
>> John Grehan
>>
>>
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu
>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard Jensen
>> Sent: Friday, May 06, 2011 9:23 AM
>> To: taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] SINES, LINES and chromosomal rearrangements
>>
>> Ah, but that was the beauty of clique analysis.  One could, without
>> reference to any tree, find the greatest number of characters in the
>> data set that were mutually congruent.  Then one could build a tree on
>> which those characters (the maximum clique) illustrated no homoplasy.
>> All other characters were, by definition, homoplasious on that tree!
>>
>> Dick J
>>
>> On 5/6/2011 9:17 AM, John Grehan wrote:
>>> Ok - I get that. As long as there is character incongruence there is
>>> homoplasy, although if one is limited to two characters then one
>> cannot
>>> make a choice as to which. That still appears to correspond to my
>> point
>>> that one has to have a tree to identify homoplasious features (and
>> also
>>> determine how much of a 'problem' the level of homoplasy depending on
>>> the strength (as measured by whatever indices) of that tree.
>>>
>>> John Grehan
>>>
>>> -----Original Message-----
>>> From: taxacom-bounces at mailman.nhm.ku.edu
>>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard
>> Jensen
>>> Sent: Friday, May 06, 2011 9:08 AM
>>> To: taxacom at mailman.nhm.ku.edu
>>> Subject: Re: [Taxacom] SINES, LINES and chromosomal rearrangements
>>>
>>> Meacham showed that one did not need a tree to determine the presence
>> of
>>> homoplasy.  The question was, could these two characters support the
>>> same tree?  He domeonstrated that one could answer that question
>> without
>>> reference to a tree.
>>>
>>> This seemed to me a valuable insight, especially if one had reason to
>>> hypothesize that one character was likely to be more informative than
>>> the other.
>>>
>>> Dick J
>>>
>>> On 5/6/2011 8:55 AM, John Grehan wrote:
>>>> I think you are just saying what I said in a different way - that
>>>> homoplasy is recognized only in relation to the product of analysis -
>>>> i.e. the tree. One has to have a result (a tree) to assess whether
>>>> individual characters correspond. Those that do not are called
>>>> homoplasies (unless I got the totally wrong).
>>>>
>>>> John Grehan
>>>>
>>>> -----Original Message-----
>>>> From: taxacom-bounces at mailman.nhm.ku.edu
>>>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard
>>> Jensen
>>>> Sent: Friday, May 06, 2011 8:49 AM
>>>> To: taxacom at mailman.nhm.ku.edu
>>>> Subject: Re: [Taxacom] SINES, LINES and chromosomal rearrangements
>>>>
>>>> Sorry, John, but that's not quite right.  As Meacham demonstrated in
>>> the
>>>> early '80's, one can determine, a priori, whether or not any  two
>>>> characters will support the same tree.  Thus, if they disagree, at
>>> least
>>>> one of them will be homoplasious on any tree. My suspicion is that
>>> this
>>>> has been much ignored because it was presented in the context of
>>>> conducting clique analyses.  But the idea extends to any data matrix.
>>>>
>>>> Dick J
>>>>
>>>>
>>>> On 5/6/2011 8:09 AM, John Grehan wrote:
>>>>> The homoplasy argument is ad hoc. The only way own knows about
>>>> homoplasy
>>>>> is after the analysis. In the case of the human-great ape
>>>>> morphogenetics, homoplasy seems to be relatively unproblematic since
>>>>> there is such a great majority of congruent characters supporting
>> the
>>>>> human-orangutan clade.
>>>>>
>>>>> John Grehan
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: taxacom-bounces at mailman.nhm.ku.edu
>>>>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth
>>>> Kinman
>>>>> Sent: Wednesday, April 06, 2011 11:48 PM
>>>>> To: taxacom at mailman.nhm.ku.edu
>>>>> Subject: [Taxacom] SINES,LINES and chromosomal rearrangements (was:
>>>>> contamination)
>>>>>
>>>>> Hi John,
>>>>>             I'll certainly agree with your second point, that
>> examining
>>>> the
>>>>> human-great ape question will be heuristically valuable and the
>>>> results
>>>>> could well surprise many researchers long convinced of an exclusive
>>>>> chimp-hominid clade.
>>>>>            However, although we agree that an exclusive
>> "chimp-gorilla"
>>>> clade
>>>>> is probably a very good bet, I would also bet that your contention
>>>> that
>>>>> there is also an exclusive "orangutan-hominid" clade is due to your
>>>>> inordinate distrust of molecular data (even SINEs and LINEs and
>> wider
>>>>> chromosomal arrangements, which are clearly more reliable than
>> simple
>>>>> indels, and undoubtedly often more reliable than a lot of
>> macroscopic
>>>>> morphologies that you seem to prefer).  Most of your arguments have
>>>> been
>>>>> directed at indels (which are clearly less reliable).
>>>>>
>>>>>              Anway, this is another middle ground approach that I
>> think
>>> is
>>>>> superior.  Large molecular sequences (SINES, the even larger LINES,
>>>> and
>>>>> the even larger chromosomal rearrangements) are where we should
>>>>> concentrate.  Simplistic indels and morphological characters are
>>> often
>>>>> too subject to homoplasy, so many on both sides of that debate
>>>>> ultimately miss the mark.
>>>>>                       -----------Ken Kinman
>>>>> P.S.  This all sort of reminds me of the political debate in
>>>> Washington
>>>>> whether the Democrats or Republicans have the best ideas.  Those few
>>>>> Independents who want to follow a middle ground approach get almost
>>> no
>>>>> media coverage whatsoever.  The media just covers the extremes
>>> because
>>>>> confrontation "sells" ot the masses in general (sort of like
>> sports).
>>>>> But the scientific media is even more negligent, because it tends to
>>>>> favor one extreme only (strict cladism) and usually ignores any
>>>>> arguments for paraphyly (be they moderate or extreme).  But I still
>>>>> think that many strict cladists will eventually be maligned like
>> Wall
>>>>> Streeters are increasing being maligned for their extreme (and often
>>>>> misleading) views on what would actually benefit the vast majority
>> in
>>>>> the long run.  But thanks to the U.S. government, many Wall
>> Streeters
>>>>> are still raking in obscene profits playing computer games with
>> other
>>>>> people's money.  Not that strict cladists (or any other biologists)
>>>> are
>>>>> sharing in that excess of governmental welfare (and lack of
>>>> regulation),
>>>>> but strict cladists certainly seem to fare a lot better than those
>>> who
>>>>> are not strict cladists.  Not because they are right, but because
>>> they
>>>>> have more clever lobbyists.
>>>>>        -------------------------------------------------------------
>>>>>
>>>>> John Grehan responded to my post:
>>>>>
>>>>>> perhaps the best bet (my hypothesis) is that an orangutan
>>>>>> clade split off next, then a hominid clade, and finally>the
>>>>>> chimp-gorilla clade.  This would explain the morphological
>>>>> similarities
>>>>>> of orangtans and hominids (great ape "plesiomorphies" of>two
>>> adjacent
>>>>>> basal clades).
>>>>> It would explain them that way only if that were the case. While Ken
>>>> may
>>>>> think it's the best bet, in my differing opinion there is no
>>> necessary
>>>>> imperative for the evidence to lead to that.
>>>>>
>>>>>> If a lot more attention were paid to proving or disproving>an
>>>>>> exclusive chimp-gorilla clade, we might actually get>somewhere,  As
>>>>> long
>>>>>> as the chimp-hominid clade is regarded as "solid", there>will be
>>>>>> researchers out there challenging that hypothesis if it is>not
>>> backed
>>>>> up
>>>>>> by strong morphological characters.  I agree with John on>that, but
>>> I
>>>>>> still doubt that this means orangutans and hominids form>an
>>> exclusive
>>>>>> clade.
>>>>> I see the human-great ape question as a heuristic for the challenge
>>> of
>>>>> dealing with incongruent sequence and morphogenetic evidence.
>> Because
>>>>> the question of human origins is so prominent the matter is not so
>>>> easy
>>>>> to sweep under the carpet as it may be with more obscure groups.
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>>
>>>>> Taxacom Mailing List
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>>>>>
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>>>>> _______________________________________________
>>>>>
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>


-- 
Pierre DELEPORTE
UMR6552 EthoS
Université Rennes 1
CNRS
Station Biologique
35380 PAIMPONT
tél (+33) 02 99 61 81 63
fax (+33) 02 99 61 81 88


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