[Taxacom] SINES, LINES and chromosomal rearrangements

Fri May 6 08:23:21 CDT 2011

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.
>>>
>>>
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-- 
Richard J. Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674