[Taxacom] SINES, LINES and chromosomal rearrangements

Fri May 6 08:08:15 CDT 2011

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