[Taxacom] SINES, LINES and chromosomal rearrangements

[John Grehan]

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


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