[Taxacom] SINES, LINES and chromosomal rearrangements (was: contamination)

[Kenneth Kinman]

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.