[Taxacom] lateral gene transfer - was Homo sapiens neanderthalensis

Kenneth Kinman kennethkinman at webtv.net
Tue Jul 6 22:24:33 CDT 2010

 joel sachs wrote: 
            Doesn't this happen every day with
lateral gene transfer amongst single-celled species?  Why would it cause
a "complication" to phylogenetics?         
Hi Joel, 
        Well, those phylogeneticists who are most
obsessed with strictly bifurcating evolution and building their strict
"cladifications" (and eliminating paraphyletic groups at any cost),
horizontal gene transfer (HGT) is particularly troubling and often
referred to as "noise". 
        In many cases that is actually too bad, because
HGT can make evolutionary history richer, more interesting and
challenging. It only becomes a major problem when researchers don't
realize that HGT is happening (a common mistake, more so in past
decades), but once that is realized, it actually can be used as an
important tool.                
       RANT ALERT (for those who don't like my rants about
the Three Domain Classification of life, it's probably best not to read
the following paragraph).    Anyway, problems in establishing a
vertical, strictly phylogenetic classification of prokaryotes (where HGT
is highest) are too often mainly blamed on HGT, and therefore ignore
other problems, especially rooting problems (which are particularly
difficult near the base of the Tree of Life).  The Three Domain
classification of life, although popular over the last 20 years, is in
my opinion the worst case of major misrooting in the history of biology.
Horizontal gene transfer just complicates the matter, but is probably
less of a problem than misrooting for prokaryotic evolution and
classification at the highest levels. It has major implications about
the nature of the earliest cellular prokaryotes, and in my opinion has
mislead increasing numbers of scientists to suggest that life on Earth
originated at high temperatures and even high pressures (such as at
"black smokers" deep in the oceans) but largely ignore more interesting
alternate proposals that life originated near freezing temperatures.
>From the standpoint of chemistry, cold temperatures, or even mild
temperatures (Darwin's warm pond) make far more sense than a
thermophilic origin of life, and yet the latter seems to be more popular
than ever. Once the so-called "Archaebacteria" (a.k.a. "Archaea") are
finally seen as derived, not "archaic", prokaryotes, all of this will
make far more sense.  But it is simplistic to place too much of the
blame on horizontal gene transfer when misrooting is still probably even
more of a problem. 

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