Continuity, reticulation, and classification

Ken Kinman kinman at HOTMAIL.COM
Mon Jul 23 17:07:25 CDT 2001

     Before getting back to viruses and gene evolution, I'll quickly address
the "human construct" issue.  Any bioclassification is a construct and
arbitrary.  Whether cladistic constructs are less arbitrary is debatable.
There is no real beginning or end to any species (especially when time is
considered as well as space).  The tree of life is a continuity, and any
cuts to divide it into taxa are arbitrary.  Cladistic classification is just
as arbitrary in a different way, and many cladists believe that sister
groups actually exist (which I find very troubling).  Its benefits are
marginal at best, and the drawbacks just keep getting more and more
     As for the clade/grade issue.  A paraphyletic group (called "grade",
especially by cladists who don't like them) can be effectively made a clade
by adding a marker for the outgroup that has been formally removed.  I does
NOT have to be an either-or situation any more.  I believe that Michael
Benton's 1997? book has a classification of reptiles in which there is
cross-referencing marker of this kind for birds, but they are formally
classified as a separate group.  I expect to see more such hybrid
classifications (cladisto-eclectic) in the future, including the
cladistically coded ones I prefer.
      Back to genes now.  Mammals genes are a complex collection from a
very, very long line of ancestors, each of which could have incorporated
horizontally transferred "prokaryotic" genetic material (passing it
vertically to their descendants).  Genes pop in and out of genomes all the
time, and occasionally they stay there and get passed on to the next
generation.  I would think most such transfers (horizontal or vertical) are
between relatively closely related organisms (e.g. mammal to mammal), rather
than plant to mammal or bacterium to mammal (which would be more rare).  Of
course widespread genetic-engineering of foods could eventually change that
balance if we rush into it too quickly.
     Anyway, reticulation is just one more reason strictly cladistic
classification fails to reflect the reality of evolutionary history.  Such
micro-reticulation can (with some difficulty) be studied with cladistic
analysis (and this will be increasingly done in the future as genomes are
sequenced fully and databases grow).  However, strictly cladistic
classification will most clearly betray its fundamental weaknesses (and
overly simplistic underpinnings) at this micro-genetic level----much more so
than at for instance the organelle level (i.e., the reticulate nature of the
eukaryotic cell where large numbers of genes were transferred in one
    A cladisto-eclectic system will work even at the micro-level of genetic
reticulation.  Classifications on that level of precision will admittedly be
complex, but they will not be impossible (as would be the case with
cladistic classifications that reduce evolution to an unrealistic binary
splitting pattern).
    Of course, most of us will not have to worry about gene classification
(and evolution) in such detail---thank goodness.  But a hybrid system will
allow some measure of stability over a wide range of detail---from the broad
evolution of organisms at kingdom and phylum levels down to minute details
of genetic variation among individuals.   No time to proofread, so please
forgive any typos.
              ------Ken Kinman
>From: "Panza, Robin" <PanzaR at CARNEGIEMUSEUMS.ORG>
>Reply-To: "Panza, Robin" <PanzaR at CARNEGIEMUSEUMS.ORG>
>Subject: Re: One origin? (viral evolution)
>Date: Mon, 23 Jul 2001 10:01:43 -0400
> >>>>From: Barbara Ertter [mailto:ertter at UCLINK4.BERKELEY.EDU] Does this
>that Homo sapiens (to use an example!) is paraphyletic unless all renegade
>DNA (aka viruses) are included therein?  Fun!<<<<
>So what does one do with viruses that infect more than one species?
>all its hosts and it (and all the other viruses of all those hosts, and all
>the other hosts of those viruses, etc.) a single species?
>I still say that a few mammalian genes does not a mammal make!  Mammalian
>viruses may be non-living (certainly, some virologists believe this). They
>may be living but, due to their minimalist nature, outside the ken of
>phylogenetic analysis.  If a couple of genes can define a taxon, then we're
>prokaryotes--it's my understanding that we've got bits of bacterial DNA
>inserted into our genomes, so we must be bacteria.  And I know humans share
>genes with many other eukaryotic species, so all life must be one big,
>Robin P.
>panzar at
>Pittsburgh, Pennsylvania, USA
>There is no job s simple that it can't be done wrong.

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