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Tuesday, October 13, 2009

Re: BRYONET: local endemics

BRYONET

Brent,
In spite of the old saw, "it is better to keep ones mouth shut and let
people think you are stupid than to open ones mouth and prove it", I ask
the
following questions.
Are you advocating not using the term species because reality is more
complex than that simple concept? Then what do we call those taxa/clades
that are worth conserving? Clade 124!7N48?
In spite of the strict monophyly in the new Jepson Manual, I bet they still
used genus, species and family designations. Why did they use them? They
used them because they are still the only sensible way to organize and
communicate the information that is the reason for the book. What is the
rankless way of naming taxa? Do we say the ruralis clade in the Syntrichia
clade? Do we say this is the Mishler clade in the laevipila clade in the
Syntrichia clade? How about the Oregon clade in the Mishler clade in the
laevipila clade in the Syntrichia clade? At a certain point we stop, and it
is necessarily an arbitrary decision.
But if you insist on a rankless system, using binomials is a copout because
you cannot use them without some concept of rank, even if it is only by
reminding us of the Linnaean ranked system. So that question needs to be
answered with a language that can be used quickly and efficiently, and one
that gives some sense of how many clades are above and below the group we
are talking about. The Linnaean system does that with different endings for
family and class names. It is crude and oversimplified, but it works for
the most part.
Everyone knows that I do not have formal training in evaluating cladistic
and genetic studies. But even I can recognize problems with using these
tools and calling the results "truth", or maybe even the best "truth we
have". I am especially wary of studies by people unable to correctly
identify the plants they are testing, and everyone is aware of horror
stories centering on GenBank. I could well be wrong, but most of these
"definitive" studies are only using one nuclear, one mitochondrial, and one
chloroplast gene. So few genomes have been completed, much less compared,
that it seems premature to say that those three genes are the best to
unveil
the evolution of the taxa. It may well be that when more complete genomes
have been mapped, that the differences and relationships these 3 genes are
showing are minor blips compared to major groupings in other groups of as
yet unexplored genes. Moreover, most of the studies I have read use one
exemplar of a particular taxon, and often one exemplar from a particular
genus (at least in the higher order studies). What if that exemplar is the
atypical one, or worse, not even correctly identified? I have also seen
that
the addition of just one taxon/ exemplar can drastically change a tree. How
about the selection of the correct out groups, that also is very important.
The trees generated by these studies can only portray probabilities of
being
correct. If probabilities are reality, then no one has ever won the
lottery.
So I ask the question: to date, do these cladistic and genetic studies
absolutely prove something that contradicts morphology? I am not yet
convinced, but from the way you write, Brent, I get the feeling that you
accept both these methods and the conclusions that they produce as "truth".
My mind is completely open to the complexity of the tree of life that
suggest that assignation of taxonomic rank is ridiculous. I see and agree
that as soon as you have one rank, you have an infinite number of ranks. I
can see to some point, the concept of monophyly so long as the ancestor is
not included in the clade. But I feel that it is premature to use genetic
and cladistic studies to "prove" that the traditional family and generic
relationships are polyphyletic, until we have done a lot more work. It is
perfectly fair in my mind to say that these studies strongly suggest
certain
conclusions, but I do not yet believe overwhelming evidence is at hand.
I also sympathize with Richard Zander's complaint with cladistic trees that
do not identify (with names) the ancestors at any particular point of
evolutionary divergence. A new clade has does not evolve from a node, it
evolves from an organism, why can't we name it? Do rankless monophyletic
cladistic trees illuminate true evolution or hide it?
Lastly, what happens when we uncover even more complex problems like
reticulated evolution, or gene transfer between taxa, or who knows what
wondrous phenomenon? How do we talk about it? Yes, we could say this clade
has had a non-branching evolution. What if the particular evolution shows
the combination of two large clades, that is to say non-nesting? This seems
a probable scenario in less complex organisms. I know that the Linnaean
system fails here as well, but a biological species concept might
eventually
apply, even if we have trouble with the higher classifications. But, as I
understand it, strict monophyly is completely destroyed in this situation.
Brent, this is an important point in my mind, and I would like to get a
better handle on it. If I am wrong here, please help me to understand. The
reason this is so critical is that if we start making exceptions to strict
rules, then the exceptions can quickly overtake the rule, and we have not
advanced the science beyond the Linnaean system.
Therefore, I believe we need to remember that both of these systems are
just
models for reality, not reality. Both models have weak points and strong
points. So until I feel better about the answers to the questions I have
raised above, I will continue to use the Linnaean system, and bear in mind
that it is only a model, and that it falls down in many places. I use it
because it is still the best way to organize and communicate my thoughts
about biological entities that I encounter in my work.
I am going to send this message now before the power goes out, it is
raining
and blowing like hell here in the Santa Cruz Mountains!
Ken
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