[Taxacom] New systematics book

[Robin Leech]

Curtis, 
You might add the following, sort of in the Berkelian Logig:
"Just because no one studied and identified different entities of nature
that we call species, it does not mean that they don't exist."
Robin

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Curtis Clark
Sent: September-08-13 10:04 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] New systematics book

First I want to say that, from all the agreement on this list that species
are not entities in nature, it seems that pattern cladistics has won, and
those of us who studied (and perhaps still study) speciation could have done
no worse by studying unicorns. All the rest of what I write is based on the
assumption that species are the result of an evolutionary process, and to
that extent (at least) are real. I surmise that you agree.

I accept paraphyletic species, and in fact my own studies suggested several
examples. What I have never understood is how the existence of paraphyletic
species provides a general justification for paraphyletic higher taxa. If
the pattern of character distribution in extant lineages showed, say, four
lineages that share a synapomorphy, three of them have distinct
autapomorphies, and the fourth has no autapomorphies, that could be
suggestive of ancient peripatric speciation. And it would be a clear case
for a polytomy in a cladogram. But paraphyletic taxa like Reptilia (sensu
antiquo)  and Dicotyledonae are most often the result of gaps in knowledge;
it's hard for me to imagine the existence of peripatric speciation
justifying them.

On 2013-09-08 1:35 PM, Richard Zander wrote:
> " ... parsimony and other optimality analyses only work with accuracy 
> with pseudoextinction (dying ancestor, two new species). The correct 
> optimality for branching analysis is that which makes the shortest 
> (most likely, most credible) tree given identified surviving ancestors 
> and their daughter taxa based on other information. This is merely, 
> MERELY less precise, correctly less precise and therefore with more 
> uncertainty about evolutionary relationships.

This is a methodological issue, not a conceptual one. There are many other
problems with parsimony as well (including long branch attraction for
molecular data). I don't see how this supports recognition of paraphyletic
groups.

One of the reasons that the results of the Angiosperm Phylogeny Group are so
widely accepted is that the groups are things we were considering anyway,
but didn't quite have the evidence for. In a previous post, I gave some
examples from Scrophulariaceae s.l.; plant taxonomists have known for years
that the family was heterogeneous, and now we have a few more lines of
evidence to convince us of that. Just because some people make
classifications from bootstrapped molecular parsimony trees with no other
input doesn't invalidate cladistics.

> "...  molecular "lineages" are molecular strains, and ancestral taxa 
> in stasis generate lots of molecular strains before and after 
> generation of one or more daughter species. The DNA continues to 
> mutate in isolation while expressed traits remain in stasis for 
> millions of years. Molecular phylogenetics gives precise sister group 
> analyses of extant strains, not taxa. Evidence? Molecular paraphyly. 
> What about extinct or unsampled strains? They could have diverged 
> molecularly long before or after any extant strain."

This is again methodological. The lack of congruence of many gene trees is
well-known, as are the evolutionary processes resulting in the lack of
congruence. Again, no basis here for general recognition of paraphyletic
higher taxa.

Within the eukaryotes, the general pattern of groups within groups is
pervasive. Peripatric speciation, hybrid speciation, and lateral gene
transfer are all fascinating processes that certainly muddy the waters, but
there are a lot of "just-so stories" lurking in Bessey's Cactus and its
descendents. Perhaps your book has a methodological framework to address
that (I presented a method for defining grades a year or two ago, but you
neither challenged nor agreed).

And as far as "phylogenetic jargon has taken a life of its own," it's
perhaps not a good idea to redefine terms like monophyly yet again.

-- 
Curtis Clark        http://www.csupomona.edu/~jcclark
Biological Sciences                   +1 909 869 4140
Cal Poly Pomona, Pomona CA 91768


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