[Taxacom] Paraphyletic species and paraphyletic higher taxa

[Chris Thompson]

Nice, Curtis,

but two points:

first on yours
"With a clade, you can always say "show me your synapomorphies". A 
paraphyletic group is argument by authority."

Not exactly as a paraphyletic group is merely clade A minus clade B. A 
polyphletic group is merely clade A minus clades B, C, etc. So, it is not 
argument by authority.

So, second, the compromise for maintaining old paraphyletic / polyphyletic 
group in a modern classification is to ANNOTATE the classification, using 
the Wiley conventions, etc. That is, for example, a paraphyletic group can 
be recognized and marked at such (paraphyletic) and then the following 
clades can be ordered sequentially, given that the cladogram is pectinate, 
etc.

Oh, well ...

Chris Thompson

from home

-----Original Message----- 
From: Curtis Clark
Sent: Tuesday, December 14, 2010 9:47 AM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Paraphyletic species and paraphyletic higher taxa

On 12/14/2010 12:31 AM, Rob Smissen wrote:
> I'm not sure if Curtis is an evolutionary cladist or not, but if so he and 
> Willi Hennig are both wrong - sometimes the smallest units of phylogeny 
> are higher taxa than species. The extent of tokogeny is considerable... at 
> least among the daisies (the largest family of flowering plants, don't 
> believe a word they say about orchids). Taxa with hybrid origins may not 
> in themselves be a problem, but if their ancestors don't go extinct they 
> leave one hell of a mess.
Uh, back before I went over to the dark side of university
administration, my research specialty was hybrid speciation in the
Asteraceae. So I've been there, done that, have the t-shirt.

For me, cladistics is a tool, not a religion. Grouping taxa by shared
apomorphy has an elegance that I never found in my pre-cladistic
systematics (a student in one of my classes once likened the Bessey
cactus to "walking in mud"). In that sense, it's like a torque wrench:
elegant at torquing bolts, but not suitable for drying oneself off after
a shower.

Verne Grant predicted in the second edition of Plant Speciation that
hybridization in the flowering plants was so pervasive that phylogeny in
that group would never be determined. And he didn't mean Hennig
phylogeny, he meant Simpson phylogeny. IMO he has been proven wrong
(depending, of course, on your meaning of "determine"): large parts of
angiosperm phylogeny are well-supported by multiple lines of
morphological, chromosome structural, and sequence data.

As a tool, grouping by shared apomorphy pretty much always works (if
you're right about the apomorphies). Assuming that groups so diagnosed
are non-overlapping doesn't have as good a track record: hybrid
speciation and lateral gene transfer (by introgression or more
"esoteric" mechanisms) does muddy the waters. Cladistics provides *a*
tool (certainly not the only tool) to explore that. It provides a null
hypothesis ("the distribution of character states in this group is the
result of cladogenesis alone") that can be falsified.

There are plenty of documented cases of hybrid speciation involving
parent species that are somewhat distantly related. We can assume that
at least some extant lineages arose from hybrid species such as those.
We recognize the possibility because of character incongruence. But
character incongruence has many sources, a major one being homoplasy:
calling something a homology that isn't. Distinguishing incongruent
homology (from hybridization) from incongruent homoplasy (from bad
interpretation) is non-trivial.

Let's say that we had established with a high degree of confidence that
a named lineage originated from a hybrid between distantly related
species in another named lineage. Would I accept the progenitor lineage
as a paraphyletic taxon? Perhaps. I don't object in principle. Did Aves
arise from Reptilia by hybrid speciation? I've never read of that
hypothesis. And there's the rub. There is no single criterion for
erecting paraphyletic groups. They can be based on evolutionary grades
(I posited in a previous Taxacom post a rationale for an entirely
grade-based taxonomy, but no one seemed interested). They can be based
on presumed tokogeny. They can be based on morphological gaps that are
subsequently narrowed by discovery of new species. They can be based on
whim. And not even Ken's notation explains which of these or other
reasons are used.

With a clade, you can always say "show me your synapomorphies". A
paraphyletic group is argument by authority.

And my biggest reason for rejecting paraphyletic groups might seem
trivial: they don't play well with others. Any classification that
accepts a paraphyletic Reptilia from which sprang a monophyletic Aves
will never contain a monophyletic Saurischia or Archosauria. The only
way to have those taxa would then be to develop an entirely new scheme
of nomenclature--we might call it "Phylocode". I'd rather see our
existing system use clades.

-- 
Curtis Clark                  http://www.csupomona.edu/~jcclark/
Director, I&IT Web Development                   +1 909 979 6371
University Web Coordinator, Cal Poly Pomona


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