[Taxacom] Paraphyletic species and paraphyletic higher taxa

[Curtis Clark]

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