[Taxacom] Phylogenetic Classification?

Richard Zander Richard.Zander at mobot.org
Fri Jul 31 15:54:09 CDT 2009

This has come up once I think. Species paraphyly is generally considered
something of a different thing than paraphyly of a genus. As far as I
can figure it out, phylogeneticists expect a species that is
paraphyletic (many exemplars with a different species coming out of the
middle of the lineage of exemplars) to eventually become a sister group
(reciprocally monophyletic is the phrase). Therefore, a paraphyletic
species should be considered different from the autophyletic species
because it will inexorably become a sister group to it as exemplars get
their act together and homogenize their molecular data through
recombination and gene conversion and whatnot.

For the time being, however, I see the paraphyletic species as ancestor
to the autophyletic one; very clearly an ancestor. Seeing the future to
imagine the former into a sister group relationship is typical of
phylogenetic insistence on a classification based only on sister groups.

Evolutionary classification is messy because evolution is messy.
Simplification of classification by eliminating macroevolution affects
not just classification, but the perceived reality of natural entities.
If they are not recognized using words, how does one talk about them?

Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
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St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
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-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Boggan, John
Sent: Friday, July 31, 2009 11:08 AM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] Phylogenetic Classification?
Maybe this has already come up but I don't have the time or patience to
wade through all the discussion in the archives.  How are paraphyletic
species to be treated in strictly cladistic classifications?  I don't
know about animals, but in plants paraphyletic species are probably
quite common, i.e., one or more morphologically distinct and
reproductively isolated species have been derived from a common and
widespread ancestral species that still exists.  Recognizing those
derived species makes the ancestral species paraphyletic, but it is
still a species (or is it?) in that it consists of interbreeding
populations that are united by gene flow while reproductively isolated
from their relatives (including the descendant species).  Should the
derivative species be synonymized under the ancestral species?  And if
not, what are the phylogenetic implications of the subsequent history of
these two taxa, one monophyletic but the other not?


Most molecular phylogenies will not reveal this problem (or at best only
hint at it) because they sample only one individual of each species.
But taking the problem to a reasonable extreme, it's theoretically
possible for a single founding individual of a species, landing on an
island, to undergo an evolutionary radiation and give rise to numerous
new genera and species even while the ancestral species still exists on
the mainland, remaining more or less unchanged.  In practice, extinction
of populations and entire species probably saves us from this problem.
But if it could be shown that the founding individual (and thus all its
descendants) was more closely related to one population of the ancestral
species than another, the classification of that group could get awfully


John Boggan

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