[Taxacom] Phylogenetic Classification?

[Richard Zander]

Phylogenetics has exemplars (one specimen) as terminals. We extend
meaning of the cladogram to the population, species, genus, etc. When
two exemplars of the same species are paraphyletic (distant on the
molecular cladogram by at least one intermediary lineage of a different
species), then the species is considered paraphyletic. Some people have
the nerve to name the molecular variants as different species with no
corroborating expressed traits.

*****************************
Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Non-post deliveries to:
Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110
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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 Stephen Thorpe
Sent: Friday, July 31, 2009 8:02 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Phylogenetic Classification?

Re paraphyletic species: phylogenetics usually has species as terminal  
taxa, not individuals, in which case there is no such thing as a  
"paraphyletic species"...

S

Quoting Richard Zander <Richard.Zander at mobot.org>:

> 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
> PO Box 299
> St. Louis, MO 63166-0299 USA
> richard.zander at mobot.org
> Web sites: http://www.mobot.org/plantscience/resbot/
> and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> Non-post deliveries to:
> Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110
> *****************************
>
> -----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
> messy...
>
>
>
> John Boggan
>
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