[Taxacom] Phylogenetic Classification?

Fri Aug 7 09:35:55 CDT 2009

Sure. I review some papers dealing in molecular cryptic species in:
Zander, R. H. 2007. When biodiversity study and systematics diverge.
Biodiversity 8: 43-48.
http://tinyurl.com/27fq62.

And in
Zander, R. H. 2008. Evolutionary inferences from non-monophyly on
molecular trees. Taxon 57: 1182--1188. http://tinyurl.com/6frd9l

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Winston Edwards
Sent: Thursday, August 06, 2009 10:29 PM
To: Taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Phylogenetic Classification?

Hi Richard,

Would it be possible for you to include a reference to a paper that
names
the molecular variants as different species using the molecular
phylogeny
only?

Thanks,

Winston T. Edwards

On Mon, Aug 3, 2009 at 10:08 AM, Richard Zander
<Richard.Zander at mobot.org>wrote:

> 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
> *****************************
>
>
> -----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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>
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