[Taxacom] Paraphyletic groups as natural units of biological
classification
John Grehan
calabar.john at gmail.com
Wed Oct 1 06:01:14 CDT 2014
2014
Where, then, is the evidence for paraphyly?
John Grehan
On Tue, Sep 30, 2014 at 8:14 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
wrote:
> I suspect that evolution is intrinsically paraphyletic, and that such
> widespread paraphyly can never be cracked, simply because there is no
> extant evidence to identify sister taxa in many cases. I'm thinking of a
> scenario along these lines: We have an obviously monophyletic group M,
> belonging to another obviously monophyletic group MM. But MM minus M is
> just a bunch of plesiomorphic species, with no one (or more) of them having
> a synapomorphy with M. There could be just a few of these species, or there
> could be a great many. Together they could be a monophyletic group (without
> any synapomorphies!), or one (or more) of them could be more closely
> related to M (but again with no synapomorphies!) We can never know. All it
> would take is for M to evolve rapidly along its own evolutionary trajectory
> (perhaps a small isolated population), and "leaving no history", so to
> speak!
>
> Stephen
>
>
> --------------------------------------------
> On Wed, 1/10/14, Kenneth Kinman <kinman at hotmail.com> wrote:
>
> Subject: RE: [Taxacom] Paraphyletic groups as natural units of biological
> classification
> To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "Curtis Clark" <
> lists at curtisclark.org>, "taxacom at mailman.nhm.ku.edu" <
> taxacom at mailman.nhm.ku.edu>, "AlanWeakley" <weakley at bio.unc.edu>
> Received: Wednesday, 1 October, 2014, 11:44 AM
>
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> Hi Stephen,
> I agree with you that
> angiosperm classification is not a typical case (having been
> so intensely studied and most of the higher taxa being
> extant). Most cases involve a basal paraphyletic remainder
> (I don't like calling them a residue) that is either too
> hard to crack or won't be cracked for a long time. But
> even in the case of angiosperms, I believe it is more
> memorable (and intuitive) and extremely useful to divide
> angiosperms into just three formal classes (Liliopsida,
> Rosopsida, and Magnolipsida%) for monocots, eudicots, and
> the paraphyletic basal remainder. As I recall, Stuessy
> (2010) recognized the same three classes, but with
> non-typified names (calling the basal remainder
> Archaeangiospermae). I suppose one could put the
> paraphyletic group in quotes, but I still prefer to mark it
> with the % symbol (and Cavalier-Smith just uses an
> asterisk).
>
> I've long thought that it would become
> obvious that the pendulum swing to purely holophyletic
> classifications ("cladifications", as Mayr called
> them) had too many drawbacks that it would become glaringly
> apparent that it was causing as much harm as good.
> Unfortumately the followers of Hennig have been swayed by
> the successes and blissfully ignore the failures.
>
> The biggest failure is the supposed holophyly of three
> Domains of life, which still has widespread support even
> though it has been thoroughly discredited by some of the
> greatest minds in biology. Such a simple explanation of
> the tree of life is just... simplistic (and the result of
> using Archaebacteria to root the Eubacteria), but the more
> likely alternative trees are unfortunately more complex and
> will take much more data and time to sway the majority.
> Only then will that majority finally return to dividing
> cellular life into its two fundamental organizational types
> (Prokaryota and Eukaryota), and finally declare that a Three
> Domain Tree based mainly on too few molecular sequences is
> (and always has been) a horrible mistake.
>
>
> Another failure is the much older debate over the
> classification and phylogeny of Metazoan phyla. The clade
> Ecdysozoa could well be truly holophyletic, but Platyzoa was
> recently shown to be paraphyletic, and I have been harping
> on the paraphyly of the supposed "clade"
> Lophotrochosa even since it was proposed almost 20 years
> ago. Of
> course, the damage has been even greater at lower taxonomic
> ranks, since there are a lot more taxa at such ranks.
> Vertebrates classes are now a taxonomic mess (even though
> heavily studied).
>
> ------------------------Ken
>
>
> ----------------------------------------------------------------------------------------------------------------
>
> > Date: Sat, 27 Sep
> 2014 20:29:39 -0700
> > From:
> stephen_thorpe at yahoo.co.nz
> > To:
> lists at curtisclark.org; taxacom at mailman.nhm.ku.edu;
> weakley at bio.unc.edu
> > Subject: Re:
> [Taxacom] Paraphyletic groups as natural units of
> biological classification
> >
> > But this example doesn't illustrate
> the terms of the debate, as I see it. As you describe the
> example, we have a rare case of an uncontroversial and fully
> determined monophyletic classification of flowering plants
> which leaves (no pun intended!) no paraphyletic residue.
> Examples of this kind are rare, I suggest, and the typical
> case involved only moderately supported phylogenies and a
> basal paraphyletic residue that is too hard to crack.
> >
> > Stephen
> >
> >
> --------------------------------------------
> > On Sun, 28/9/14, Weakley, Alan
> <weakley at bio.unc.edu> wrote:
> >
> > Subject: Re: [Taxacom] Paraphyletic
> groups as natural units of biological classification
> > To: "Curtis Clark"
> <lists at curtisclark.org>,
> "taxacom at mailman.nhm.ku.edu"
> <taxacom at mailman.nhm.ku.edu>
> >
> Received: Sunday, 28 September, 2014, 3:09 PM
> >
> > Here seems to
> be
> > "the thing".
> >
> > The "basal
> angiosperms" or
> > "primitive
> dicots" or "ANITA and the
> >
> Magnoliids" or... are clearly a basal grade to
> other
> > angiosperms, based on all recent
> analyses. Amborellales
> > sister to all
> other angiosperms. Then Nymphaeales sister
> > to all the rest, then... ETC. Whether
> you have access to
> > all the papers, a
> good summary of the current consensus can
> > be had online at the Angiosperm Phylogeny
> Website, at MoBot,
> > compiled by Peter
> Stevens. This clearly shows a grade of
> > various orders (all small, currently) and
> then also the
> > magnoliids (mostly
> small, currently, except especially, the
> > Lauraceae and somewhat less so the
> Piperaceae).
> >
> >
> So, the "basal
> > angiosperms"
> are not monophyletic. And yet, it is
> >
> "useful" and "convenient" to refer to
> > them as a group -- to classify them as a
> unit. In
> > teaching, and in floras
> (Flora of Virginia 2012, Flora of
> > the
> Southern and Mid-Atlantic States 2014)), it is
> > "handy" ("useful") to
> divide the
> > vascular flora into:
> Lycophytes, Ferns, Basal Angiosperms,
> >
> Monocots, and Eudicots. It seems
> >
> "disproportionate" to treat 4 or more units
> > (small, currently, a genus or two, a
> hundred species or
> > less, each) at
> equivalent rank to Monocots or Eudicots,
> > which have many more orders, families,
> genera, and
> > species. Especially, as
> their morphological differences
> > seem
> relatively obscure, abstruse, and non-obvious. If the
> > morphological distinctions were
> completely obvious, maybe we
> > would be
> more accepting -- no-one seems to have a hard time
> > with Ginkgo or Welwitschia as (modern)
> monotypes:
> > uncontroversial monotypic
> orders.
> >
> > So,
> Judd et al., for instance, in their
> >
> textbook, Plant Taxonomy: a Phylogenetic Approach, use
> > quotes to indicate units that are not
> monophyletic but yet
> > are
> "useful". There is an interesting tension
> > here between "strict monophyly"
> and
> > "intuitive (useful)
> classification
> > units". Units
> with quotes seem to flag
> > something
> like "this is not monophyletic but sure is
> > handy so we will keep using it
> informally".
> >
> > I'm not taking sides here
> > (I am conflicted). But... it may be
> instructive to
> > contemplate that other
> "intuitive (useful)
> >
> classification units" ("plants",
> > "animals", "algae",
> "fungi",
> > "birds",
> "bacteria",
> >
> "slime-molds", ) have fared increasingly poorly
> > over time as real classification units.
> I was taught as a
> > college botany
> student in the 1970s that there were 2 main
> > types of algae (a kind of plant):
> prokaryotic
> > ("blue-green
> algae") and eukaryotic (green, red,
> > brown, etc., algae) -- several decades
> on, this looks
> > laughable (and in no
> way "useful" or
> >
> "convenient" in any respect). On the other
> hand,
> > the "Basal
> Angiosperms" seem a "useful"
> > unit for teaching and organization and
> classification, even
> > if monophyly is
> uncertain or even disproved...
> >
> > -----Original Message-----
> > From: Taxacom
> [mailto:taxacom-bounces at mailman.nhm.ku.edu]
> > On Behalf Of Curtis Clark
> > Sent: Saturday,
> >
> September 27, 2014 9:29 PM
> > To:
> taxacom at mailman.nhm.ku.edu
> > Subject:
> Re: [Taxacom] Paraphyletic groups as
> >
> natural units of biological classification
> >
> > On 2014-09-27 6:59
> AM, John
> > Grehan wrote:
> > > Since you have some
> > expertise and strong opinions on
> paraphyly I
> > > presume you have
> read the citation of
> > Stuessy (2010) on
> basal
> > > angiosperms
> > being a paraphyletic group. As I do not
> have immediate
> > > access to that
> paper perhaps you could
> > describe in
> what way that group was paraphyletic.
> >
>
> > Some of its members
> > (Austrobaileyaceae?) are more closely
> related to the rest of
> > the angiosperms
> than others are. (Same definition as
> >
> usual.)
> >
> > --
> > Curtis Clark
> http://www.csupomona.edu/~jcclark
> >
> Biological Sciences
> > +1 909 869 4140
> > Cal Poly
> > Pomona,
> Pomona CA 91768
> >
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