[Taxacom] Paraphyletic groups as natural units of biological classification

John Grehan calabar.john at gmail.com
Thu Oct 2 05:52:24 CDT 2014


My question was aimed at the issue of whether or not paraphyletic groups
can be identified in the absence of evidence that shows that they are
artificial divisions within a monophyletic group (i.e. that artificially
exclude some members, usually because the subdivision is based on a
preference for plesiomorphies). If there is no direct evidence for
sustaining a paraphyletic grouping that represents the actual sequence of
phylogenetic relationship (as then known according to the systematics
evidence), then paraphyletic groups have no real existence in terms of
phylogenetic sequence. I would say that we would know that MM minus M (and
I had no problem with the language here) is paraphyletic if the group MM
plus M is already shown to be monophyletic. Of course, it is always
possible that subsequent research may reveal sufficient character evidence
(molecular or morphological) to change the phylogeny where MM becomes a
monophyletic group and M is its sister taxon. Admittedly my knowledge of
systematics theory is pretty limited so I will not be surprised if the
above is found to be nonsense, but I would then be interested to understand
why.

John Grehan

On Wed, Oct 1, 2014 at 3:28 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
wrote:

> Explain the question a bit more, please! I was trying to say that the
> remainder (MM minus M) may or may not be paraphyletic, and we could never
> know. There would not however be any evidence for monophyly, either
>
> Stephen
>
> --------------------------------------------
> On Wed, 1/10/14, John Grehan <calabar.john at gmail.com> wrote:
>
>  Subject: Re: [Taxacom] Paraphyletic groups as natural units of biological
> classification
>  To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
>  Cc: "Curtis Clark" <lists at curtisclark.org>, "taxacom at mailman.nhm.ku.edu"
> <taxacom at mailman.nhm.ku.edu>, "AlanWeakley" <weakley at bio.unc.edu>,
> "Kenneth Kinman" <kinman at hotmail.com>
>  Received: Wednesday, 1 October, 2014, 11:01 PM
>
>  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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