[Taxacom] Paraphyletic groups as natural units of biological classification

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Wed Oct 1 14:28:10 CDT 2014

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


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
 On Tue, Sep 30, 2014 at
 8:14 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
 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!
 On Wed, 1/10/14, Kenneth Kinman <kinman at hotmail.com>
  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
  #yiv5322393153 #yiv5322393153 --
  .yiv5322393153hmmessage P
  #yiv5322393153 body.yiv5322393153hmmessage
  Hi Stephen,
          I agree with you that
  angiosperm classification is not a typical case (having
  so intensely studied and most of the higher taxa being
  extant).  Most cases involve a basal paraphyletic
  (I don't like calling them a residue) that is either
  hard to crack or won't be cracked for a long time. 
  even in the case of angiosperms, I believe it is more
  memorable (and intuitive) and extremely useful to
  angiosperms into just three formal classes (Liliopsida,
  Rosopsida, and Magnolipsida%) for monocots, eudicots,
  the paraphyletic basal remainder.  As I recall,
  (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
  with the % symbol (and Cavalier-Smith just uses an
           I've long thought that it would
  obvious that the pendulum swing to purely holophyletic
  classifications ("cladifications", as Mayr
  them) had too many drawbacks that it would become
  apparent that it was causing as much harm as good.
   Unfortumately the followers of Hennig have been swayed
  the successes and blissfully ignore the failures.    
      The biggest failure is the supposed holophyly of
  Domains of life, which still has widespread support
  though it has been thoroughly discredited by some of
  greatest minds in biology.  Such a simple explanation
  the tree of life is just... simplistic (and the result
  using Archaebacteria to root the Eubacteria), but the
  likely alternative trees are unfortunately more complex
  will take much more data and time to sway the majority.
   Only then will that majority finally return to
  cellular life into its two fundamental organizational
  (Prokaryota and Eukaryota), and finally declare that a
  Domain Tree based mainly on too few molecular sequences
  (and always has been) a horrible mistake.          
       Another failure is the much older debate over
  classification and phylogeny of Metazoan phyla.  The
  Ecdysozoa could well be truly holophyletic, but Platyzoa
  recently shown to be paraphyletic, and I have been
  on the paraphyly of the supposed "clade"
  Lophotrochosa even since it was proposed almost 20
  ago.    Of
  course, the damage has been even greater at lower
  ranks, since there are a lot more taxa at such ranks.
   Vertebrates classes are now a taxonomic mess (even
  heavily studied).   
  > 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
  example, we have a rare case of an uncontroversial and
  determined monophyletic classification of flowering
  which leaves (no pun intended!) no paraphyletic
  Examples of this kind are rare, I suggest, and the
  case involved only moderately supported phylogenies and
  basal paraphyletic residue that is too hard to crack.
  > Stephen
  > On Sun, 28/9/14, Weakley, Alan
  <weakley at bio.unc.edu>
  >  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
  >  "the thing". 
  >  The "basal
  angiosperms" or
  >  "primitive
  dicots" or "ANITA and the
  Magnoliids" or...  are clearly a basal grade to
  >  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
  So, the "basal
  >  angiosperms"
  are not monophyletic.  And yet, it is
  "useful" and "convenient" to refer
  >  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)
  >  uncontroversial monotypic
  >  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"
  >  "intuitive (useful)
  >  units".   Units
  with quotes seem to flag
  >  something
  like "this is not monophyletic but sure is
  >  handy so we will keep using it
  >  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",
  >  "birds",
  "slime-molds", ) have fared increasingly
  >  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): 
  >  ("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
  >  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
  >  > 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
  >  --
  >  Curtis Clark       
  Biological Sciences               
  >     +1 909 869
  >  Cal Poly
  >  Pomona,
  Pomona CA 91768
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 Celebrating 27 years of Taxacom in 2014.

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