[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

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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  >  The Taxacom Archive back to 1992 may
 
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  >  Celebrating 27 years of
 
  >  Taxacom in 2014.
 
  >
 
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  >  The Taxacom Archive back to 1992 may
 
  be
 
  >  searched at:
 
  http://taxacom.markmail.org
 
  >
 
  >  Celebrating 27 years of
 
  >  Taxacom in 2014.
 
  >
 
 
 
  >
 
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  > The Taxacom Archive back to 1992 may be
 
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  >
 
  > Celebrating 27 years
 
  of Taxacom in 2014.
 
 
 
 
 
 
 
 
 
 
 
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