[Taxacom] Paraphyletic groups as natural units of biological classification

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Thu Oct 2 15:33:14 CDT 2014


John,
I think what you are saying is that a paraphyletic group is one which has no known synapomorphies (e.g. MM minus M), even though it could later be shown to be monophyletic (i.e. sister taxon to M) if synapomorphies were discovered. My point, however, is such paraphyletic groups may be commonplace, and it may never be possible to discover synapomorphies. Therefore, if we were to try to force a Linnean classification to be strictly monophyletic, we would have a problem. One possible solution is to reject Linnean classification in favour of a rankless phylogenetic classification, but this has the major disadvantage of rendering a vast amount of published information obsolete. I think it is far more sensible to retain Linnean classification, with formally names and ranks for paraphyletic groups. All we need to do is tag these names somehow as being paraphyletic, such as by putting the name in double quotes (e.g. "Reptilia"), but they are still formal names,
 governed by the appropriate code of nomenclature (actually not in the case of Reptilia, which is unregulated by the ICZN). This way, the results of phylogenetic studies is not necessarily to change the classification, but just to tag names for paraphyletic taxa. A reclassification may still be appropriate in cases with very high phylogenetic support. The problems arise when people start rejecting formally named taxa just because they are paraphyletic according to your definition (i.e. based on no known synapomorphies). Not sure how much sense this makes, and apologies for any "using words any old way I like" ...
Stephen
--------------------------------------------
On Thu, 2/10/14, 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: Thursday, 2 October, 2014, 10:52 PM
 
 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
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
   #yiv5322393153 #yiv5322393153 --
 
 
 
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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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   >  Celebrating 27 years of
 
 
 
   >  Taxacom in 2014.
 
 
 
   >
 
 
 
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   >  Taxacom Mailing List
 
 
 
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   http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 
 
 
   >  The Taxacom Archive back to 1992 may
 
 
 
   be
 
 
 
   >  searched at:
 
 
 
   http://taxacom.markmail.org
 
 
 
   >
 
 
 
   >  Celebrating 27 years of
 
 
 
   >  Taxacom in 2014.
 
 
 
   >
 
 
 
 
 
 
 
   >
 
 
 
   _______________________________________________
 
 
 
   > Taxacom Mailing List
 
 
 
   >
 
 
 
   Taxacom at mailman.nhm.ku.edu
 
 
 
   >
 
 
 
   http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 
 
 
   > The Taxacom Archive back to 1992 may be
 
 
 
   searched at: http://taxacom.markmail.org
 
 
 
   >
 
 
 
   > Celebrating 27 years
 
 
 
   of Taxacom in 2014.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  _______________________________________________
 
 
 
  Taxacom Mailing List
 
 
 
  Taxacom at mailman.nhm.ku.edu
 
 
 
  http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 
 
 
  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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