[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

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" ...
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
 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
 John Grehan
 On Wed, Oct 1, 2014 at 3:28
 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
 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>
  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
  widespread paraphyly can never be cracked, simply
  there is no extant evidence to identify sister taxa in
  cases. I'm thinking of a scenario along these lines:
  have an obviously monophyletic group M, belonging to
  obviously monophyletic group MM. But MM minus M is just
  bunch of plesiomorphic species, with no one (or more)
  them having a synapomorphy with M. There could be just a
  of these species, or there could be a great many.
  they could be a monophyletic group (without any
  synapomorphies!), or one (or more) of them could be
  closely related to M (but again with no synapomorphies!)
  can never know. All it would take is for M to evolve
  along its own evolutionary trajectory (perhaps a small
  isolated population), and "leaving no history",
  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
   so intensely studied and most of the higher taxa
   extant).  Most cases involve a basal paraphyletic
   (I don't like calling them a residue) that is
   hard to crack or won't be cracked for a long
   even in the case of angiosperms, I believe it is more
   memorable (and intuitive) and extremely useful to
   angiosperms into just three formal classes
   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
   with the % symbol (and Cavalier-Smith just uses an
            I've long thought that it would
   obvious that the pendulum swing to purely
   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
   the successes and blissfully ignore the failures.  
       The biggest failure is the supposed holophyly
   Domains of life, which still has widespread support
   though it has been thoroughly discredited by some of
   greatest minds in biology.  Such a simple
   the tree of life is just... simplistic (and the
   using Archaebacteria to root the Eubacteria), but the
   likely alternative trees are unfortunately more
   will take much more data and time to sway the
    Only then will that majority finally return to
   cellular life into its two fundamental organizational
   (Prokaryota and Eukaryota), and finally declare that
   Domain Tree based mainly on too few molecular
   (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
   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
   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
   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
   >  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
   >  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,
   >  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
   >  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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