[Taxacom] Paraphyletic groups as natural units of biological classification

John Grehan calabar.john at gmail.com
Wed Oct 1 06:01:14 CDT 2014


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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