[Taxacom] Paraphyletic groups as natural units of biological
classification
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Thu Oct 2 18:00:24 CDT 2014
2014
John,
>My view is that there is no problem of Linnean classification if it is limited to being applied to monophyletic groups<
I think you may have possibly missed the point. If P= MM minus M is paraphyletic, then, in order to have a Linnean classification which recognises M, you also need to recognise P (or else elevate all the species in P to the same rank as M). This is the problem!
> If one wants to apply a name or label to a paraphyletic assemblage then there is nothing to prevent that usage, only with the proviso that it is an artificial grouping – in my opinion<
That was the point of tagging, yet you have some sort of objection to tagging!
Stephen
--------------------------------------------
On Fri, 3/10/14, 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: Friday, 3 October, 2014, 10:18 AM
Hi Stephen,
With respect to your
comment “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. “
My counter point is that a
paraphyletic group is not a group
at all in the natural sense of monophyly.
“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.”
My view is that there is
no problem of Linnean classification
if it is limited to being applied to monophyletic groups. If
one wants to apply
a name or label to a paraphyletic assemblage then there is
nothing to prevent
that usage, only with the proviso that it is an artificial
grouping – in my
opinion.
“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.”
Personally I would not add
paraphyletic labels to a
phylogenetic assemblage in any formal way. Informal I would
have no problem with.
“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).”
One either rejects the
formal name, or extends it to include
all members encompassed by the defining synapomorphy or
synapomorphies.
“Not sure how much sense
this makes, and apologies for any
"using words any old way I like" .
Stephen”
I’m never sure how much
sense I make and periodically some people say as much - ha
ha. So no worries.
John Grehan
On Thu, Oct 2, 2014 at 4:33
PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
wrote:
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
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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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