[Taxacom] A Cladist is a systematist
who seeks a natural classification
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Sun Apr 8 15:46:08 CDT 2018
2018
Speaking of molecular taxonomy, here is a good example of something that I suggest we really don't want to see!
Balke, M.; Hájek, J.; Hendrich, L. 2017: Generic reclassification of species formerly included in Rhantus Dejean (Coleoptera, Dytiscidae, Colymbetinae). Zootaxa, 4258(1): 91-100.
Genera have been defined in accordance with molecular results, but with no way of morphological diagnosis (so the keys only work at best for "most cases")
Cheers, Stephen
--------------------------------------------
On Mon, 9/4/18, Richard Zander <Richard.Zander at mobot.org> wrote:
Subject: RE: [Taxacom] A Cladist is a systematist who seeks a natural classification
To: "Elena Kupriyanova" <Elena.Kupriyanova at austmus.gov.au>, "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "taxacom" <taxacom at mailman.nhm.ku.edu>, "Kenneth Kinman" <kinman at hotmail.com>
Received: Monday, 9 April, 2018, 7:14 AM
"Subsequent testing" is an interesting
desideratum.
Morphological cladograms use all data
on shared traits for the whole species, which is sampled
lots of times during revisions.
Molecular cladograms are commonly based
on one or more recently a very few samples of a species.
Sampling sequences is not the same as sampling individuals
in a species. Given evidence from the few studies using
multiple samples of a species, what you are really sampling
are molecular races.
Now if the distribution is simple, a
sample of only a few specimens of a genus (say, 15 to 30)
may be sufficient. If one has multiple races, each with
divergent sequences, then the number of samples must very
much larger. How large? Sufficient to cover the expected
range of variation, which, from what I've seen in published
mult-sample molecular studies, is five or so. But ... what
if some of the races are extinct? This may be expected in
older species. Molecular systematics can be informative
about evolution, but the details are very problematic. Stick
to morphology, which is much better sampled.
-------
Richard H. Zander
Missouri Botanical Garden – 4344 Shaw
Blvd. – St. Louis – Missouri – 63110 – USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and
http://www.mobot.org/plantscience/resbot/
-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
On Behalf Of Elena Kupriyanova
Sent: Saturday, April 07, 2018 6:58 PM
To: Stephen Thorpe; taxacom; Kenneth
Kinman
Subject: Re: [Taxacom] A Cladist is a
systematist who seeks a natural classification
Therefore, what advantage does
cladistics/phylogenetic analysis have over any other method
for generating hypothesis, such as "taxonomic intuition"?
Sorry, I would really love to know what
these other methods for generating hypotheses, other than
cladistics/phylogenetic analysis and "taxonomic
intuition" are
Dr. Elena Kupriyanova
Senior Research Scientist
Marine Invertebrates
Associate Editor,
Records of the Australian Museum
Australian Museum Research Institute
1 William Street Sydney NSW 2010
Australia
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61402735679Â f 61 2 9320 6059
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Inspiring the exploration of nature and
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-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
On Behalf Of Stephen Thorpe
Sent: Sunday, 8 April 2018 7:04 AM
To: taxacom <taxacom at mailman.nhm.ku.edu>;
Stephen Thorpe <stephen_thorpe at yahoo.co.nz>;
Kenneth Kinman <kinman at hotmail.com>
Subject: Re: [Taxacom] A Cladist is a
systematist who seeks a natural classification
Ken said: "there is no problem with
cladistic analysis as an hypothesis generator"
Actually, I think that there is a
problem. A method for generating hypotheses does just that,
i.e. generates hypotheses, and nothing more. Now, it doesn't
actually matter where a hypothesis comes from (i.e. it
doesn't matter how it is generated). The (only) value of any
hypothesis lies in subsequent testing. Therefore, what
advantage does cladistics/phylogenetic analysis have over
any other method for generating hypothesis, such as
"taxonomic intuition"?
Stephen
--------------------------------------------
On Sun, 8/4/18, Kenneth Kinman <kinman at hotmail.com>
wrote:
Subject: Re: [Taxacom] A Cladist is a
systematist who seeks anaturalclassification
To: "taxacom" <taxacom at mailman.nhm.ku.edu>,
"Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
Received: Sunday, 8 April, 2018, 1:23
AM
Hi all,
    There is
no problem with cladistic analysis as
an hypothesis generator. The problem is that
phylogenetic systematists only formally recognize taxa
which are clades. By branding paraphyletic taxa
as unnatural
 and refusing to recognize any of
them, they often fail to put in the added work of
incorporating divergence information into their
classifications when it would make them more stable
and usable (as advocated by Mayr, Ashlock,Â
Cavalier-Smith, and other evolutionary
 systematists).
   This is
especially true of higher taxa
(families to kingdoms). It is therefore no
surprise that it is at the level of Kingdoms, Phyla,
and Classes that the debate between evolutionary
systematists and phylogenetic
 systematists is most
heated. Phylogenetic systematists have too often
generated instability at those levels, and thus
severely affecting usability.
    That is
why Ernst Mayr called them
cladifications (not classifications). At the
level of species and genera, cladifications often turn
out to be good classifications, but the same is too
often not true at higher
 taxonomic levels. The
worst case is the Three Domain cladification which was
(and continues to be) horribly simplistic. It is
people like Cavalier-Smith who is putting in the hard
work of attempting to construct more natural, stable,
and usable classifications.
    Â
 --------------Ken
From: Taxacom
<taxacom-bounces at mailman.nhm.ku.edu>
on behalf of Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Sent: Saturday, April 7, 2018 1:01 AM
To: taxacom; John Grehan
Subject: Re: [Taxacom] A Cladist is a
systematist who seeks a natural classification
The issue
that I still haven't been able to get
a clear answer to is whether cladistics is just a way
of generating hypotheses for future testing (which, as
we all know, is ongoing and never conclusive), or
whether it somehow generates
 something which can be more or
less thought of as a "fact", i.e. something which is
at least more likely to be "true" than not. My own
suspicion is the former, i.e. just a hypothesis
generator, based on various assumptions (such a s
parsimony) and given values
 of certain variables
(weightings, etc.) which may themselves be quite
subjective.
Stephen
--------------------------------------------
On Sat, 7/4/18, John Grehan <calabar.john at gmail.com>
wrote:
 Subject: [Taxacom] A Cladist is
a systematist who seeks a natural  Â
classification
 To: "taxacom"
<taxacom at mailman.nhm.ku.edu>
 Received: Saturday, 7 April,
2018, 6:10 PM
 Since there are at various times
some strong
 opinions on cladistics and on
 natural classification I have
pasted
 below the text of a recent
article
 that might be of interest to
some (some
 typos may have crept in during
the
 copy/paste).
 Biol Philos (2018) 33:10
 https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1007%2Fs10539-018-9621-7&data%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata=y%2B6CxsAe2d11lHup48VafBHkoDbW6ffkpe3lGDkxcNQ%3D&reserved=0
 David M. Williams & Malte C.
Ebach
 A Cladist is a systematist who
seeks a
 natural classifcation: some
comments
 on Quinn (2017)
 Abstract. In response to Quinn
(Biol
 Philos, 2017.
 https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1007%2Fs1053&data%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata=%2FVgLke31Lm48sIrfxwLaU9%2BCuCX5Pul5125joI3eTgg%3D&reserved=0
 9-017-9577-z) we identify
cladistics to
 be about natural
classifications
 and their
 discovery and thereby propose to
add an
 eighth cladistic defnition to
 Quinn’s list,
 namely the systematist who seeks
to
 discover natural
classifications,
 regardless of their
affiliation,
 theoretical or methodological
 justifications.
 Derived from various
permutations of
 phylogeny, biology, philosophy,
 methodology, sociology, loyalty
etc.,
 Aleta Quinn recently proposed
“seven
 specific definitions that
capture
 distinct contemporary uses� of
cladistics
 (Quinn 2017, p. 1). Our own
efforts,
 based on the same criteria,
yielded a
 further seven, which we do not
intend
 to bore our readers with here.
We are
 sure more could be found and
more
 people could be found who
 subscribe/correspond to them.
Suffice
 to say, one might find
definitions
 for anything—and in any case,
Quinn
 was clear about her motives:“I
do not
 intend to classify individuals,
ideas,
 or research programs. Rather, I
 clarify distinct things that
speakers
 mean by the term
‘cladist’� (Quinn
 2017, p. 1). Depending on
one’s
 outlook—philosopher,
historian, biologist,
 even sociologist (Hull
1988)—the
 definitions might help progress
their
 subject. As biologists, we found
much
 to think about but rather than
 dissecting the minutiae, we seek
to
 clarify by attempting to
simplify.
 We need first to dispense with
one
 misconception. Quinn draws upon
a
 commonly preconceived notion,
namely
 that systematics requires
evolution as
 a prior condition:1
 “What that theoretical
foundation may
 have been [in reference to de
 Candolle’s
 view on characters] is not
relevant to
 my points about contemporary
 systematics,
 whose conceptual framework
presupposes
 the concept of evolution�
(Quinn
 2017, footnote 11).
 Consider the concept of a
cladogram,
 which everyone might agree is a
 branching diagram commonly
included as
 part of the results of a
cladistic
 analysis. One might derive from
this
 diagram which taxon is more
closely
 related to itself than to any
other.
 One might explain this
relationship by
 common descent. The cladogram,
however,
 need not be constructed with
any
 evolutionary assumptions in
mind;
 rather, the evolutionary
assumptions
 serve to explain why one taxon
is more
 closely related to itself than
any
 other.
 The search for a natural
classifcation
 was established prior to the
 adoption of
 any theory of evolution. In
fact
 Augustin P. de Candolle’s had
a great deal
 to say
 on the matter, especially the
 differences between natural and
artificial
 classifications (Candolle 1913).
But de
 Candolle was working some time
ago,
 so what, if anything, might be
his
 relevance today? Methods of
systematics
 change as time passes. But all
methods
 fnd cladograms, in the sense
that
 the results yield sets of
 relationships, either as a
branching diagram or
 as a written classification.
Regardless
 of method, which of these
 relationships might be
considered to
 reflect something that actually
 exists, rather than a product
(an
 artefact) of the method? How can
any
 method achieve that without
knowing the
 answer beforehand? Obviously it
 can’t. One might play around
with
 simulation studies to judge the
 performance of any suite of
methods, or
 one might delve into philosophy
to
 create justification, but in the
court
 of last resort all that remains
are
 sets of cladograms that either
agree or
 disagree to a greater or lesser
 extent in terms of common
relationships
 found. That is, they agree in
the
 cladistic parameter, the
relationships
 specified—that the signal to
noise
 ratio is working in our favour,
as is
 evident from classifications of
the
 past. Here we might argue that
natural
 classification is the result
derived
 from several cladograms,
regardless as
 to how they were arrived at;
 artificial classifications are
derived
 from a specific method, be that
 Wagner parsimony, UPGMA,
maximum
 likelihood and so on, or from a
specific
 source of data (DNA,
 ultrastructure, etc.), and so
on. Why are these
 artificial? Because a method,
any
 method, assumes the results that
are
 required (the shortest tree; or
the
 most similar taxa grouped
together; or
 the most similar taxa grouped
together
 via a weighted model of
character
 change, etc.); for a data
source, they
 assume those data are
privileged
 over other data (DNA must be the
source
 of ‘true’ relationships,
etc.).
 Cladistics, in its most general
sense,
 does not associate with any one
 method, or any one data source.
It
 applies to sets of
relationships—it is
 the set of relationships. This
is
 effectively what de Candolle
argued for,
 and has been the basis of
systematics
 for decades, if not centuries:
 “For the last 50 years
and
 more—even now continuing into
the realm of
 nomenclature—in the name of
the
 modern and the new, Visionaries
aim, as
 it were, to confine the past to
a
 dustbin of history, and to bolt
and lock
 the
 lid upon it. As if without it,
we be in
 some way better, even born
again
 more
 whole-some; as if Carl Linnaeus
really
 were among the last of the
Ancients,
 and not, rightly, the first of
the
 moderns, and so related to
us—of a group
 inclusive of us� (Annual
Review of
 the Linnean Society, 2001).
 These words, not readily
accessible,
 were spoken by Gareth Nelson
after
 receiving the Linnean Gold Medal
and
 re-cast above as part of the
2001
 Annual Review of the Linnean
Society,
 London. Linnaeus as the first of
the
 moderns? Among other matters,
Linnaeus
 spoke of the differences
between
 artificial and natural
classification,
 a subject taken up and developed
by
 de Candolle (1913). One might
cast that
 debate in very simple terms:
 artificial classifications are
found by
 imposition, natural
classification
 is discovered. Imposition
implies some
 method or motivation to erect a
 particular classification, such
as a
 field guide or handbook for
 identifying specimens—today it
is
 more likely those would be
websites, or
 online interactive guides. There
is
 nothing wrong with artificial
 classifications. We both use
them all
 the time, almost every day (
 https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.trilobites.info%2F&data%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata=U8%2BPeMIgalve2cDuEoerguLRMisn6iiK5M%2FuoBGoeFU%3D&reserved=0;
 https://apac01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fnaturalhistory.museumwales.ac.uk%2Fdiatoms%2F&data%7C01%7CElena.Kupriyanova%40austmus.gov.au%7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30cfd6%7C0%7C1%7C636587318368915357&sdata¹qbuc4IMI1W9%2FUYuDgO6DE1yCez%2Bo5dq%2BPkUA0TZ2I%3D&reserved=0).
But
 whatever merits they
 have, and there are many, they
 are created by acts of
imposition. We
 ask our readers, then, if they
would
 consider analysis of some data
with one
 or another statistical program,
or
 with one or another parsimony
program,
 or with one or another phenetic
 program, whether this is an act
of
 imposition or an act of
discovery? We
 see it as an act of imposition.
How
 could it be otherwise?
Cladistics,
 then, is about discovery, about
finding
 repeating patterns,finding the
same
 relationships, finding
relationships
 that are not method dependent,
finding
 relationships that are
reflections of
 the world as it is:
 “What, then, of cladistics in
 relation to the history of
systematics? If
 cladistics
 is merely a restatement of the
 principles of natural
classifcation, why has
 cladistics been the subject of
 argument? I suspect that the
argument is
 largely
 misplaced, and that the
misplacement
 stems, as de Candolle suggests,
from
 confounding the goals of
artifcial and
 natural systems� (Nelson 1979,
p.
 20).
 For us, cladistics is about
natural
 classifcations and their
discovery, an
 activity
 that occurs with or without
 “knowledge of process�. Look
in museums,
 herbaria,
 universities and other
institutions
 that still hire systematists and
you
 will see:
 Cladist (viii): A cladist is a
 systematist who seeks to
discover natural
 classifications.
Â
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