[Taxacom] A Cladist is a systematist who seeks a natural classification
John Grehan
calabar.john at gmail.com
Mon Apr 9 09:35:52 CDT 2018
Some comments, but with the caveat that these are made with full
appreciation of my ignorance on systematics (I know, I know, if so ignorant
why say anything at all? Inflated ego I suppose)
"Consider the scenario of one species generating four descendant species.
First off, cladists cannot conceive or countenance such an idea."
My understanding is that the theorized origin is not relevant to examining
relationships
"What happens is that a cladogram based on morphological data commonly
shows either a multification from an unknown shared ancestor of all taxa,
or an entirely or partially "resolved" tree of dichotomous relationships.
These trees are hypotheses of what?"
Hypotheses of relationship that are not fully resolved. But that is not to
say that further resolution is necessarily possible (i.e. a multicotomy may
represent the actual origin)
"Molecular analysis can give you dichotomous trees of these taxa,"
Not always. Molecular analyses can give unresolved branching as well.
"Cladistic analysis has abandoned evolutionary theory and is stuck in a
structuralist hole."
My understanding of cladistic analysis is that it is a method of pattern
analysis. What one makes of the relationships is a separate matter. If it
is so defunct then no doubt some other method will take over.
I'm open to other approaches if they make sense to me (and I can comprehend
their principles). For now cladistics works for me for morphology (but
appreciating that there are molecular systematists out there who argue that
Hennig's type of morphological cladistics is not true cladistics where one
only analyzes patterns of derived character relationships within the
ingroup).
John Grehan
On Mon, Apr 9, 2018 at 10:03 AM, Richard Zander <Richard.Zander at mobot.org>
wrote:
> Perhaps one should examine what a cladistic hypothesis really is. I think
> such is an attempt to wrench evolutionary relationships between species
> into a dichotomous tree with relationships between unknown shared ancestors.
>
> Consider the scenario of one species generating four descendant species.
>
> First off, cladists cannot conceive or countenance such an idea. What
> happens is that a cladogram based on morphological data commonly shows
> either a multification from an unknown shared ancestor of all taxa, or an
> entirely or partially "resolved" tree of dichotomous relationships. These
> trees are hypotheses of what?
>
> Molecular analysis can give you dichotomous trees of these taxa, all
> species derived from a postulated four additional unknown shared ancestors,
> because the species are probably generated from one progenitor species at
> different times. This means what? What is the hypothesis?
>
> Cladistic analysis has abandoned evolutionary theory and is stuck in a
> structuralist hole. This sort of hierarchical cluster analysis is 30-year
> old technology. As millennials say, "It's so yesterday."
>
>
> -------
> 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
> Stephen Thorpe
> Sent: Saturday, April 07, 2018 10:27 PM
> To: taxacom; Kenneth Kinman; Elena Kupriyanova
> Subject: Re: [Taxacom] A Cladist is a systematist who seeks a natural
> classification
>
> Elena,
> That really isn't the point. The point is that too many phylogenetists go
> on to say something along the lines of "the results of the phylogenetic
> analysis indicate that X is paraphyletic wrt Y, so we hereby synonymise
> X=Y". This makes little sense if the results of the phylogenetic analysis
> are merely a hypothesis.
> Stephen
>
> --------------------------------------------
> On Sun, 8/4/18, Elena Kupriyanova <Elena.Kupriyanova at austmus.gov.au>
> wrote:
>
> Subject: RE: [Taxacom] A Cladist is a systematist who seeks a
> natural classification
> To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "taxacom" <
> taxacom at mailman.nhm.ku.edu>, "Kenneth Kinman" <kinman at hotmail.com>
> Received: Sunday, 8 April, 2018, 12:57 PM
>
> 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
> t 61 2 9320 6340 m
> 61402735679 f 61 2 9320 6059
> Visit: http://www.australianmuseum.net.au
> Like: http://www.facebook.com/australianmuseum
> Follow: http://www.twitter.com/austmus
> Watch: http://www.youtube.com/austmus
> Inspiring the exploration of nature and cultures
>
>
>
> -----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,
> 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.
>
>
> --------------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 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=
> 02%7C01%7CElena.Kupriyanova%40austmus.gov.au%
> 7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30
> cfd6%7C0%7C1%7C636587318368915357&sdata=y%2B6CxsAe2d11lHup48VafBHkoDbW6f
> fkpe3lGDkxcNQ%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=02%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=02%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=02%7C01%7CElena.Kupriyanova%40austmus.gov.au%
> 7Ca8296606ea304383f56608d59ccb0f99%7C6ee75868f5d64c8cb4cda3ddce30
> cfd6%7C0%7C1%7C636587318368915357&sdata=b9qbuc4IMI1W9%
> 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.
>
>
> _______________________________________________
>
>
>
>
>
>
>
>
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> Nurturing Nuance while Assaulting Ambiguity for 31 Some Years, 1987-2018.
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> Nurturing Nuance while Assaulting Ambiguity for 31 Some Years, 1987-2018.
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