[Taxacom] Alternative method of generating evolutionary hypotheses for classification purposes
John Grehan
calabar.john at gmail.com
Mon Apr 9 09:25:32 CDT 2018
This links were not very helpful in a practical sense. A lot of theoretical
arguments and theorizing about probabilities and Bayes methods or whatever
(as obscure to me as most of the modelling that goes into molecular
phylogenetics). Nearest I found to something straightforward was the
statement
"The deciban method of determining monophyly uses both data sets of shared
traits (preliminary cladogram) and those of unique or adaptive traits
(superoptimization of the cladogram). It is capable of distinguishing
serial macroevolutionary changes (rather than branch order excepting
parallelism) and can provide a probabilistic basis for evaluation of such
changes. The ultimate result is a caulogram (Besseyan cactus) with a Bayes
factor assigned to each descendant, or a deciban differential for the first
two most likely species when Bayes factors are inconclusive."
So at present this deciban method is out of reach for me to utilize as a
practical method. Please give some citations of other systematists who have
published practical applications of this method (not books as these are not
accessible to me).
John Grehan
On Sun, Apr 8, 2018 at 2:05 PM, Richard Zander <Richard.Zander at mobot.org>
wrote:
> One method of generating hypotheses for evolution-based classifications is
> "macroevolutionary systematics":
>
> See
> http://www.mobot.org/plantscience/ResBot/Repr/Zander-Framework.pdf
> http://phytoneuron.net/2014Phytoneuron/78PhytoN-MonophylyPart1.pdf
> http://phytoneuron.net/2014Phytoneuron/79PhytoN-MonophylyPart2.pdf
> http://phytoneuron.net/2014Phytoneuron/80PhytoN-MonophylyPart3.pdf
> Also latest:
> https://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%
> 3Daps&field-keywords=zander+macroevolutionary&rh=i%3Aaps%
> 2Ck%3Azander+macroevolutionary
>
> Basically, instead of expecting a dichotomous tree to represent/model/give
> information on evolution, expect radiations of specialized species from
> more generalized progenitors, these progenitors in a series. You get a
> tree like a series of mini-explosions. A genus is then definable as each
> explosion of short lineages of radiating specialized species from a central
> progenitor. This is an empirical definition of a genus.
>
> Unless one can see nothing but cladograms, anyone familiar with a group
> can intuitively identify one or more central species around each of which
> there is a cloud of apparent descendants that are more similar to the
> progenitor than to each other. This can be nailed down by creating a
> spreadsheet with putative progenitors in one column and their descendants
> in the column to the right. If the descendants have descendants of their
> own, use a third column. You should be able to create such a spreadsheet
> with no or few reversals.
>
> Each trait of a descendant that represents an advance over its ancestral
> species gets one informational bit (Shannon entropy). Bits are directly
> translatable to Bayesian posterior probabilities: 1 bit = 0.67 BPP (nearly
> 1 standard deviation); 2 bits = 0.80 BPP; 3 bits = 0.88 BPP, 4 bits = 0.94
> BPP, (nearly 2 standard deviations); etc. Given that a species requires at
> least 2 new traits (linked by some process like genetic isolation) to
> distinguish it from its ancestor (one trait could just be an allele
> wandering through the genome), then support for a lineage is commonly very
> high indeed.
>
> Go ahead, give it a try.
>
>
> -------
> 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
> 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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