[Taxacom] Alternative method of generating evolutionary hypotheses for classification purposes
Richard Zander
Richard.Zander at mobot.org
Sun Apr 8 13:05:26 CDT 2018
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
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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, 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%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=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%7C6ee75868f5d64c8cb4cda3ddce30cfd6%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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