[Taxacom] On genera

Richard Zander Richard.Zander at mobot.org
Thu Jul 18 10:55:49 CDT 2013


Excellent, John. On the other hand, one might say that the generalized species and specialized species were all daughter species of an irascible deity, or were polyphyletic, or were all part of the One Being.

 

In the first place, I advance a scientific theory, descent with modification from a species at hand with a clear and known evolutionary process, specialization into particular habitats. Otherwise, inventing ad hoc, unnamed and unnameable, invisible explanations for a natural phenomenon is a step back. The only reason to advance an unidentified ancestral species is when all the taxa involved are specialized into particular habitats.

 

Richard

 

____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA  
Web sites: http://www.mobot.org/plantscience/resbot/ <http://www.mobot.org/plantscience/resbot/>  and http://www.mobot.org/plantscience/bfna/bfnamenu.htm <http://www.mobot.org/plantscience/bfna/bfnamenu.htm> 
Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm <http://www.mobot.org/plantscience/resbot/21EvSy.htm> 
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA

________________________________

From: John Grehan [mailto:calabar.john at gmail.com] 
Sent: Thursday, July 18, 2013 10:22 AM
To: Richard Zander
Cc: Stephen Thorpe; JF Mate; Taxacom
Subject: Re: [Taxacom] On genera

 

Try it. Lots of subgenera commonly have some one wide-ranging species of generalized morphology with some closely related species specialized into more recent habitats. A theory could be developed if one was not a cladist that these are all daughter species of the more generalized species.

 

Or one might say that the generalised species and specialized species are all daughter species of a shared common ancestor.

 

John Grehan

 

On Thu, Jul 18, 2013 at 11:15 AM, Richard Zander <Richard.Zander at mobot.org> wrote:

Aha, good response, Stephen. Exactly!



Inferring monophyly solely by (maximizing) synapomorphies leads to evolutionary paraphyly.



Suppose we have a bunch of taxa terminal on a clade. Two are most terminal with shared synapomorphies. The next taxon down, however, clearly, derived from the same ancestral taxon as the two most terminal taxa. Asserting that the two most terminal taxa are monophletic splits the ancestral taxon.



Try it. Lots of subgenera commonly have some one wide-ranging species of generalized morphology with some closely related species specialized into more recent habitats. A theory could be developed if one was not a cladist that these are all daughter species of the more generalized species.



It is a fallacy that all daughter species must occur as polychotomies, since, in morphological analysis, given few important traits, some will reverse and some will be duplicated given false (aleatory) resolution. In molecular analysis, extinct and unsampled molecular strains confound resolution totally when one ancestral species gives rise to two or more other taxa (lineages may survive from any point in the cladogram the ancestral taxon has occupied).



The fact that cladistics has promoted recognition of evolutionary paraphyly (while damning phylogenetic paraphyly) has been one of those things right in front of us for thirty years. We've ignored it because of our blinding greed for the perquisites of hard science.



Richard







____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
Web sites: http://www.mobot.org/plantscience/resbot/ <http://www.mobot.org/plantscience/resbot/>  and http://www.mobot.org/plantscience/bfna/bfnamenu.htm <http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm <http://www.mobot.org/plantscience/resbot/21EvSy.htm>
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA

________________________________

From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
Sent: Wednesday, July 17, 2013 8:22 PM
To: Richard Zander; JF Mate; Taxacom
Subject: Re: [Taxacom] On genera



Richard:

I don't know what you are on about, but naming, or not, a shared ancestor is not likely to affect anything! Monophyly is inferred from the existence of synapomorphies, though the assessment of these is fallible (as is everything!) ...

Stephen



From: Richard Zander <Richard.Zander at mobot.org>
To: JF Mate <aphodiinaemate at gmail.com>; Taxacom <taxacom at mailman.nhm.ku.edu>
Sent: Thursday, 18 July 2013 8:20 AM
Subject: Re: [Taxacom] On genera


Jason:

You seem an articulate spokesman for phylogenetics, and have a balanced view on many associated topics.

So, would you reply directly to my assertion that cladistics, because it will not name shared ancestors, cannot infer monophyly?

You say you "think that taxonomy has benefited from phylogenetics/cladistics in one major way and that is the persecution of polyphyly." I say that if cladistics (and by extension the more evolution-oriented phylogenetics) cannot infer monophyly, then it also cannot infer polyphyly and paraphyly and etc. Unless by definition, such as every clade is monophyletic.

Richard



____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
Web sites: http://www.mobot.org/plantscience/resbot/ and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of JF Mate
Sent: Monday, July 15, 2013 1:42 PM
To: Taxacom
Subject: Re: [Taxacom] On genera

I cannot claim to be right or wrong because this whole argument is about what is more or less desirable. Nevertheless I will begin by saying that we should not confuse evolution with book keeping. I am all for making them mutually compatible but not surrendering one to the other. i think that taxonomy has benefited from phylogenetics/cladistics in one major way and that is the persecution of polyphyly.
Having said that a tree, is not a classification per se, there is a major component of common sense and practicality involved and that is what I think is missing from the taxonomic discourse nowadays, with every an opportunity for naming and renaming groups.
On the other hand, the pursuit of "meaningful" higher taxa has lead to provincialism and oversplitting. By this I mean that the longer and harder you look at something the more you see of it but the less around it and this leads taxonomists along the the path of believing that their group is so unique that it deserves a classification to match.
The point is that we are in major splitting phase, and it seems to me a combination of cladification and pronvicialism. But the classification is not just for the few who make it, it is for those who use it and I think that  a major dose of pragmatism is in order.

Best


On 15 July 2013 20:14, Richard Zander <Richard.Zander at mobot.org> wrote:

> Good point, Jason. Are you suggesting that if no info was available to
> base theories on evolutionary trajectories, etc., then
>
> 1. We should leave standard taxonomy be. I agree. Unless cladistics is now
> standard taxonomy.
>
> 2. We should do cladistic clustering because such are stable and easy to
> use. I disagree with such, because wrong is wrong and easy to use wrong is
> not right.
>
>
>
> ____________________________
> Richard H. Zander
> Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
> Web sites: http://www.mobot.org/plantscience/resbot/ and
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> Modern Evolutionary Systematics Web site:
> http://www.mobot.org/plantscience/resbot/21EvSy.htm
> UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:
> taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of JF Mate
> Sent: Monday, July 15, 2013 11:22 AM
> To: Taxacom
> Subject: Re: [Taxacom] On genera
>
> My biggest objection to a generic concept that seeks more than practical
> outcomes is that it can lead to over-splitting if not tamed by the needs of
> users. Further, "meaningful" concepts require a lot of information which is
> mostly lacking except for the cute and cuddly, so entomologists (for
> example but not exclusively) would be left in the cold. I´m afraid that it
> will come down to users voting with their feet for stability and ease of
> use.
>
> Best
>
> Jason
>
>
> On 15 July 2013 17:43, Richard Zander <Richard.Zander at mobot.org> wrote:
>
> >  Okay, that's two of you who assume a genus concept as I proposed would
> > result in a mass of monotypic genera. Why? Is it because you maybe think
> > that a genus (or species) concept must apply to all genera (or species)
> > across the board as impressed on nature by human will and our need to
> > categorize along absolute lines? Or maybe you don't but you expect others
> > will. I don't think so little of others.****
> >
> > ** **
> >
> > I think nature teaches us (if we will but learn) why genera are cohesive,
> > or at least coherent, and that we will find that different genera are
> > coherent for different reasons, different evolutionary processes. ****
> >
> > ** **
> >
> > ____________________________
> > Richard H. Zander
> > Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
> > Web sites: http://www.mobot.org/plantscience/resbot/ and
> > http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> > Modern Evolutionary Systematics Web site:
> > http://www.mobot.org/plantscience/resbot/21EvSy.htm
> > UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA****
> >
> >  ------------------------------
> >
> > *From:* Raymond Hoser - The Snakeman [mailto:viper007 at live.com.au]
> > *Sent:* Sunday, July 14, 2013 5:32 PM
> > *To:* Stephen Thorpe; Richard Zander; JF Mate; Taxacom
> > *Subject:* RE: [Taxacom] On genera****
> >
> > ** **
> >
> >  I was thinking the same thing (see below)
> >
> > > >A genus may be defined, at least for some taxa, as a set of closely
> > related species that evolves as a group<
> > >
> > > Sounds like a recipe for multitudes of monotypic genera!!
> >
> > Snakebustersâ <http://www.snakebusters.com.au/> - Australia's best
> reptiles
> > â
> > The only hands-on reptilesâ shows that lets people hold the animalsâ.
> > Reptile partiesâ <http://www.reptileparties.com.au/>, events, courses
> > Phones: 9812 3322
> > 0412 777 211
> >
> >  ****
> >
> > > Date: Sun, 14 Jul 2013 13:40:54 -0700
> > > From: stephen_thorpe at yahoo.co.nz
> > > To: Richard.Zander at mobot.org; aphodiinaemate at gmail.com;
> > taxacom at mailman.nhm.ku.edu
> > > Subject: Re: [Taxacom] On genera
> > >
> > > >A genus may be defined, at least for some taxa, as a set of closely
> > related species that evolves as a group<
> > >
> > > Sounds like a recipe for multitudes of monotypic genera!!
> > >
> > >
> > > ________________________________
> > > From: Richard Zander <Richard.Zander at mobot.org>
> > > To: JF Mate <aphodiinaemate at gmail.com>; Taxacom <
> > taxacom at mailman.nhm.ku.edu>
> > > Sent: Monday, 15 July 2013 8:19 AM
> > > Subject: Re: [Taxacom] On genera
> > >
> > >
> > >
> > > Yes, "Others may disagree."
> > >
> > > A genus may be defined, at least for some taxa, as a set of closely
> > related species that evolves as a group. Perhaps they all seem move in
> > response to environmental change (say, all the cold-climate species die
> > out, which changes the circumscription of the genus). Or perhaps one
> > ancestral species gave rise to many specialized species. One CAN make
> good
> > hypotheses based on data that may be non-phylogenetically informative.
> > >
> > > These less than exact definitions should be considered because
> > cladistics cannot determine monophyly since no ancestral nodes are named.
> > Phylogenetic monophyly then is done by definition, not by empirical
> > inference; that is, every clade is monophyletic, period.
> > >
> > > What drives people to accept this nonsense?
> > >
> > >
> > > 
> > >
> > > ____________________________
> > > Richard H. Zander
> > > Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
> > > Web sites: http://www.mobot.org/plantscience/resbot/and
> > http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> > > Modern Evolutionary Systematics Web site:
> > http://www.mobot.org/plantscience/resbot/21EvSy.htm
> > > UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA
> > >
> > >
> > > -----Original Message-----
> > > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:
> > taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of JF Mate
> > > Sent: Thursday, July 11, 2013 9:22 PM
> > > To: Taxacom
> > > Subject: [Taxacom] On genera
> > >
> > > ... what is a genus? I would say that divergence times are irrelevant.
> My
> > > own view is that a genus is just a convenient monophyletic grouping of
> > > species, i.e. not too big, not too small, and easily recognisable.
> Others
> > > may disagree ...
> > >
> > > I would strongly agree that it is a taxonomic convenience so we can
> > > communicate better and break down biodiversity for our understanding. I
> > > would disagree with the need for monophyly though, and rather push for
> > > non-polyphyletic genera, at least until taxonomists show some restraint
> > > naming genera, or at least an equal enthusiasm for synonymizing them.
> > > Otherwise simplicity and ease of use will be jeopardised in the name of
> > > phylogenetic correctnes. As a final note, when we talk about easily
> > > recognisable, maybe it should be stressed that it is for the
> > non-specialist
> > > (in the particular group that is).
> > >
> > > My two cents
> > >
> > > Jason
> > > _______________________________________________
> > > Taxacom Mailing List
> > > Taxacom at mailman.nhm.ku.edu
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> > >
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> > >
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