[Taxacom] On genera

JF Mate aphodiinaemate at gmail.com
Fri Jul 19 00:36:10 CDT 2013


Thanks Stephe, you are correct, modern cladistics seeks monophyly but I
think after a while most practitioners soften-up towards paraphyly (in
classification), as a practical approach to transitions between
monophyletic clades ( a case of "do as I say, don´t do as I do"). As Rich
says, nature is fuzzy, and sometimes the fuzzy, paraphyletic rind is best
retained around your monophyletic groups. And since more sampling just
makes the problem worse, a pragmatic compromise between our dichotomous
minds and reality seems more appropriate.

Best

Jason


On 18 July 2013 22:44, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:

> Well, my understanding of (phylogenetic) systematics, which may not be
> entirely accurate, is that it seeks to "eliminate" paraphyly, though this
> must be understood as seeks to minimize paraphyly. The bird/reptile example
> is a good one. Birds are clearly monophyletic, but are nested within more
> generalized reptiles, so traditional Reptilia is a paraphyletic group. But,
> forgetting mammals for a moment, reptiles+birds are a monophyletic group.
> The problem though, which is presumably what you are alluding to, is that
> there probably isn't a way of reclassifying the group such that all named
> subtaxa are monophyletic ... there will always be some paraphyletic residue
> (basal reptiles?), but that is why I say "minimize" paraphyly, rather
> than "eliminate" ...
>
> Stephen
>
>   *From:* Richard Zander <Richard.Zander at mobot.org>
> *To:* Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; JF Mate <
> aphodiinaemate at gmail.com>; Taxacom <taxacom at mailman.nhm.ku.edu>
> *Sent:* Friday, 19 July 2013 3:15 AM
>
> *Subject:* RE: [Taxacom] On genera
>
>   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/ 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:* 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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