[Taxacom] Elimination of paraphyly: sensible or not?

Thu Feb 8 20:58:01 CST 2018

I agree. But at the end that affects nomenclature at a larger scale. 
Lack of nomenclatural stability also influences how those non-taxonomists look at our work. At least in my case, working aside forestiers and rangers and doing taxonomy intended to help the management and conservation of ecosystems, the continuous change in names is not well received. 
I love the advancement of science and I respect phylogenetical studies. The new information is exciting and it is great to know the real relationships among organisms. But we shall remember that the information that we generate is used by many other people and that some stability would help. As crazy as it sounds, why not to report in a paper that such and such genera are not in a monophyletic group but left the names stay? I know that this is not acceptable for ortodox phylogenetists. But I know excellent ones that have kept the names untouched...

M. Socorro Gonzalez ElizondoHerbario CIIDIRInstituto Politecnico NacionalSigma 119 Fracc. 20 de Noviembre IIDurango, Dgo., 34220 MEXICOTels. (618) 814 4540, (618) 814 6802; (55) 5 729 6000 ext. 82609

      De: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
 Para: Mary Barkworth <Mary.Barkworth at usu.edu>; "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>; Michael A. Ivie <mivie at montana.edu>; Socorro Gonzalez <herbario_ciidir at yahoo.com.mx> 
 Enviado: Jueves, 8 de febrero, 2018 20:28:43
 Asunto: Re: [Taxacom] Elimination of paraphyly: sensible or not?

Lumping supraspecific taxa (genera etc.) is totally different to lumping at the species level!

--------------------------------------------
On Fri, 9/2/18, Socorro Gonzalez <herbario_ciidir at yahoo.com.mx> wrote:

 Subject: Re: [Taxacom] Elimination of paraphyly: sensible or not?
 To: "Mary Barkworth" <Mary.Barkworth at usu.edu>, "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>, "Michael A. Ivie" <mivie at montana.edu>
 Received: Friday, 9 February, 2018, 3:16 PM

 I
 totally agree Mary. Lumping is the easiest way. Or,
 as Leme (2003) put it, lumping may cause "nominal
 extinction". 
 Taxonomists
 have a lot of responsibility on the fate of organisms. If we
 reduce to synonymy a name we shall be totally certain that
 it is just part of the variation of the taxon under we are
 puting it. But it is common to lump because people see
 "gradients" when in reality there are two or more
 different taxa involved. In many cases, those lumped names
 represent endemic or scarcely known species. After that,
 they are not longer included in official lists of taxa for
 conservation or in ecological and floristic lists. That
 contributes to reduced evaluations of the biodiversity and,
 at long, to its actual reduction.
 Cheers,

 Socorro

 Source: Leme, E.M.C. 2003. Nominal extintion
 and the taxonomist's responsibility: the example of
 Bromeliaceae in Brazil. Taxon 52(2): 299‑302.
 _________________________________

 M. Socorro Gonzalez
 Elizondo
 Herbario CIIDIR
 Instituto Politecnico Nacional
 Sigma 119 Fracc. 20 de Noviembre II
 Durango, Dgo., 34220 MEXICO
 Tels. (618) 814 4540, (618) 814 6802; (55) 5
 729 6000 ext. 82609

 ________________________________
  De: Mary Barkworth
 <Mary.Barkworth at usu.edu>
 Para: Stephen
 Thorpe <stephen_thorpe at yahoo.co.nz>;
 "taxacom at mailman.nhm.ku.edu"
 <taxacom at mailman.nhm.ku.edu>; Michael A. Ivie
 <mivie at montana.edu> 
 Enviado: Jueves,
 8 de febrero, 2018 19:32:47
 Asunto: Re:
 [Taxacom] Elimination of paraphyly: sensible or not?

 But lumping (wide scoped supraspecific taxa)
 can also result in loss of understanding. There are no magic
 answers. Your wide scoping is my lumping and potential death
 by nomenclature - failure to identify the subsumed taxa into
 subsequent studies and/or failure to include them because
 they are not distinct.

 Mary

 -----Original Message-----

 From: Taxacom
 [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
 Stephen Thorpe

 Sent:
 Friday, February 9, 2018 4:22 AM

 To: taxacom at mailman.nhm.ku.edu; Michael A. Ivie
 <mivie at montana.edu>

 Subject: Re: [Taxacom] Elimination of
 paraphyly: sensible or not?

 At any rate, the basic problem
 appears to be that "understanding" is always
 inconclusive and in flux (and may not even be able to be
 defined very precisely if you mean some sort of collective
 understanding by the entire scientific community). So, the
 question is how much inconclusivity and/or flux do we want
 in taxonomic classification? My preference is to try to
 minimise it. I would go for more wide scoped supraspecific
 taxa (genera, families, etc.) There is nothing worse than
 oversplitting of genera, etc. This just leads to more
 instability as a result of phylogenetic studies.

 Stephen

 --------------------------------------------

 On Fri, 9/2/18, Michael A.
 Ivie <mivie at montana.edu> wrote:

 Subject: Re: [Taxacom]
 Elimination of paraphyly: sensible or not?

 To: "Stephen Thorpe"
 <stephen_thorpe at yahoo.co.nz>,
 taxacom at mailman.nhm.ku.edu

 Received: Friday, 9 February, 2018, 2:09 PM

 OK, I
 misunderstood you, but you

 misunderstood me as well.  "... in the 
 face of ever advancing understanding of the  evolution of
 life on earth" 

 is
 not

 meant to be just
 phylogenetics, but all aspects of biology  that  is bring
 more and more sense to the  universe every day (expect in 
 understanding  voting patterns or political
 motivations).

 Mike

 On 2/8/2018 6:02 PM,
 Stephen

 Thorpe wrote:

 > Mike said: "...
 in

 the face of ever
 advancing understanding of the evolution of  life on
 earth"

 >

 > It is a moot point
 whether

 cladistics/phylogenetics does in fact advance
 understanding  of the evolution of life on earth! It seems
 to me to be  little more than a paint by numbers approach
 which can in  theory be replicated by anyone else who uses
 the same  character weightings, etc., but replicability
 alone does not  imply that we are actually advancing
 understanding of the  evolution of life on earth"!

 >

 > You also misunderstood my comments about 
 retaining birds and mammals as named taxa. They ARE 
 monophyletic, and I didn't say to necessarily retain 
 them as taxa of equal rank to reptiles (so subtaxa of 
 reptiles are indeed fine to me also), I just meant that we 
 don't want to simply dump them into reptiles such that 
 Reptilia simply contains various subtaxa from each in a
 way  that doesn't group bird (or mammal) subtaxa
 together  under a name.

 >

 >

 I'm surprised that anyone
 finds "interesting"

 the inconclusive and ephemeral results of
 phylogenetic  studies!

 >

 >

 Stephen

 >

 >

 --------------------------------------------

 > On Fri, 9/2/18, Michael
 A. Ivie <mivie at montana.edu>

 wrote:

 >

 >   Subject:

 Re: [Taxacom] Elimination of
 paraphyly: sensible or not?

 >   To: taxacom at mailman.nhm.ku.edu

 >   Received: Friday, 9
 February, 2018,

 12:56 PM

 >

 >   Hi

 Stephan,

 >

 >  
 It

 seems to me that you
 have this premise

 >  
 backwards.  Rather than there

 >   being a

 >   cabal

 of rabid cladists obsessed with eliminating
 paraphyly,  >   I  >   think there  is a cabal
 of rabid  >   revanchists  obsessed with hanging on
 to  >   familiar  paraphyletic taxa in the face of
 ever  >

   advancing
 understanding

 >   of
 the

 evolution of

 >   life on earth. 
 In

 actual practice, most
 advocates

 >   of a

 monophyly standard continue to
 use and

 >   propose
 taxa that cannot be

 >   shown to be

 >

 monophyletic, but if we have evidence, why not
 use it?

 >

 >   You say

 "We wish to

 >   retain birds and

 also mammals as useful
 monophyletic

 >

 taxa, for obvious
 reasons."  How, if you  >   mean as  > 
 nomenclaturally-recognized taxa at  >   a  level
 equal to reptiles, is this  >  obvious,  >   or
 to be wished for?  We  have the words "birds"

 >   and

 "mammals"

 >   for the folk

 >   taxonomy, but why not
 recognize them  for what they really  >  >   are?
 Subtaxa of Reptiles works fine  for  >   me.

 >

 >   As for why look for

 >   monophyletic
 lineages?  Because

 scientifically,

 >   doing phylogenetics

 is INTERESTING.  I myself

 >   do mostly

 alpha taxonomy,

 >   because I

 >   don't have the
 skill set to be a

 leading

 >   phylogeneticist, but

 >   I find their
 results

 >   to be very
 thought provoking,

 interesting and even

 >   exciting.  It

 is not that they get too much

 >

 funding, it is that

 >   faunistics and

 taxonomy

 >   get to little.

 >

 >  
 Mike

 >

 >

 >

 >  
 On

 >   2/8/2018 3:07
 PM, Stephen Thorpe

 wrote:

 >   >

 >

 Hi
 all,

 >   > I have
 been giving some

 thought

 >   to the cladistic
 obsession

 of eliminating
 paraphyly in

 >

 taxonomic classification. For
 many taxa (above species),  the  >   subtaxa consist
 of one or more  clearly monophyletic groups,  >  
 plus a  possibly paraphyletic residue (i.e. no apomorphies
 to  >   bind the residue together into a 
 monophylum). So, if we must  >  eliminate paraphyly (or
 possible paraphyly), the only  >   options are to
 either: (1) subsume the  monophyletic subtaxa  >  
 into the  paraphyletic residue; or (2) break up the 
 >   paraphyletic residue into monophyletic  subtaxa.
 Effectively  >   the two options  may actually be
 equivalent. An example might  >   help to illustrate
 my point. Let's  take a simplistic  >   view of
 reptiles  as scaly tetrapods, birds as feathery  >

   winged bipeds derived from
 reptiles, and mammals as  hairy  >   tetrapods
 derived from  reptiles. So, amniotes (reptiles,  > 
 birds and mammals) are a monophyletic group, as are birds 
 >   and also mammals, but not reptiles  (reptiles
 being the  >  "paraphyletic residue"). We
 wish to retain  birds  >   and also mammals as
 useful  monophyletic taxa, for obvious  >  reasons.
 So, what to do? Luckily, within reptiles there  are 
 >   some monophyletic subgroups of  sufficient
 diversity to be  >   useful,  but this might not have
 been the case if all  >   reptiles were just
 basically  "skinks", with only  >  species
 or perhaps also generic differences between them.

 >   Had this been so,
 amniotes would have  to be taxonomically  >   split
 between  numerous (maybe hundreds) virtually identical 
 >   taxa of "skinks", plus birds  and also
 mammals as  >   just two taxa at  the same level (not
 necessarily a ranked  >   level, but direct child taxa
 of  amniotes). Would this be a  >   useful 
 classification of amniotes? I suggest that it would 
 >   be far more useful to recognise a  single
 paraphyletic taxon  >   of  reptiles (all the
 "skinks" in the hypothetical  >   example),
 plus birds and also mammals  (i.e. just 3 direct  >  
 child taxa of  amniotes). I wonder for plants, fungi and
 also  >   invertebrates, if there might be many  taxa
 analogous to the  >   above  hypothetical example,
 with a paraphyletic residue  >   consisting of
 hundreds of  "skinks", but also with  > 
 just one or two very distinct and diverse monophyletic 
 >   subtaxa? If so, would it be sensible to  eliminate
 paraphyly  >   or best just to  live with a known
 paraphyletic residue as a  >   unified subtaxon? Given
 the amount of  limited resources  >   which are
 being  allocated to projects to eliminate  > 
 paraphyly, to the detriment of alpha taxonomy, it would 
 be  >   nice to think that there was a  clearly good
 reason for the  >  elimination of paraphyly, but
 I'm not so sure that  there  >   is! The usual
 argument seems  to be that you cannot make  > 
 meaningful predictions from paraphyletic taxa, but how 
 much  >   biology does rely on the making  of
 predictions based on  >   taxon  membership, and what
 proportion of those predictions  >   end up being true
 anyway? For example,  you might predict  >   that a
 newly  discovered braconid is a parasitoid, but a few 
 >   braconids are phytophagous anyway. So,  I guess
 that the main  >   question that  I am posing is
 whether we think that the  >   benefits of monophyly
 justify the  spending of so much  >   limited 
 resources on the elimination of paraphyly? Perhaps 
 >   the elimination of paraphyly is being  driven
 instead by  >   economic factors,  doing phylogenies
 being a more cost  >  efficient way for institutional
 scientists to spend their  >   time on than alpha
 taxonomy?

 >   >

 >   Stephen

 >   >

 >

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 --

 >

 __________________________________________________

 >

 >   Michael A.

 Ivie, Ph.D.,

 >   F.R.E.S.

 >

 >  
 NOTE: two

 >  
 addresses with different Zip Codes

 depending on carriers

 >

 >  
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 >   Montana Entomology Collection

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 50

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 >

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 >   UPS, FedEx, DHL Address:

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 Collection

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 Labs, Room 50

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 >

 >

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 >

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 >

 >

 >

 _______________________________________________

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 Taxacom at mailman.nhm.ku.edu,

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 for 31 Some Years,
 1987-2018.

 >

 > .

 >

 --

 __________________________________________________

 Michael A.
 Ivie, Ph.D.,

 F.R.E.S.

 NOTE: two

 addresses with different Zip
 Codes depending on carriers

 US Post Office Address:

 Montana Entomology
 Collection

 Marsh Labs, Room
 50

 PO Box

 173145

 Montana State University

 Bozeman, MT 59717

 USA

 UPS, FedEx, DHL Address:

 Montana Entomology Collection

 Marsh Labs, Room 50

 1911 West

 Lincoln Street

 Montana State University

 Bozeman, MT 59718

 USA

 (406)

 994-4610 (voice)

 (406) 994-6029 (FAX)

 mivie at montana.edu

 _______________________________________________

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