[Taxacom] What taxon corresponds to "birds'?

Tue Nov 29 22:11:18 CST 2016

Hi Stephen,

       Yes, cladistic nomenclature is perhaps popular, not so much because it is superior, but because it opened up a whole new avenue of getting published and getting grant money.  I am stunned to learn that the clade Crocopoda is not based on any synapomorphies whatsoever, but is instead based on a single symplesiomorphy.  Apparently it's sister group (Choristodera) lost the prominent calcaneal tuber, but Crocopoda retained it.  That loss could be a synapomorphy, but one can't really create a clade "Acrocopoda", because it would be redundant (a synonym of Choristodera).   Anyway, I quote from the original paper:

     "Crocopoda means “crocodile foot” and is derived from the Latin word “crocodilus” and the Greek word “pous.” This name refers to the fact that members of this clade possess a prominent calcaneal tuber, which is a plesiomorphic characteristic retained by the crocodile-line of Archosauria. It should be noted that the presence of a calcaneal tuber is a character-state that currently diagnoses Crocopoda, but it does not define it."

       It just seems like useless clutter to be naming clades like this.  But as long as PhyloCode is regarded as possibly becoming a reality, it's priority provision is probably going to continue to tempt workers to name clades before someone else beats them to it.  And there are already lots of clade names that are clearly synonyms of other clade names.  What a big fat mess and it just continues to get worse.  I am already regretting having spent so much time on this today.
                    ----------------Ken
P.S.  Shouldn't the clade name Pantestudines be hyphenated (Pan-Testudines)?  Same for Pan-Aves?  Panaves (without a hyphen) is just too similar to Paraves.  Paraves is obviously an important clade, but I can't say Pan-Aves is of much value.

________________________________
From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Sent: Tuesday, November 29, 2016 9:00 PM
To: Kenneth Kinman; John Grehan
Cc: deepreef at bishopmuseum.org; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] What taxon corresponds to "birds'?

" ...why bother proposing the tree in the first place"

I once asked a taxonomist this very question, relating to a published phylogeny which lacked any conclusions whatsoever. I don't think the person I asked was an author of the paper, but anyway he replied [quote]Well, people have to eat[unquote]! In other words, phylogenetics is "just a job", and you need to "publish or perish"..

Stephen

--------------------------------------------
On Wed, 30/11/16, John Grehan <calabar.john at gmail.com> wrote:

 Subject: Re: [Taxacom] What taxon corresponds to "birds'?
 To: "Kenneth Kinman" <kinman at hotmail.com>
 Cc: "deepreef at bishopmuseum.org" <deepreef at bishopmuseum.org>, "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
 Received: Wednesday, 30 November, 2016, 3:54 PM

 So I get
 the impression from your comments Ken that you object to too
 many taxonomic categories being proposed by (which could
 apply to any group with many branches regardless of whether
 cladistic or otherwise). Can sympathize, although there is
 no objective way to impose a limit.
 Interesting converse to taxonomic
 categories that are not shown on the tree is where a new
 phylogeny proposed breaking up numerous taxa (such as
 genera), but no formal change to the generic classification.
 One wonders if the authors are in such doubt about their
 results why bother proposing the tree in the first place.

 John
 Grehan
 On Tue, Nov 29, 2016 at
 8:14 PM, Kenneth Kinman <kinman at hotmail.com>
 wrote:
 Hi
 Stephen and Richard,

       Yes, I agree.  Frankly, I love splintered
 cladograms and trees.  However, when that splintering is
 incorporated into classifications (often prematurely), such
 classifications become less and less useful.

        I just found one example in the Wikipedia article
 for Archosauriformes.  It has both a tree and a
 classification, but the classification has taxa not shown in
 the tree (and vice versa).  And the classification already
 contains a new clade Eucrocopoda proposed this year, so not
 much time for others to test this hypothesis.  And to get
 to Crocopoda you have to jump back above clade
 Archosauriformes, which is weird, and Eucrocopoda is between
 Archosauriformes and Archosauria (equally weird).

         But perhaps weirdest of all, birds are now
 members of clades Crocopoda and Eucrocopoda:  https://en.wikipedia.org/wiki/
 Archosauriformes

                      ---------------Ken

 P.S.  Don't ask me how many clade names there are
 between Crocopoda and Aves, because I don't have time to
 count them all.   Might make for an interesting tree, but
 it makes for a very messy, splintered classification.

 ______________________________ __

 From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>

 Sent: Tuesday, November 29, 2016 6:07 PM

 To: 'John Grehan'; 'Kenneth Kinman'; deepreef at bishopmuseum.org

 Cc: taxacom at mailman.nhm.ku.edu

 Subject: Re: [Taxacom]
 What taxon corresponds to "birds'?

 Rich,

 Yes, one major problem involves people trying to
 "formalize" every phylogenetic hypothesis into a
 classification! I'm really confused about one major and
 fundamental issue relating to phylogenies, which has
 considerable bearing on this issue. Are phylogenies merely
 hypotheses (to be tested, which is an ongoing process
 without a clear endpoint) or are they already the nearest
 things we can get to "facts"? If they are merely
 hypotheses, then it makes little or no sense to use them to
 alter classifications.

 Cheers,

 Stephen

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

 On Wed, 30/11/16, Richard Pyle <deepreef at bishopmuseum.org>
 wrote:

  Subject: Re: [Taxacom] What taxon corresponds to
 "birds'?

  To: "'John Grehan'" <calabar.john at gmail.com>,
 "'Kenneth Kinman'" <kinman at hotmail.com>

  Cc: taxacom at mailman.nhm.ku.edu

  Received: Wednesday, 30 November, 2016, 12:16 PM

  > I have seem

  > innumerable molecular phylogenies

  generating many branching points

  >

  involving many taxa, but as long as the tree is presented
 I

  am not sure what

  > you see to be so

  complicated or splintered. With respect to splintered
 are

  you

  > saying some phylogenetic

  relationships should remain unresolved so the

  > pattern is 'simple'?

  I can't answer for Ken,

  but one point I have been making for many years is that
 if

  you want to represent inferred evolutionary
 relationships

  among organisms, then cladograms and similar
 branch-type

  diagrams are an extremely effective tool for
 communicating

  them.  I think the problem happens when people have
 tried

  to use a hierarchcal classification and nomenclatural
 system

  originally developed by a creationist (aka, Linnean

  nomenclature) as a system explicitly for communicating

  hypothesized inferred evolutionary relationships.
 Such

  names and classifications have a history spanning more
 than

  two and a half centuries (a century before Darwin), and

  benefit to some degree on stability of usage over time.

  Thus, let's use line

  drawings like cladograms to communicate our specific
 ideas

  about inferred evolutionary relationships, and leave
 the

  nomenclature to the function it has very effectively

  fulfilled for many years.  Clearly there is (and
 should

  be!) a very high degree of congruence between the two

  systems of communication.  But attempts to use the
 latter

  as a strict communication tool to represent the former
 often

  (usually?) serves neither goal effectively. Birds are a

  great example of this.

  Aloha,

  Rich

  Richard L. Pyle, PhD

  Database Coordinator for Natural Sciences |

  Associate Zoologist in Ichthyology | Dive Safety
 Officer

  Department of Natural Sciences, Bishop Museum,

  1525 Bernice St., Honolulu, HI 96817

  Ph:

  (808)848-4115, Fax: (808)847-8252 email: deepreef at bishopmuseum.org

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