[Taxacom] What taxon corresponds to "birds'?

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Tue Nov 29 21:00:38 CST 2016

" ...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"..


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.
 On Tue, Nov 29, 2016 at
 8:14 PM, Kenneth Kinman <kinman at hotmail.com>
 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/
 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'?
 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.
 ------------------------------ --------------
 On Wed, 30/11/16, Richard Pyle <deepreef at bishopmuseum.org>
  Subject: Re: [Taxacom] What taxon corresponds to
  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
  am not sure what
  > you see to be so
  complicated or splintered. With respect to splintered
  > 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
  you want to represent inferred evolutionary
  among organisms, then cladograms and similar
  diagrams are an extremely effective tool for
  them.  I think the problem happens when people have
  to use a hierarchcal classification and nomenclatural
  originally developed by a creationist (aka, Linnean
  nomenclature) as a system explicitly for communicating
  hypothesized inferred evolutionary relationships. 
  names and classifications have a history spanning more
  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
  about inferred evolutionary relationships, and leave
  nomenclature to the function it has very effectively
  fulfilled for many years.  Clearly there is (and
  be!) a very high degree of congruence between the two
  systems of communication.  But attempts to use the
  as a strict communication tool to represent the former
  (usually?) serves neither goal effectively. Birds are a
  great example of this.
  Richard L. Pyle, PhD
  Database Coordinator for Natural Sciences |
  Associate Zoologist in Ichthyology | Dive Safety
  Department of Natural Sciences, Bishop Museum,
  1525 Bernice St., Honolulu, HI 96817
  (808)848-4115, Fax: (808)847-8252 email: deepreef at bishopmuseum.org
 staff/staffimages/pylerich.jpg ]<http://hbs.bishopmuseum.org/
 HBS Staff - RLPyle<http://hbs.
 bishopmuseum.org/staff/ pylerichard.html>
 The State Museum of Cultural and Natural History, Honolulu,
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