[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
Kenneth Kinman
kinman at hotmail.com
Thu Jul 9 17:16:54 CDT 2015
2015
Hi Stephen,
Logically, we must remember that Reptilia (before birds evolved from them in the Mesozoic) was once a holophyletic (strictly monophyletic) taxon. But having so much success and given rise to so much diversity and numbers of taxa (especially after their dinosaur ancestors were wiped out), birds were naturally regarded as distinct from reptiles and thus given their own Class. Amphibians likewise are classified as distinct from their sarcopterygian fish ancestors. And embryophytes (metaphytes) are classified as distinct from their charophyte ancestors, so much so that they are usually given their own Kingdom Metaphyta (or Plantae sensu stricto).
Therefore, it has always seemed to me logical not to give a new name to Reptilia, but to simply add an exgroup marker {{Aves}} to show where the birds branched off cladistically within the theropod dinosaurs. Same with a {{Metaphyta}} marker within Charophyta, and a {{Tetrapoda}} exgroup marker within Class Sarcopterygii. This is not only more informative, but it avoids most of the instability that "strict" cladism has caused in its continued assault on perfectly good paraphyletic taxa. The Linnean hierarchy has managed to hold on in spite of the increasing strain this assault has placed on it, but just barely. Why bioinformatics so often gravitates to the strictly cladistic methodology, which is inherently unstable, continues to baffle me. Exgroup markers are much more logical, and if you want to add a coding system to show cladistic relationships, all the better (but you certainly can't do that with an alphabetical listing).
---------------Ken
------------------------------------------------------------------------------------------------------
> Date: Thu, 9 Jul 2015 13:44:54 -0700
> From: stephen_thorpe at yahoo.co.nz
> Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
> To: releech at telus.net; tonyrees49 at gmail.com; kinman at hotmail.com
> CC: taxacom at mailman.nhm.ku.edu
>
> Logically, Reptilia should be given a new name (say Pertilia) if Aves are included in it, for what the paraphyly really amounts to is to show that reptiles don't exist, except as a group of convenience. So, reptiles should just become an informal name for nonavian pertiles. However, systematists are rarely logical ...
>
> Stephen
>
>
> --------------------------------------------
> On Fri, 10/7/15, Kenneth Kinman <kinman at hotmail.com> wrote:
>
> Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
> To: "Robin Leech" <releech at telus.net>, "'Tony Rees'" <tonyrees49 at gmail.com>
> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Received: Friday, 10 July, 2015, 4:54 AM
>
>
>
>
> Hi Tony and Robin,
> I have to disagree. I
> don't think this was inevitable (or wise or brave). We
> have long known (since Archaeopteryx) that birds evolved
> from reptiles, but that is not a good reason to subsume one
> into the other. By such reasoning, we could argue that
> Amphibia and the other tetrapod classes should be subsumed
> into Sarcopterygii. Or subsuming all the higher plant
> phyla into Phylum Charophyta. Or how about dumping all the
> insects into the Crustacea. Such reasoning is just as
> unwise with respect to Aves as it is with these and many
> other examples. So I don't think it is inevitable that
> birds have to be dumped in with their reptile (dinosaur)
> ancestors, any more than it is would be inevitable that we
> dump tetrapods in with the sarcopterygian fish (or Insecta
> into Crustacea).
> ----------------Ken
> ------------------------------------------------------------------------------------------------------------------------------------------------
> > From: releech at telus.net
> > To: tonyrees49 at gmail.com;
> kinman at hotmail.com
> > CC: taxacom at mailman.nhm.ku.edu
> > Subject: RE: [Taxacom] New paper: Ruggiero
> et al. "A Higher Level Classification of All Living
> Organisms"
> > Date: Thu, 9 Jul 2015
> 10:01:56 -0600
> >
> >
> Tony,
> > Probably inevitable - the more
> we find out, the closer the two (reptiles and birds) seem to
> be.
> > Robi
> >
> > -----Original Message-----
> > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
> On Behalf Of Tony Rees
> > Sent: July-09-15
> 1:10 AM
> > To: Kenneth Kinman
> > Cc: taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] New paper: Ruggiero
> et al. "A Higher Level Classification of All Living
> Organisms"
> >
> > I
> note that (class) Aves has now been subsumed into class
> Reptilia for the first time - brave or inevitable??
> >
> > - Tony
> >
> > On Thu, Jul 9, 2015
> at 1:26 PM, Kenneth Kinman <kinman at hotmail.com>
> wrote:
> > >
> > >
> Hi Stephen, My
> biggest problem with this
> > >
> classification (and many others) is that the subtaxa within
> a taxon
> > > are alphabetically
> arranged, which automatically and immediately
> > > affects their naturalness from the
> start. Paleognathae is thus placed
> >
> > after Neognathae, and worse yet Aves is placed before
> all the other
> > > reptiles. The
> Superclass Angiospermae is a mess, which for some
> > > reason they only classify as a single
> Class. Therefore, the subtaxa
> > >
> are an unnatural mess. Although I nitpick about the
> details of the
> > > cladistic
> classifications of angiosperms, at least they are fairly
> natural (even with their unnatural rejection of a
> > > few very natural and useful taxa).
> Neomycota
> > > is listed as Dikarya, so it comes
> before Eomycota. And they don't
> >
> > even mention the name Eumycota (which has always been
> more informative
> > > than
> "Fungi"). The mammal orders Cingulata and Pilosa
> aren't listed
> > > together at
> all, and how many non-mammalogists even know what animals
>
> > > those taxa include? And totally
> separating Archaebacteria from their
> >
> > relatives Posibacteria is a horrible oversight that has
> plagued
> > > classifications for well
> over 20 years.
> > >
> ---------------Ken----------------------------------------------------
> > >
> ----------------------------------------------------------------------
> > >
> --------------------------------------
> >
> >
> > > > Date: Wed, 8 Jul 2015
> 18:11:57 -0700
> > > > From: stephen_thorpe at yahoo.co.nz
> > > > To: Taxacom at mailman.nhm.ku.edu;
> tonyrees49 at gmail.com
> > > > Subject: Re: [Taxacom] New
> paper: Ruggiero et al. "A Higher Level
> > > Classification of All Living
> Organisms"
> > > >
> > > > The problem with it being
> "followed in future by both ITIS and
> > > > Catalogue
> >
> > of Life" is that new developments, based on
> scientific evidence, will
> > > not be
> considered (at least not until some big revised version of
> the
> > > present paper is published).
> So, bioinformatics and science part ways for a while.
> > > It is really just a case of
> "choose your own classification", and if
> > > you wish to choose to follow Ruggiero
> et al.'s paper, you can, but
> > >
> there may be better alternatives.
> > >
> >
> > > > Stephen
> > > >
> > > >
> --------------------------------------------
> > > > On Thu, 9/7/15, Tony Rees <tonyrees49 at gmail.com>
> wrote:
> > > >
> >
> > > Subject: [Taxacom] New paper: Ruggiero et al.
> "A Higher Level
> > >
> Classification of All Living Organisms"
> > > > To: "taxacom" <Taxacom at mailman.nhm.ku.edu>
> > > > Received: Thursday, 9 July,
> 2015, 12:52 PM
> > > >
> > > > Dear Taxacomers,
> > > >
> > > >
> Since I did not see this mentioned on Taxacom earlier
> (perhaps I
> > > > missed it),
> list members may be interested to know that Michael
> > > > Ruggiero et al.'s paper
> "A Higher Level Classification of All
> > > > Living Organisms" has
> been out in PLOS One since 20 April 2015,
> > > > the link is here:
> > > >
> > >
> >
> > > http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119248
> > > >
> > > >
> This is an internally consistent treatment of
> "all" extant
> > > > taxa
> down to the
> > > > level of Order
> (in most cases), to be followed in future by
> > > > both ITIS and
> > > > Catalogue of Life I
> understand. For those interested in
> >
> > > going further to
> > >
> > the level of family, I have come across a spreadsheet
> with
> > > > the latter
> > > > information prepared by the
> same authors (possibly slightly
> > >
> > earlier
> > > > version)
> labelled "GGI family data" at http://ggi.eol.org/downloads .
> > > >
> > > >
> Of course the above treatments do not include fossil
> > > > orders/families but
> > > > maybe these will be in scope
> at some point in the future
> > > >
> (??)
> > > >
> >
> > > Hoping this is of interest to at least some
> Taxacom
> > > > readers,
> > > >
> > > >
> Best regards - Tony Rees, New South Wales, Australia
> > > >
> _______________________________________________
>
>
>
>
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be
> searched at: http://taxacom.markmail.org
>
> Celebrating 28 years of
> Taxacom in 2015.
>
More information about the Taxacom
mailing list