[Taxacom] Protist systematics

Ken Kinman kinman at hotmail.com
Fri Jan 24 10:53:18 CST 2014


Hi John and Fred,       John, I have never bashed monophyly (holophyly).  It is an important component of classifications.  What we object to is restricting classifications to holophyly ONLY (which is what strict cladists do when they don't allow any paraphyly at all).         And Fred, I think Linnaean categories are (and always have been) a good, useful tool.  The human brain organizes things by using categories, and Linnaean categories give classifications a much needed structure.                   -----------Ken                

Date: Sat, 25 Jan 2014 00:17:24 +1300
Subject: Re: [Taxacom] Protist systematics
From: calabar.john at gmail.com
To: kinman at hotmail.com
CC: brpatric at dwu.edu; taxacom at mailman.nhm.ku.edu

Ken said "Too bad limited paraphyly is still seen as a bad thing, and those who bash paraphyly can still get rewarded for doing so."

One might rephrase to say that "Too bad monophyly is seen as a bad thing, and those who bash monophyly can still get rewarded for doing so." Point here is that there is a difference of opinion about structuring natural groups. Either is bad only depending on one's point of view. And one is "rewarded" only by the measure of acceptance among colleagues. Maybe its "too bad" that at particular times and places some views predominate and others do not, but that's the way the real world works. If paraphyly is so great it will be up to the proponents to keep making the case or demonstrating its application. Its always possible that paraphyly has merit that is not measured by level of acceptance (as the history of science shows, the degree to which a view (theory, hypotheses etc) is believed is not necessarily a proof of that view). That is true of any minority point of view. 

John Grehan


On Fri, Jan 24, 2014 at 3:54 PM, Ken Kinman <kinman at hotmail.com> wrote:

Hi all,



       I was just comparing my 2011 classification (see below) with that of Adl et al. 2012.  They are phylogenetically almost the same, except that Adl still recognizes a broader Excavata as a single clade, while I separate them as a paraphyletic grouping, into two adjacent, but separate, clades (Euglenozoa and Excavata sensu stricto), as does Thomas Cavalier-Smith.


      Otherwise, it is mainly minor semantic differences.  They refer to Clade 3 as Amorphea, whereas it is better known as Unikonta (and a better name in my opinion).  And for what Cavalier-Smith has refered to as the photokaryotes (Clades 4 to 10), they now propose the more formal name Diaphoretickes.  Seems to me Photokaryota would be easier to remember and understand.  Diaphoretickes sounds more like an arachnid that might bite you and suck your blood (sorry, I couldn't resist that one).


      I couldn't help but notice that Adl (et al.) gave PhyloCode definitions for their new taxa.  And this no doubt indicates they are opposed to the recognition of any paraphyletic taxa however useful they might be.  I guess that is still a popular band-wagon to hop onto.  Will be interesting to see if their broad Excavata actually turns out to be paraphyletic (how embarrassing that would be).


      Anyway, given that paraphyly is really a natural product of evolution, I am always surprised to see how far some will go to "appear" to avoid paraphyly.  And yet in the process, they often end up proprosing paraphyletic groupings that are less useful than the paraphyletic taxa they themselves oppose (such as Kingdom Protista).  At these highest levels of classification in particular, strict "cladifications" are about as unnatural as it gets.  Too bad limited paraphyly is still seen as a bad thing, and those who bash paraphyly can still get rewarded for doing so.


                 -----------------Ken Kinman





                KINGDOM PROTISTA



   1   Euglenozoa

  2A   Percolozoa

   B   Loukozoa

   C   Metamonada

  3A   Amoebozoa

   B   Apusozoa

   C  Choanozoa%%

            1A  Cristidiscoidea

            1B  {{Eumycota}}

            2   Ichthyosporea

            ?   Corallochytrea

            3   Filasterea

            4   Choanoflagellatea

            5   {{Metazoa}}

 _a_   {{Kingdom EUMYCOTA}} (true fungi)

 _b_   {{Kingdom METAZOA}}

  4A   Glaucophyta

   B   Rhodophyta

   C   Chlorophyta%

 _a_   {{Kingdom METAPHYTA}} (embryophytes)

  5A   Cryptophyta

   B   Haptophyta

   6   Rhizaria

   7   Heterokonta (stramenopiles)

   8  Ciliophora

   9   Dinozoa (or Dinophyta)

  10   Sporozoa



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

NOTES: Clades 5-10 make up the "SAR" clade (Cavalier-Smith's Chromista

sensu lato). Clades 4-10 form the photokaryote clade.   Clades 3-10

form Cavalier-Smith's "Neozoa"; Clades 2-10 form Cavalier-Smith's

"neokaryotes".   Clade 3 is "Unikonta" and Clade 3B (Choanozoa and its

two exgroups) form the Opisthokonta clade of which we are a part).

    ADDED NOTE:  And as noted above, Clades 7-10 have been named Clade

Halvaria.



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



> From: kinman at hotmail.com

> To: brpatric at dwu.edu; taxacom at mailman.nhm.ku.edu

> Date: Thu, 23 Jan 2014 19:36:52 +0000

> Subject: Re: [Taxacom] Protist systematics

>

> Hi Brian,

>

> Some of us still prefer a single Kingdom Protista, but recognizing some newly discovered Phyla within it. In my last classification of Protista which I posted on Taxacom in 2011, I recognized 17 Phyla. It shows that Chromalveolata must be either split up or expanded (especially to include Phylum Rhizaria). Either way, I never liked either Chromista or Chromalveolata. Here's a weblink to my 2011 classification:


>

>

>

> http://mailman.nhm.ku.edu/pipermail/taxacom/2011-August/073326.html

>

>

>

> ---------------Ken Kinman

>

> ------------------------------------------------------------------------------------------------------------------

>

>

> > From: brpatric at dwu.edu

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

> > Date: Thu, 23 Jan 2014 14:28:10 +0000

> > Subject: [Taxacom] Protist systematics

> >

> > Dear colleagues,

> >

> > The classification of protists has changed a great deal in the last decade or so. Most introductory textbooks still refer to older classification systems because the protist classifications rapidly change. However, there seems to be some growing consensus that at least a couple of new kingdoms have been introduced (e.g., Chromalveolata).


> >

> > Are there any papers that have addressed the higher level classifications of the protists? If so, might someone suggest a few such papers?

> >

> > Thank you for your time!

> >

> > Best regards, Brian

> >

> > ----------------------------------------------------------------

> > L. Brian Patrick, Ph.D.

> > Assistant Professor of Biology and Chair

> > Department of Biological Sciences

> > Dakota Wesleyan University

> > 1200 W. University Ave.

> > Mitchell, SD 57301

> >

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> The Taxacom Archive back to 1992 may be searched with either of these methods:

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