[Taxacom] Prokaryota (was: All levels of organisation and manifestation ...)

Ken Kinman kinman at hotmail.com
Sun Nov 11 19:35:29 CST 2012


























Hi again David,
        I already discussed a paraphyletic Kingdom Protista a few days ago.  Now I would even more strongly challenge your statement that "Prokaryota is better replaced with the Eubacteria and Archaebacteria."  I assume that this is based on the still somewhat popular 3 domain trees in which Eubacteria is shown as strictly monophyletic (holophyletic).  However, that tree is very badly out-of-date (22 years) and was always an overly simplistic view based on ribosomal RNA sequences (as a warmed over version of the discredited Three Urkingdoms).  It is little more than a one-character classification, and we know how misleading those can be.    
       But there is increasingly strong evidence from much more molecular data, as well as morphological data (including fossil evidence, which includes chemical signatures), that Eubacteria are older than either Archaebacteria or Eukaryota (the latter two which form the Neomura clade), and that Eubacteria is very paraphyletic with respect to the Neomura clade.  Indeed there is a growing consensus that one particular subclade of Eubacteria (the gram-positive Actinobacteria) is closest to Neomura.  Cavalier-Smith has been continually testing and retesting his ideas on bacterial evolution (for decades now) with more and more evidence, and very eloquently presented these multiple lines of evidence in his 2006 paper (which uses very insightful transition analyses), but it has not received nearly as much attention as it deserves.  Here's a weblink to that paper:  http://www.biology-direct.com/content/1/1/19    
       For those of you who don't want to read all the details in that paper, below I present just a brief classification showing Cavalier-Smith's basic phylogeny of prokaryotes.  He calls it Kingdom Bacteria (sole kingdom in Empire Prokaryota).  However, I will call it Kingdom Prokaryota, since the name Bacteria was used as a Domain name and Domain Bacteria only includes the eubacteria.     
Kingdom Prokaryota             1   Chlorobacteria   2   Hadobacteria   3   Cyanobacteria (and chloroplasts)  4A  Spirochaetae   B   Sphingobacteria   C   Proteobacteria (and mitochondria)   D   Planctobacteria   5   Eurybacteria   6   Endobacteria   7   Actinobacteria   8   Archaebacteria (I still prefer Metabacteria)    9   {{Eukaryota}} (Protista, thence to Metazoa, Eumycota, and Metaphyta)

       Note that Eubacteria includes clades 1-7; Negibacteria includes clades 1-5; Posibacteria includes clades 6-7; Neomura includes clade 8-9.  Anyway, if one is trying to completely cladify prokaryotes and avoid paraphyly, dividing them into Eubacteria and Archaebacteria will clearly not get the job done.  To completely cladify them, you would have to divide the eubacteria into at least 7 separate clades (Domains?), for a total of 9 Domains instead of 3.  Might have to add at least one more if Actinobacteria is itself paraphyletic, and perhaps yet another if Archaebacteria is paraphyletic (as in Lake's "eocyte hypothesis).  And Chlorobacteria at the base could be paraphyletic as well.
      Fighting paraphyly is too often a never ending process which is destabilizing and leads to either excessive lumping or excessive splitting (just look at the classification of dinosaurs along the theropod lineage which gave rise to birds).  There never was anything wrong with the 5 Kingdom classification of life, and trying to eliminate the paraphyly of two of those Kingdoms has just created a big fat mess that was totally unnecessary (even Cavalier-Smith's eukaryotic Kingdom Chromista, which I never liked, although it was less harmful than the 3 Domains).    And I really, REALLY wish textbook publishers would stop publishing those simplistic 3 Domain trees.                
                                              -------------------Ken       
Date: Thu, 8 Nov 2012 11:45:28 -0700
Subject: Re: [Taxacom] All levels of organisation and manifestation should be acknowledged for the classificatory and evolutionary value that is inherent in them
From: dpatterson at mbl.edu
To: kinman at hotmail.com
CC: nicholasa at ukzn.ac.za; richard.zander at mobot.org; taxacom at mailman.nhm.ku.edu

I can comment on protists which I know a little about.
You may wish to look at the most recent global classification of protists - J. Eukaryot. Microbiol., 52(5), 2005 pp. 399–451 - 'Protista' has been rejected.

Prokaryota is better replaced with the Eubacteria and Archaebacteria. 
Perhaps folk with expertise in the other taxa can see if Ken's view is consistent with the authoritative perspectives?

David

On Thu, Nov 8, 2012 at 11:11 AM, Ken Kinman <kinman at hotmail.com> wrote:





Hi David,        The higher level paraphyletic taxa are probably the most useful, since they have a very wide user pool.  (1)  Kingdom Prokaryota (or rank it as Empire or Domain, if you will).  (2) Kingdom Protista is a major example, since trying to get rid of that one has done nothing but create needless confusion.   (3) Phylum Bryophyta.  (4) Class Sarcopterygia.  (5) Class Amphibia.   (6) Order or Superorder Dinosauria, for the so-called "non-avian dinosaurs".    

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

Date: Thu, 8 Nov 2012 10:23:41 -0700
Subject: Re: [Taxacom] All levels of organisation and manifestation should be acknowledged for the classificatory and evolutionary value that is inherent in them

From: dpatterson at mbl.edu
To: kinman at hotmail.com
CC: nicholasa at ukzn.ac.za; richard.zander at mobot.org; taxacom at mailman.nhm.ku.edu


If 'many other do too', I'd be surprised.  Some, certainly. But the majority see little value in preserving paraphyletic taxa.  But perhaps some of the advocates for retention (nay, adoration) of paraphyly could suggest some 'taxa' that they believe serve us better than holophyletic taxa.


David Patterson

On Thu, Nov 8, 2012 at 8:58 AM, Ken Kinman <kinman at hotmail.com> wrote:



Hi Ashley,

      Here, here.  Agree completely, and many others do too.  Not that our heads would go on the chopping block, but our heads do get sore banging up against that brick wall (of holophyly worship coupled with paraphyly bashing).  You would think branding paraphyletic taxa with a "Scarlet letter" P would satisfy them (Thomas Cavalier-Smith uses a * symbol, and I use a % symbol for paraphyletic taxa).  But explicit marking of paraphyletic taxa doesn't satisfy them, and they just want to destroy them (not just bash them), no matter how informative and useful such taxa can be.  Few of them seem willing to even discuss possible compromise of any sort on this subject.



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





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

> From: Nicholasa at ukzn.ac.za

> To: Richard.Zander at mobot.org; taxacom at mailman.nhm.ku.edu

> Date: Thu, 8 Nov 2012 14:56:50 +0000

> Subject: [Taxacom] All levels of organisation and manifestation should be acknowledged for the classificatory and evolutionary value that is inherent in them

>

> Right - let me put my head on the chopping block!

>

>

>

> One of the disturbing things about modern classificatory paradigms is that a whole level of organisation (organismal morphology) is being written off as scientifically worthless. Am I the only one who is scared by empirical scientific implications of this?



>

>

>

> I personally think this is bad science. Biodiversity presents us with information at the molecular, genetic, organismal, physiological and ecological levels and data from all level gives us important information about how organisms manifest and change with time. The acceptance of strict monophyly is allowing scientists to discount groups of organisms defined by unique morphologies. These groups are valid and could easily be accepted under a paraphyletic classification. This is possibly arguable, but if we are to create classifications in which data from all levels of organisation are acknowledged for the value that is inherent in them, then we must accept paraphyly. Besides all new major evolutionary lines start off as paraphyletic side branches -- and paraphyly says a great deal about the way in which organisms and groups evolve. By removing paraphyly we remove the possibility of investigating some very intriguing evolutionary questions - that I feel need to explored rathe



 r than ignored.

>

>

>

> Everyone seems focused on the morphological versus molecular and monophyletic versus paraphyletic battlefields. There are other levels of organization which we neglect at our scientific peril.

>

>

>

> At the end no matter the evidence used (morphological or molecular) classifications that are extrapolated from this evidence only hypotheses. Hypotheses are merely concepts out there for further verification or falsification. They are not the truth. Despite what outsiders may think scientists live in a world of uncertainty and all good scientists will embrace this fact.  As a professional taxonomist I live (in my head) in a world of multiple taxonomies and classifications base on the same organisms. Why are we so fixated on having only one classification? I wish other scientists and funders would stop trying to put me into either the morphological or molecular box. As a scientist I refuse to limit myself like this -- the organismal diversity I walk through when I am in the bush is more than just morphology and molecules. I do not see any good scientific reason to abandon information from other levels of manifestation.



>

>

>

> Ashley

>

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

>

> Ashley Nicholas (PhD)

>

> Associate Professor & Curator Ward Herbarium

>

> School of Life Science,  Westville Campus

>

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>

> Private Bag X54001,

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> Tel.:+27-31-260 7719 Fax.: +27-31-260 2029

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> nicholasa at ukzn.ac.za

>

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

>

> Let's not continue to fool ourselves, we are no longer sititing at the edge of the cliff of "environmental disaster", we have gone over that edge. - Ashley Nicholas (at the moment six cities the size of Johannesburg are added to the world every year)



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