[Taxacom] Catalogue of Life (CoL) management classification draft document

Mon Jul 20 08:34:27 CDT 2009

Tony

I am interested in knowing what makes treatments palatable (or unpalatable).

As you say, the eutree structure is a working structure.  It's purpose is to gather taxa together in line with our understanding of relatedness, AND specifically not to group together taxa if they are not known to be related.

the consequence is a working structure that many find unpalatable.  Among the issues that contribute are:

- ranking
- names
- familiarity
- convenience
- representation of unrelatedness

I have just edited the structure to make it into the format below in order to address the latter issue.

thoughts from you or others on this would help us work up a strategy

thanks

David Patterson

Eukaryota
# Amoebozoa
# Excavates
# Glaucocystophytes
# Opisthokonts (incl. Choanoflagellates+animals, Chytrids+fungi+microspora, plus more)
# Rhodophyta
# SAR hypothesis (=Alveolates and Stramenopiles+Rhizaria)
# Viridaeplantae 

# Unassigned lineages
    # Residua (includes acritarchs, residual algae, residual amoebae, chitinozoa plus more)
    # Micronuclearia
    # Paramyxea
    # Breviatea
    # Ancyromonas
    # Apusomonads
    # Centroheliozoa
    # Cryptomonads+kathablepharids
    # Telonemidae
    # Haptophytes

----- Original Message -----
From: "Tony Rees" <Tony.Rees at csiro.au>
To: dpatterson at eol.org
Cc: taxacom at mailman.nhm.ku.edu
Sent: Monday, July 20, 2009 3:34:23 AM (GMT-0500) America/New_York
Subject: RE: [Taxacom] Catalogue of Life (CoL) management classification draft document

Dear David, all,

I've taken a look at the classification at http://eutree.lifedesks.org/ bearing in mind that as you say, it is a working rather than a reference structure. For example, the highest level categories under "Eukaryota" look like this:

Eukaryota

# Amoebozoa
# Ancyromonas
# Apusomonads
# Breviatea
# Centroheliozoa
# Cryptomonads+kathablepharids
# Excavates
# Glaucocystophytes
# Haptophytes
# Micronuclearia
# Opisthokonts (incl. Choanoflagellates+animals, Chytrids+fungi+microspora, plus more)
# Paramyxea
# Residua (includes acritarchs, residual algae, residual amoebae, chitinozoa plus more)
# Rhodophyta
# SAR hypothesis (=Alveolates and Stramenopiles+Rhizaria)
# Telonemidae
# Viridaeplantae

I think you will agree, though, that it may not be very suitable for porting into the CoL style of hierarchy which really works around the kingdom/phylum/class/order system, unless you are happy for all of the above to be phyla (or perhaps kingdoms...) Is there anything from the above that would be a better fit for CoL needs than the alternative suggested in Dennis' paper?

I guess the other issue for CoL is that they probably need to cite a "published" classification (e.g. with versioning) that can be superseded at some later point, than a continuously evolving web product (however accurate this may be)...

Regards - Tony

-----Original Message-----
From: David Patterson [mailto:dpatterson at eol.org] 
Sent: Saturday, 18 July 2009 11:38 PM
To: Rees, Tony (CMAR, Hobart)
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Catalogue of Life (CoL) management classification draft document

Folks

To answer Tony's question, No there is still no consensus over how to handle the protists.  Molecular analyses have tended to add a fair bit of noise to the picture, this has led to many speculations expressed in the form of classificatory structures, and the consequence is a lot of confusion.  Some parts of the scheme appear to be increasingly robust, although the scope and definition of the taxa remain uncertain.  Survivors at the top level seem to be the Opisthokonts (animals, fungi and close protistan relatives), Amoebozoa and Rhizaria.  Excavates go in an out of favor, while chromalveolates and Archaeplastida are not solid.  Similarly, at more distal points in the conceptual tree, some taxa, such as Chromists, are unsupported by much beyond wishful thinking and so are contentious.  

Ideally, the application of phylogenetic principles as criteria for retention or dismissal of taxa would be wonderful, and protistologists have been somewhat slow to move in this direction.

A protist classification that is more consistent with currently available data can be found at eutree.lifedesks.org.  It is a working structure rather than a reference structure.  In that system, if relationships are unclear, the contestants for most proximate neighbors are placed as sister groups to minimize the risk of producing polyphyletic taxa.

As an interesting aside, the eutree classification was built from a decade-old classification that had been based mostly on premolecular data.  The conversion required fewer than 100 edits.  Those edits included the addition of several previously missing genera and species. That is, the somewhat costly molecular studies of the last decade have led to about 70 discrete improvements in our knowledge of this area.

Thanks for the opportunity, Tony

David Patterson

----- Original Message -----
From: "Tony Rees" <Tony.Rees at csiro.au>
To: taxacom at mailman.nhm.ku.edu
Sent: Saturday, July 18, 2009 2:49:56 AM (GMT-0500) America/New_York
Subject: [Taxacom] Catalogue of Life (CoL) management classification draft document

Dear Taxacomers,

For those who may not have yet come across it, I thought it might be worth mentioning that a draft discussion document entitled "Towards a management hierarchy (classification) for the Catalogue of Life" by Dennis Gordon is now available on the CoL website (and also the CD-ROM distribution version for 2009) at the following URL:

http://www.catalogueoflife.org/annual-checklist/2009/info_hierarchy.php

There is no stated procedure for commenting on this draft or to whom such comments should be addressed, but it makes good reading for those interested in such matters, and might stimulate some relevant discussion as well, updated since the last time this issue was raised on the list around one year ago. I'd be particularly interested in the question of whether a consensus now exists to follow e.g. Cavalier-Smith in treating the protists, or whether there are other views on this that are also worthy of consideration (since I would appreciate some guidance in this area myself).

Regards - Tony Rees

________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Adolf & Oluna Ceska [aceska at telus.net]
Sent: Saturday, 18 July 2009 1:28 AM
To: 'TAXACOM'
Subject: [Taxacom] Drawing of Myriophyllum fruits

I am looking for drawings of fruits ("mericarps") of the following
water-milfoil (Myriophyllum) species:

Myriophyllum heterophyllum

Myriophyllum pinnatum

Myriophyllum quitense

Myriophyllum ussuriense

I would greatly appreciate if some of those botanists who like to have their
feet wet could help me.

Many thanks,

Adolf Ceska, Victoria, British Columbia, Canada

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