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

Tue Jul 21 19:28:53 CDT 2009

Dear David, all,

Well, I have some opinions on your question, though no claim to the ultimate answers, or special status as a commentator, but here goes.

I look upon biological classifications as serving two purposes - first, to illustrate our current best guess/es as to the relationships between organisms, and second, to provide a recognisable navigation structure so that persons entering the classification can (hopefully) find their way to their particular organisms of interest. You can focus on one to the detriment of the other, or try to find a pragmatic middle ground where most people with general exposure to biology in the past will not feel too lost (to take a geographic analogy: we can cope with a few countries changing their name - Ceylon/Sri Lanka, Burma/Myanmar, but if everyone changed at once it would be total chaos). Take home message #1: familiar reference points are good.

Also I will admit a couple of personal preferences at the outset: first, I have no problem with paraphyly - admitting that birds and mammals evolved from reptiles is fine by me, so is pygmy sperm whales (Kogiidae) from sperm whales (Physeteridae), reptiles from amphibians, and all the way back to the primordial slime; and second, I prefer ranked to rankless classifications - to use the geo analogy again: if I live in Sandford (suburb) << Hobart (city/town) << Tasmania (state) << Australia (country) << Australasia/South Pacific (geo region) << Earth (planet) it is quite helpful (to me at least) to be able to make at least partially useful comparisons at the same level (rank), and navigate quickly to the planet / country / town / whatever of interest for a particular purpose while ignoring other possibilities.

(Maybe that is messages #2 and #3).

Message #4 is that, while there is much that is interesting about the evolution of protists (and I have spent much more of my working life looking at them down microscopes than studying larger vertebrates or angiosperms), I feel that the reality is that the majority of educated public or even professional biologists are scarcely concerned with them, and certainly would find it unpalatable to have multiple protist kingdoms (for example) while the higher plants, animals and fungi become very small twigs on a mighty protistan bush (sorry, but that's just the way it is). The lens of biology and also popular culture is always going to be on the more prominent and charismatic fauna and flora that we interact with every day, however small a portion of evolutionary divergence and geologic time this may represent in fact.

So my feeling is that we cannot get away from the usage of "kingdoms" for higher plants, metazoan animals, and fungi sens. strict.; hopefully we can at least take comfort that the latter appear all to be monophyletic, at least, and we can either have one kingdom or two for prokaryota or bacteria and archaea. This leaves the problem of what to do with the protists and algae, small and large; the chlorophyte algae and charophytes seem to be flexible as to whether to put them in a green plant grouping sens. lat., or keep them as honorary protists by analogy with the rhodophytes and brown algae, which are also largely macroscopc and multicellular (although of course there are micr- as well as macro- green algae).

With the protists, I see a few options: (a) no kingdom - they become honorary plants or animals (just like old textbooks and university departments of botany and zoology - pigmented ones to the botanists, remainder to the zoologists) - I think this is probably a non-option these days; (b) one kingdom - Protista or Protoctista (nobody seems to like the latter name, fine by me); (c) 2 kingdoms - the Cavalier-Smith solutions - Protista and Chromista - the latter comprising Cryptomonads, Haptophytes, and heterokonts/stramenopiles, the former everything else; and (d) more than 2 kingdoms - e.g, maybe one each for all the currently supposed eukaryote supergroups e.g. Rhizaria, Unikonts, Excavates, Chromalveolates, and non-green "plants" (red algae and glaucophytes) - or maybe one each for the latter.

It seems to me that if you don't like option (c) - and there are questions about whether cryptomonads and haptophytes really do group with heterokonts/stramenopiles or not, and if not, is the remainder enough to be a kingdom - or is it enough even with the first mentioned groups too), then you have to jump one way, either to (b) - single kingdom for protists - or (d) - lots of kingdoms. However (d) does really work against message #4 above, so I am back to (b) - a single kingdom for Protists sens. lat. (with green algae and charophytes up for discussion as to whether they belong here or with the other green plants).

So now, going with message #3 (ranks are good), we are down to e.g. phylum level, or some intermediate between phylum and kingdom if we run out of ranks too quickly. Actually the latter looks quite useful - why not pull out the eukaryote super/megagroups at subkingdom level (as they are mostly unfamiliar to lay users and also unstable at present), and look for stability/recognisability at phylum level. So you could have a subkingdom Excavata with among its phyla Euglenozoa, Jakobids, and other groups to taste, a subkingdom Unikonta from which a couple of other kingdoms emerge of course (animals and fungi), but that's life (pun intended!!), a subkingdom Viridaeplantae from which land plants emerge as their own kingdom, and so on. Subkingdom Chromalveolata (if you believe it) would contain Heterokonts as a phylum with classes beneath, Cryptomonads and haptophytes are probably phylum level, alveolates would probably be separate phyla but could perhaps be grouped at a rank like superphylum or infrakingdom if it exists, and so on.

Probably what I have said above represents a monumental effort in fitting square pegs into round holes, but anyway, food for thought perhaps.

I think the main tension is between classifications that are very flat with lots of apparently random (or alphabetically arranged) children at the next level - hard to navigate - and classifications that are very hierarchical (easier to navigate) but which obscure, or make false assumptions about, true relatedness of organisms. Treading a middle path seems eminently desirable, while at the same time not disenfranchising those misguided souls who think big things are all that matters :-)

Hope the above may at least stimulate some more discussion on this,

Best regards - Tony

Tony Rees
Manager, Divisional Data Centre,
CSIRO Marine and Atmospheric Research,
GPO Box 1538,
Hobart, Tasmania 7001, Australia
Ph: 0362 325318 (Int: +61 362 325318)
Fax: 0362 325000 (Int: +61 362 325000)
e-mail: Tony.Rees at csiro.au
Manager, OBIS Australia regional node, http://www.obis.org.au/
Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm
Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566

-----Original Message-----
From: David Patterson [mailto:dpatterson at eol.org]
Sent: Monday, 20 July 2009 11:34 PM
To: Rees, Tony (CMAR, Hobart)
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Catalogue of Life (CoL) management classification draft document

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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