PROTISTA - let's move on

[David at]

Ken (et al)

You will find a comprehensve to genus classification of
the protists at http://microscope.mbl.edu.  You may find
this a useful way of checking for gaps in coverage.

The micro*scope classification is conservative in that it
excludes all groups which are controversial (such as all
but one of the more recently articulated supergroups
excepting opisthokonts - because they have been falsified
by various studies - and also excluding the chromists for
which there is no sound evidence at all. The underlying
logic from which this classification emerged is described
in the Patterson 1999 paper - referred to by Laura Katz in
her recent mailing.

I am concerned that taxonomic schemas that are built from
an arbitrary subset of the relevant organisms, and
assembled into schemas without disciplining principles,
 does not distinguish the process or product from those
who chose not to apply science to the history of life.

I list below the taxa that you listed but are unsound. In
a phylogenetically informed classification, these elements
need to be replaced:

PROTISTA - obsolete because of inherent paraphyly.  There
is no replacement at this time. The colloquial term
'protists' has a value, but not in any critical dialogue
of phylogeny.

Choanozoa (= Mesomycetozoa) the equation of these two taxa
is inexplicable and we should avoid using one name
(Mesomycetozoa) to mean both a small group that contains
just a handful of genera, and a very extensive group that
embraces true fungi and animals.

The clade that includes the true fungi, the animals and
their microbial sister taxa is usually referred to as the
opisthokonts. Unfortunately, the term has been used with
differing scopes. This is the only 'supergroup' that has
survived critical scrutiny (cf the two which follow).

Amoebozoa - this hypothesis has been falsified many times.

Rhizaria - this hypothesis has been falsified many times.

Loukozoa (jakobids and allies). Many taxonomic concepts
have been associated with this term.  From the narrower
sense of the term, - there is no evidence that the taxa
usually assigned to this group are more closely related to
each other than to other taxa. It is probably for this
reason that the group is not used in any critical
dialogue. The component parts are usually assigned to the
larger grouping, the excavates - which seems to correspond
broadly with Group 4.  The excavate hypothesis is not
supported robustly  by the evidence to date. I am of the
view that we will make more progress if we break this into
the subtaxa, and then seek specific sister group
relationships.

Metamonada (incl. Parabasalia) - this term has many
meanings. It is best to break this into the subtaxa for
which monophyly is not disputed.

Percolozoa - I presume this to be the Heterolobosea, a
term that is more established and well defined. The
Heterolobosea seem to be sound

Group 5 Cryptophyta Haptophyta and stramenopiles. This is
the territory normally referred to as Chromists. It takes
quite a bit of contortion to get the data to support this,
and most studies have falsified this group and have done
so more or less from its inception.

Heterokonta (stramenopiles). Heterokonts and stramenopiles
are not conceptually equivalent. Stramenopiles were
defined to be compliant with phylogenetic thinking.
Heterokonts emerged about a hundred years ago to refer to
the rather small algal group - Xanthophytes (or
Tribophyceae if you prefer typified names) - and has since
expanded considerably but generally is restricted to taxa
with chloroplasts, thereby excluding some or all of the
most immediate ancestral stramenopiles as well as derived
taxa that have relinquished their palstids.

Ciliophora - can be assigned to the alveolates along with
the dinoflagellates and apicomplexan sporozoa, perkinsids,
and colpodellids.

Dinozoa (or Dinophyta) - can be assigned to the alveolates
along with the ciliates and apicomplexan sporozoa,
perkinsids, and colpodellids.

Sporozoa - an obsolete term historically used for 4 groups
of organisms that are not closely related, microsporidia,
myxozoa, haplosporidia and apicomplexa. Presumably here
intended to refer to the apicomplexa.

And as indicated above, many taxa are not covered in this
schema.  They can be identified by comparing this listing
with the one in the micro*scope environment.

The comments refer to the anterokont clade,
corticoflagellates, chromalveolates, and  "crown group" -
none of which are consistent with the data that we have
available.

David Patterson



On Sun, 5 Mar 2006 17:08:19 -0600
  Ken Kinman <kinman2 at YAHOO.COM> wrote:

Dear All,
      Since the 5-Kingdom system has been so popular for
so long, I'm going to (temporarily?) give it a try here.
To convert it to my preferred 4-Kingdom system, you can
simply replace the exgroup marker {{EUMYCOTA}} with the 3
eumycotan Phyla----Eomycota (incl. microsporidians),
Ascomycota, and Basidiomycota. In any case, I will not use
the name "Fungi" as a formal taxon name (Eumycota is far
more precise for the true fungi). And I certainly will not
recognize a 6th Kingdom for the Chromista clade
(Cryptophyta, Haptophyta, and Heterokonta). Following the
classification, I will further discuss various subclades
of Protista.

     Anyway, the total is 16 Phyla of protists (and it
would be 19 phyla if you included the 3 phyla of
Eumycota). The Apusozoa may need to be split off from
Rhizaria, but I expect virtually all of the other
"candidate" phyla will actually turn out to fit nicely
into one of the phyla listed below. We certainly do NOT
need a bunch of new eukaryotic kingdoms. As always, the
main clades are numbered in the order in which they split
off phylogenetically.

                   KINGDOM PROTISTA

  1 Choanozoa (= Mesomycetozoa)
_a_ {{EUMYCOTA}}
_b_ {{METAZOA}}
  2 Amoebozoa
  3 Rhizaria
  4 Loukozoa (jakobids and allies)
  B Metamonada (incl. Parabasalia)
  C Percolozoa
  D Euglenozoa
  5 Glaucophyta
  B Rhodophyta
  C Chlorophyta
_a_ {{METAPHYTA}}
  6 Cryptophyta
  B Haptophyta
  C Heterokonta (stramenopiles)
  7 Ciliophora
  8 Dinozoa (or Dinophyta)
  9 Sporozoa
----------------------------------------------
    NOTES: Clade 1 is the opisthokont clade, which is
sister to the anterokont clade (clades 2-9). Phylum
Amoebozoa is sister to the bikonts (clades 3-9). Phylum
Rhizaria is sister to the corticoflagellates (clades 4-9).

    Clade 4 is made up of the four excavate phyla (of
which Percolozoa and Euglenozoa make up a discicristate
subclade). Excavates are sister to the photokaryotes
(clades 5-9). Clade 5 is the plant clade, which
Cavalier-Smith calls Plantae, and it also equals the
Archaeplastida clade of Adl et al., 2005. And finally we
have the chromalveolates (three phyla of chromists and
three phyla of alveolates)---still the "crown group" after
all these years. :-)
      ------Cheers,
                   Ken Kinman

P.S. I've forgotten who coined the term "exgroup". I did a
google search for paraphyletic + exgroup, but all the hits
lead to various posts by mine (but I didn't coin the term
myself). Anyway, an exgroup is simply the taxon which one
removed from a mother group (making the latter
paraphyletic). Reptilia has two exgroups (Mammalia and
Aves), thus making it doubly paraphyletic.


David J Patterson
Bay Paul Center
Marine Biological Laboratory
Woods Hole
Massachusetts 02543
USA

1 508 289 7260

http://www.mbl.edu/microscope
http://www.mbl.edu/research/resident/lab_baypaul.html