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Re: Protista (vs. rat race)



>      Correction!!!  Protista perhaps represent more than 95% of the
> diversity of:  eukaryotic "rRNA sequences" (not of eukaryotic "life").
> There's a big difference.  And Woese's Three Domain Trees are "Trees of
> Ribosomes", not true "Trees of Life".   Metazoans have slowly evolving
rRNA
> genes.  Big deal----all those other genes more than make up for it by
orders
> of magnitude.  One-character classifications like the Three Domains have a
> long history of failure, and this currently popular bandwagon will be no
> different.
[snip -- see below]
>      You may be horrified to learn that I have gone back to including all
> the fungal groups in Kingdom Protista.  If you want to recognize a Fifth
> Kingdom, best to call it Eumycota, because "Fungi" is highly polyphyletic
> (which we all agree is bad).  And guess what---- microsporidians (which
you
> mentioned) aren't true sporozoans or even archaeoprotists----they are
> eumycotans!!!   How shocking that is to most biologists----I was
delighted,
> but certainly not surprised.

There is a wonderful IMHO article in some Science from November (I've copied
it, but §$%$&%§$§ lost it, so I can't give the full citation) called "A
Kingdom-Level Phylogeny of Eucaryotes" IIRC. This paper presents a cladogram
based on 4 genes (not rRNA). It doesn't use Protista as a taxon name at all
and gives kingdom rank to various clades (I'd say they have deserved it,
lumping all eukaryotes into just 3 kingdoms contradicts the whole idea of
ranks*). Microsporidians ARE mushrooms in this cladogram, and this at least
seems to have become fully accepted. One of the 2 picoplankton articles in a
recent Nature has an rRNA tree, in which microsporidians are basal
eukaryotes, and suspects that damn old long-branch attraction has clouded
their tree, "as has occurred with Microsporidia". One surprising outcome is
that cellular and plasmodial slime molds along with some "amoebas", together
Mycetozoa, are a monophyletic sister group of Opisthokonta, which is (Fungi
+ (Choanoflagellata + Animalia). Large groups such as Alveolata,
Ramicristata and Discicristata are recognised, I've just forgot their
contents :-) .
        It really looks like that in, say, 5 years we will have an accepted
consensus phylogeny of eukaryotes, which may even enter textbooks.
        Fungi are only polyphyletic, AFAIK, if you include
Oomycota/-mycetes -- these belong to Heterokonta, along with yellow, golden
and brown algae, diatoms and some others, such as *Blastocystis hominis*
(what is that?).

*Of course there is no possibility to test, or otherwise achieve consensus,
whether they "deserve kingdom rank" -- the Same Old Argument for abandoning
ranks altogether.

>      Simply stated, I define Kingdom Protista as all eukaryotes after the
> removal of Metaphyta and Metazoa, and yes that does make it paraphyletic.
> Cladists get out your crosses and exorcise it.  But while you're at it, go
> after Woese's two prokaryotic Domains, because they are paraphyletic too.

While I don't know for Bacteria, I'm quite sure that Archaea has some
autapomorphies (such as the ether-bond cell membranes), and that Eukarya and
Archaea are sister groups. (This is rather negative evidence, but AFAIK the
oldest fossil records for these are both 2,7 Ga old...) If good evidence for
Bacteria turns up (I don't follow that literature apart from Nature and
Science), cladists will surely "rat race" about who tears Bacteria apart
first and best.

>       A separate kingdom for saprophytes? (sorry, it doesn't exist).  The
> shift from a 4-Kingdom System to a 5-Kingdom System has caused nothing but
> trouble and confusion for 30 years, and it has eventually inspired
> additional Kingdoms, Superkingdoms, and then those awful Domains.  When
the
> new Bergey's Manual comes out and we have about a dozen prokaryotic
> Kingdoms, the protistologists will respond in kind, and we'll have so many
> kingdoms that most future students will have no idea how they are all
> related (because many of their professors will be confused as well).
> Taxonomic inflation is not a good idea.  It's a nomenclatural rat race.
>       Even with the fungal groups included, Kingdom Protista should be
> subdivided into about a dozen phyla,

Only? And Metazoa alone has over 30 (if you're picky and give phylum rank to
groups like Tullimonsterida, you easily hit 60)?!? This is even considerably
worse than giving class status to Aves, IMNSHO. If you want to use ranks,
and you find 20 groups that are large enough, then why not give them kingdom
rank?
        Here in Vienna University at least, a few selected "protist" groups
and their life cycles are simply thrown at our heads, and NO idea of any
kind how they are related is presented at all.

> ********************************************************
> Tim Williams wrote:
> >
> >I hope the term "Protista" will soon disappear from usage as well.  Those
> >single-celled blobs and creepy-crawlies which _Homo sapiens_ have
> >traditionally lumped together as the "Protista" represent more than 95%
of
> >the diversity of eukaryotic life.  The multicellular "higher" eukaryotes
> >(animals, plants, fungi) each occupy a little twig on the tree which we
> >share with diplomonads, microsporidians, trichomonads, trypanosomes,
> >euglenoids, slime molds, ciliates, dinoflagellates and diatoms.  Each are
> >each as different from each other as they are from animals, plants and
> >fungi.
> >
> >And they're just the ones we know about.  The mind boggles thinking about
> >how many gut-infesting, fecal-ingesting, blood-infecting little
"protists"
> >might have gone extinct with the dinosaurs.

There are still lots around now that we don't know about. The picoplankton
articles I mentioned have found whole clades as large as Dinoflagellata by
just sequencing rRNA from deep-sea water!