What is a protist? The Eukaryotic Tree of Life

There seems to be lots of confusion as to what a protist really is. This is quite understandable, since the chaos has deep historical roots.

The definition (guideline) that most protistologists tend to follow is:

Any eukaryote that is not a plant, an animal, or a fungus.


ie., the other ~98% of eukaryote diversity!

Let's take a look at this diversity: (Keeling et al. 2005, Trends Ecol. Evol.) (free access)




Assignment: Find animals and land plants. Note relative significance and diversity!

And before a microbiologist wanders by and launches a massive attack on my eukaryocentric ego, I'll put things into perspective: (Ciccarelli et al. 2006, Science) (free access)


K, now that this is over with, back to ignoring prokaryotes...


Why is Protista such a cladistic mess?

Historical reasons, mainly. Only a couple centuries ago, people still classified life into things that were motile (animals) and sessile (plants). Fungi were plants because they didn't walk. (molecular evidence shows they're actually the sister clade to animals). Microscopic life was unknown at that point, so there was very little reason to suspect any of those strange organisms even existed. And seaweeds were plants as far as anyone was concerned. Not like it's actually obvious without examining the cell structure and molecular data.

Eventually, this system failed, and attempts at patching it up eventually led us to a tangle of taxonomic chaos. Thankfully, molecular biology has allowed the eukaryotic phylogeny to be resolved quite a bit better (but still with plenty of vagueness).

Another problem is convergent evolution screwing up morphology-based taxonomy. Before molecular biology became possible, organisms were sorted by their appearance and special structural features. Unfortunately, some of those features tended to evolve independenly multiple times. A good example is the heliozoa -- sun-shaped microorganisms. Turns out the group actually was spread over three kingdoms -- chromalveolates, rhizaria and the green algae! (Nikolaev et al. 2004, PNAS)

Actually, the entire non-photosynthetic stramenopile group mostly consists of stuff that were confused with something drastically different:
- Labyrinthulids and Oomycetes -- thought to be fungi
- Blastocystis (can cause disease in humans) -- thought to be yeast (fungi) -- looks like yeast morphologically!
- Actinophryids -- a remnant of Heliozoa
- Opalinids (amphibian gut endosymbionts) -- used to be confused with ciliates
- Bicoecids -- easy to confuse with generic small things with two different flagella. The fact that there's a genus Pseudobodo might hint at something... (Bodo is a kinetoplastid in the Excavate kingdom, relative of the trypanosome with its awesome kDNA)

I'll elaborate on this at a later date... exam season is near!


Main points:
- Protista = Eukaryotes that are not Plants, Animals or Fungi
- Multicellularity arose several time independently and is therefore not a relevant trait... kelps are huge and multicellular, but are still protists (brown algae)
- Size does not matter: aside from seaweeds, there are plenty more macroscopic protists. Some unicellular ones get quite huge!

Hope this clears up a little bit of confusion...


And apologies for irregular updates... too much stuff going on at this time of the year!