Clickable Tree of Eukaryotes (Katz Lab)

For a while I've been contemplating on considering to con someone into making a clickable tree for me, allowing one to zoom in and click genus names leading to further info/pictures/whatever. Of course, I'd be far too lazy to actually execute such a project, especially given my lack of programming skills, and lack of faith in the stability of current phylogenies... luckily, I recently discovered some nice people already took care of that, and produced a really awesome tree:

The genus names lead to their respective Micro*scope pages (with pictures)! (Parfrey and Katz, http://www.science.smith.edu/departments/Biology/lkatz/EuTree2009/Eutree09.html; relevant literature: Parfrey et al. 2006 PLoS Genet, 2010 Syst Biol)

This is the eukaryotic tree of life sensu Katz Lab. Being on the opposite side of the continent, the people here have some differing opinions on the subject (my diagram – seriously due for an update – kind of reflects local influences). As you may have noticed from the bounty of polytomies (multiple branches at a single node indicating uncertainty in branching order), the Parfrey and Katz tree is quite conservative, which is probably a good thing. For pedagogical purposes, however, I still think it's better to go ahead with the supergroups, while mentioning the frailty of some, as it helps organise the organisms and dispells the common notion of Protista being just an amorphous grab-bag of microbial crap that doesn't fit. They run the show, it is WE who 'don't fit'...

For research purposes, one must strive to keep track of the certainty of each and every piece of data or hypothesis one works with. Of course, that's overwhelming to n00bs people outside the field, so the shakiness of some models tends to be glossed over. Also, most people don't care.

Speaking of things normal people don't care about, I was quite shocked by the disappearance of Archaeplastida as a clade -- the locals give off the impression Archaeplastida is among the healthier of the supergroups. Excavates, on the other hand, are acknowledged to be somewhat 'meh' as a clade by some of the people working on them. Hacrobia is rumoured to be practically dead anyway, so I'm just keeping that label for the sake of categorising things that may at best turn out to be paraphyletic (which I'm ok with informally), or at worst, grotesquely polyphyletic in ways that would make Heliozoa and Rhizopodia cry. Also, the Stramenopiles are sister to Rhizaria as opposed to Alveolata ("our" order goes (Rhiz,(Stram,Alv))). I find that weird. Although, on the second though, why the hell not. But local folklore has it that Stram+Alv are a pretty solid grouping. Then again, local folklore sings praises to the Chromalveolate Hypothesis... As an innocent, defenseless cell biologist, I'll just hide in the corner until this blows over...

Also, note that the tattered remnants of the 'supergroups' themselves are horribly politomised. Recall how the animal phylogeny tends to have a comb-like branch structure along the 'base' -- ie, among the earlier divergence events, only one group went on to diversify in ways we notice. Then, shortly before the Cambrian diversification event ('explosion' my ass), a bunch of divergences happened that later did lead to multiple lineages that became diverse, in ways we notice. But prior to that, it seems that animal evolution proceeded at a fairly "gradual" pace, according to some anyway. In terms of extant descendants anyway. But in any case, there are ample opportunities for an illiterate journalist (or scientist) to commit the "primitive animal" fallacy.

This error comes much more difficult in the eukaryotic evolution scenario, that is, if only those illiterates knew a thing or two about the modern phylogenies. This is because apparently, very few early-branching 'undiversified' taxa exist, if none at all. Hard to explain without a tree to show, but it seems like the major eukaryotic supergroups rapidly exploded, either soon after the origin of eukaryotes, or all the earlier-diverging clades disappeared without a trace.

This is a question of the 'tempo and mode' of evolution -- the rate and extent of diversification. It's a rather fuzzy concept, as it's quite difficult to establish what diversity is and how to measure it. Considering we biologists don't even know what a species is (and linguists, I'm told, know not what a word (or language), is...), comparing diversity is very difficult. There are some vague tendencies, but that's all they are. Or so it seems anyway -- perhaps I missed something. I guess it's hard to compare the extent of diversity when you reject ranked taxonomy. Zoologists, at least in the past, have used phyla as an indicator, which were somewhat based on the body plan. Whether it's a valid indicator is a whole other topic, but we lack such luxuries in the microbial realm anyway. This topic deserves a proper post someday...

What I was trying to get at, before almost drowning in caveats and disclaimers there, is that the major clades of eukaryotes have arisen rapidly and seem to have left no residual 'basal'/'stem' taxa, making it very difficult to resolve the relationships between them. Resolving recent 'explosions' is quite doable, as is resolving more gradual evolution in the distant past...rapid explosions in the distant past are one hell of a bitch to deal with, which is why much of the deep phylogeny remains a mystery.

How I managed to go off on this tangent eludes me. I see trees, I start chatting about them, ain't nothin' I can do 'bout that.

It being the start of the school year accompanied by an ominous influx of undergrad cooties *shudder*, I'm going to be on slow blogging mode for another week or so. So use that tree to entertain yourselves -- in fact, this tree and ToLweb make my blogging kind of redundant =P (shhh...) Fear not, since I still need to feel useful from time to time, my protists shall keep on coming.

Relevant papers to the Parfrey & Katz tree: (should be accessible)
Parfrey, L., Barbero, E., Lasser, E., Dunthorn, M., Bhattacharya, D., Patterson, D., & Katz, L. (2006). Evaluating Support for the Current Classification of Eukaryotic Diversity PLoS Genetics, 2 (12) DOI: 10.1371/journal.pgen.0020220

Parfrey, L., Grant, J., Tekle, Y., Lasek-Nesselquist, E., Morrison, H., Sogin, M., Patterson, D., & Katz, L. (2010). Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Systematic Biology DOI: 10.1093/sysbio/syq037