Our very own Tree of Eukaryotes

Time to unveil what I've been up to for the past several Friday nights. I figured that after nearly a year and a half, and almost 20K page views, it's time for our blog to grow up a bit. What we need is our very own tree.

Remember how I often refer to the Keeling et al 2005 tree when pointing out where some obscure organism lies on the 'map'? Well, that tree is 5 years out of date now. In fields like molecular biology and genomics, a lot can change in five years; compounded with how the protistan phylogeny was still in murky, squishy swamp of a mess only about 10-15 years ago, the current tree is far from static. But five years is a little too old for now, don't we think? Especially after there's been some massive 'kingdom'-level rearrangements lately, like Rhizaria being shoved amidst the Chromalveolates, and Cryptophytes+Haptophytes+Centrohelids forming a sizeable clade of their own -- Hacrobia. Protist phylogeny and taxonomy is rather volatile.

But there's another reason I decided to go ahead and make my own tree. Outdatedness will eventually haunt pretty much any hypothesis or model ever made, so that's not too much of a worry. But I really really wanted my very own tree, in vector format, that I can fiddle with and modify at whim to illustrate my point, or map characters onto it, or rearrange stuff, add taxa, etc. You can't really do that with someone else's tree, especially since you seldom have the original. After all, while I still have limited experience and lack qualifications, I do have access to volumes upon volumes of protistology literature, and even more importantly, some rather prominent members of the field. Thus, armed with PowerPoint, insanity and reduced sleep, I've ended up with a monster of a tree. And while it's nowhere near finished, and probably never will be (since science itself escapes ever being 'finished'), here is the first installment:

A tree of eukaryotes, v1.0. Not a real phylogeny (that is, no sequences were harmed aligned in the making of this diagram), just my own interpretation of the various sources listed at the bottom -- subject to error, and change. Please don't take this tree too seriously! (or any other tree, for that matter...) Feel free to use, modify and distribute, as long as the attributions are left intact =D
A Tree of Eukaryotes by Psi Wavefunction is licensed under a Creative Commons Attribution-Non-Commercial-Share Alike 2.5 Canada License.
CORRECTIONS (to come in V1.1):
1)Branching order of kinetoplastids + diplonemids messed up when moving things around; supposed to be: (diplonemids,(bodonids,trypanosomatids))
2) Oxymonad phylogeny mostly unresolved, must collapse clade (thanks, Opisthokont!)
3)Extra copy of Gonyaulocoids floating around outside the tree -- will remove
4) unsquish some taxa...if possible

If you see anything definitively wrong, please let me know. As for the particularly murky groups, I had to go by some hypothesis, so some branchings are actually quite contested. Some messy spots were lazily sketched out as giant polytomies (eg. Cercozoa). The number of taxa per clade is not in any way meant to represent its actual diversity, which I consider to be fundamentally arbitrary and pointless unless you have all the species, and have the same standard of 'species' across all groups. Good luck with that. The representative taxa were picked rather arbitrarily, and the width of the clades is largely influenced by my own tastes.

Ok, enough with the disclaimers -- just enjoy!

One very interesting group, the incertae sedis, were unfortunately left out -- for they do not have a home. While we go about our daily lives content with knowing our place in the tree (or so we think anyway), these poor creatures are left alone in the cold, unloved and unclassified. I think we should all take a moment to reflect upon their plight, and perhaps spare some change and help find at least some of them a home...look how cute and fluffy they are!

I was going to someday add pictures to go along with at least the more prominent taxa -- would that be helpful?

Not gonna cite all 33 sources with ResearchBlogging, but here's some of the major ones:

CAVALIERSMITH, T. (2003). Phylogeny and Classification of Phylum Cercozoa (Protozoa) Protist, 154 (3-4), 341-358 DOI: 10.1078/143446103322454112

Cavalier-Smith, T., & Chao, E. (2006). Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista) Journal of Molecular Evolution, 62 (4), 388-420 DOI: 10.1007/s00239-004-0353-8

James, T., Kauff, F., Schoch, C., Matheny, P., Hofstetter, V., Cox, C., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H., Rauhut, A., Reeb, V., Arnold, A., Amtoft, A., Stajich, J., Hosaka, K., Sung, G., Johnson, D., O’Rourke, B., Crockett, M., Binder, M., Curtis, J., Slot, J., Wang, Z., Wilson, A., Schüßler, A., Longcore, J., O’Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P., Powell, M., Taylor, J., White, M., Griffith, G., Davies, D., Humber, R., Morton, J., Sugiyama, J., Rossman, A., Rogers, J., Pfister, D., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R., Serdani, M., Crous, P., Hughes, K., Matsuura, K., Langer, E., Langer, G., Untereiner, W., Lücking, R., Büdel, B., Geiser, D., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D., Lutzoni, F., McLaughlin, D., Spatafora, J., & Vilgalys, R. (2006). Reconstructing the early evolution of Fungi using a six-gene phylogeny Nature, 443 (7113), 818-822 DOI: 10.1038/nature05110

KEELING, P., BURGER, G., DURNFORD, D., LANG, B., LEE, R., PEARLMAN, R., ROGER, A., & GRAY, M. (2005). The tree of eukaryotes Trends in Ecology & Evolution, 20 (12), 670-676 DOI: 10.1016/j.tree.2005.09.005

Lewis, L., & McCourt, R. (2004). Green algae and the origin of land plants American Journal of Botany, 91 (10), 1535-1556 DOI: 10.3732/ajb.91.10.1535

PAWLOWSKI, J., & BURKI, F. (2009). Untangling the Phylogeny of Amoeboid Protists Journal of Eukaryotic Microbiology, 56 (1), 16-25 DOI: 10.1111/j.1550-7408.2008.00379.x

Taylor, F., Hoppenrath, M., & Saldarriaga, J. (2007). Dinoflagellate diversity and distribution Biodiversity and Conservation, 17 (2), 407-418 DOI: 10.1007/s10531-007-9258-3

And many more!