A problem with doing this kind of thing while hanging out in this corner of the world is that as soon as you put up a tree, everyone stops you in the hallway and rants about how cruely their pet clade has been mistreated. Ok, I'm exagerrating a bit, well, a lot, but it was still quite amusing. Someone didn't like the reds, someone else didn't like the apis, multiple people pointed out that my microsporidia were screwed up, etc. In other words, instant peer review!
So here's version 1.1, definitely subject to further changes, and in need of more rigorous peer review. Does something bother you? Please let me know!
A Tree of Eukaryotes, v1.1 (Please keep the references box) Feel free to contact me for a higher res image, Blogger seems to shrink large images when uploading...
Changes include:- redoing the apicomplexan clade (it's even more of a mess than I thought...)
- adding Komokiacea (they're too cute!) and Synurophytes (someone insisted on it...)
- removed the random floating 'Gonyaulacoids' outside the tree
- rebranched kinetoplastids et al. as (diplonemids,(bodonids(p),trypanosomatids)) (must've been asleep when I grouped diplonemids with bodonids...what the hell?)
- reorganised the chlorophytes to make a little more sense visually
- Opalinid clade goes (blastocystis,(opalinea, proteromonas)), not (protero,(blasto,opalinea))
- Collapsed oxymonad clade to please Opisthokont.
- After having been nagged by about 5 different people about it, unbranched Microsporidia from Rozella (again, what was I thinking? Although some papers do put it there...but I consciously disagree with that!) and polytomised with Zygomycetes, as suggested by some local microsporidia geeks + source [26].
- indicated paraphyly for chytrids, bangiophytes and bodonids; removed paraphyly tag from dinophyceae.
Changes I haven't made yet:
- expanding forams (space constraints, see "expansion pack" though)
- adding pteridiophytes to the land plants (everyone seems to be obsessed with them!) -- again, no space!
- adding Collodaria -- space...
- completely change the amoebozoa based on some new unpublished data off a poster, which pretty much changes everything there. Grrrr. I'll get on that after the break...
- adding images -- no time yet! Again, after the break...
Enjoy!
Hyphochytriomycetes are conspicuous by their absence. Also: Prymnesiales, not Premnysiales; dictyochophytes, not dichtyochophytes. And aren't desmids a subgroup of Zygnemophyceae?
ReplyDeleteI'm sorry, this gives far too much weight to the microscopic. I had to hunt for ages to find something I could kick ;0).
ReplyDeleteDo you happen to know of a source that would allow superimposition of the distribution of meiosis among these groups?
Hmmm... Perhaps some of John Logsdon's work? IIRC they've done some analyses around the tree (searching for meiosis-related genes in genomic data), but I don't recall a tree compiling it all.
ReplyDeleteI do intend to start mapping characters after the phylogeny itself is more or less [sort-of] settled for the time being (a few corrections to make...) -- ONCE I HAVE TIME! -- and meiosis is definitely on that list.
So far it seems like all or most eukaryotes are at least ancestrally sexual (or did/do meiosis). Prokaryotes are not. Very peculiar...
Spot on, thanks (insert "cheers" emoticon here). A wealth of good stuff - I almost paid for a paper.
ReplyDelete... and it does indeed look provisionally as if the whole tree may be coloured red (or whatever the colour is for sex) on the evidence of ancestral meiosis-specific genes. Plenty of secondary loss, and an interesting paper about how to tell long-term abstinence from crypsis.
ReplyDeleteRegarding meiosis, please refer to my three papers below. Future work will show more breadth of meiotic genes in genomes. In a nutshell, the meiosis-specific genes did evolve prior to the divergence of extant eukaryotes, and not all protists have actually been "caught in the act" of meiosis because we have not yet looked at all the parts of their life cycles.
ReplyDeleteMalik S.-B., Pightling A.W., Stefaniak L.M., Schurko A.M. and J.M. Logsdon Jr. (2008) An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. Public Library of Science - One, 3(8): e2879. doi:10.1371/journal.pone.0002879.
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002879
Malik S.-B., Ramesh M.A., Hulstrand A.M. and J.M. Logsdon Jr. (2007). Protist homologs of meiotic Spo11 genes and topoisomerase VI reveal an evolutionary history of gene duplication and lineage-specific loss. Molecular Biology and Evolution, 24:12:2827-2841.
http://mbe.oxfordjournals.org/cgi/content/full/24/12/2827
Ramesh M.A.*, Malik S.-B.* and J.M. Logsdon Jr. (2005) A phylogenomic inventory of meiotic genes: Evidence for sex in Giardia and an early eukaryotic origin of meiosis. Current Biology, 15:2:185-191.
http://euplotes.biology.uiowa.edu/web/jmlpubls/rml05.pdf