There arose a need for a new tree for a parasitology meeting, so after almost five years, I finally updated the tree of eukaryotes. There are still things that need to be changed, and new orphan lineages that should be added, but here's an updated version showing predominantly parasitic lineages in bold, and lineages known to contain parasites and/or opportunists marked with an asterisk. Since the citations box from the older editions is hard to keep updated, I've removed it, and hope to replace it with references and further reading on this site, where it can be easily modified.
Once again, note that this tree, which incorporating real data, is an inherently subjective synthesis, and should be used with caution. As always, comments and suggestions welcome.
References and further reading to be added shortly, once I have more time ;-)
(The first edition was half a decade ago... time flies!)
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Welcome back!
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ReplyDeleteHow do you generate the graphics (and the tree)? Is that done manually? Is there a computable (computer-readable) version?
ReplyDeleteRosie: Thanks! I hope to pick things up again... once I get a transcriptome going! ;-)
ReplyDeleteArlin: Did it entirely manually... first, five years ago, via Powerpoint (may have been slightly insane), but now editing and modifying it with Illustrator. It's a synthesis, not a real tree, one a rather subjective one. But if, for whatever reason, you need a computer-readable one, just email me! I'm hesitant about making one and putting one up because, again, it's not *directly* based on real data, and I'm afraid that people may treat it as such if I post a Newick version.
That said, it is based on literature and input from experts in this area. The problem with real data trees is that every tree lies, but between many differently-lying trees you can start to assemble the truth, somewhat ;-)
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ReplyDeleteI think it would be interested to see how much of this is covered in OpenTree's synthetic tree (opentreeoflife.org). The way to do this is in a blog that I wrote about OpenTree web services last fall: http://blog.opentreeoflife.org/2014/10/07/tree-for-all-hackathon-series-introduction/
ReplyDeleteFor instance, you can query with a set of names:
curl -X POST http://api.opentreeoflife.org/v2/tnrs/match_names -H "content-type:application/json" -d'{"names":["angiosperms","gymnosperms", "floridiophytes", "Naegleria"]}'
and this will try to match against a taxonomy database. In this case, the floridiophytes are not included. Then you can take the IDs (the ottId values, specifically), and run a query against the tree:
curl -X POST http://api.opentreeoflife.org/v2/tree_of_life/induced_subtree -H "content-type:application/json" -d '{"ott_ids":[592507, 99252, 641875]}'
And you'll get back the sub-tree:
('Naegleria_ott641875',('Gymnosperma_ott592507','Magnoliophyta_ott99252'))
where Magnoliophyta is the favored synonym for angiosperms.
The reason I was asking about automation is that there are a lot of people out there who are interested in more reproducible, automatable ways to annotate trees and render them (e.g., see discussion at https://github.com/OpenTreeOfLife/tree-illustrator/wiki/Design-notes). These are not sophisticated enough for your purposes, but your tree could serve as a challenging use-case.
ReplyDeleteThis is certainly a useful tool, any plans to expand it?
ReplyDeleteSeems like a great looking tree! It's great to see the information spread like this. If you update it again, please share with us!
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