Open Tree of Life

Open Tree of Life aims to construct a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. The project is a collaborative effort between 11 PIs across 10 institutions. Funding is from NSF AVAToL #1208809.

Browse the tree and leave feedback: Click on nodes to move through the tree, and click on nodes or edges to see more information about taxonomies and phylogenies that contain / support that node. If you have feedback about the relationships that you see, use the "Add Comment" button.

Contribute data: You can contribute to the synthetic tree by uploading trees through our curation interface. These can be trees from TreeBASE or trees uploaded from your computer. There will be a delay before uploaded trees appear in the synthetic tree. Up to summer 2015, the release cycle has been months between new versions of the synthetic tree, but this should shorten in the future.

Contact us using one of the methods on the Contact page.

Cite the Open Tree of Life: Hinchliff, Cody E., et al. "Synthesis of phylogeny and taxonomy into a comprehensive tree of life." Proceedings of the National Academy of Sciences 112.41 (2015): 12764-12769. + https://doi.org/10.1073/pnas.1423041112

Postdocs & students
Joseph Brown
Ruchi Chaudhary
Lyndon M. Coghill
Jiabin Deng
Bryan Drew
Romina Gazis
Jessica Grant
Cody Hinchliff
Dail Laughinghouse
Emily Jane McTavish
Chris Owen
Ben Redelings
Developers
Jim Allman
Joseph Brown
Karen Cranston
Cody Hinchliff
Mark Holder
Jonathan Leto
Emily McTavish
Peter Midford
Ben Redelings
Richard Ree
Jonathan Rees
Stephen Smith
Principal investigators
Gordon Burleigh
Keith Crandall
Karen Cranston
Karl Gude
David Hibbett
Mark Holder
Laura Katz
Richard Ree
Stephen Smith
Doug Soltis
Tiffani Williams

Comments

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  • opentreeoflife vs. onezoomon GitHub

    I am writing a book about evolution and I see there is two life trees, opentreeoflife and onezoom. They differ in many places. Is there a reason why? - or is one of them not updated with the latest news? Please answer. Kind regards Aage Nicolaisen Silkeborg, Denmark aage.nic@mail.dk

    • Yes. We got that email too. I'll answer and post here too.

    • This is what I've replied to Aage. Do add other comments if you have any.

      At OneZoom we essentially rely on the OpenTree 'phylogeny' for most of the tree of life, after pruning away subspecies and a few inappropriate taxa like those with ‘.cf’ in their names. The current version of OneZoom uses OpenTree 7, but we are upgrading to OpenTree 9.1 in a few weeks.

      The OneZoom tree, however, does differ from the OpenTree in two major respects:

      (1) the current OneZoom view only displays bifurcations, so where the OpenTree has a multifurcation ('polytomy'), we split the branches at random. Note that in a month or two we will have other views of the tree that retain these polytomies, so this will cease to be a major difference. Also note that the polytomies in the OpenTree are not polytomies in the same sense as those shown in (e.g.) a consensus phylogeny. There has been a recent discussion about this on the OpenTree discussion group (see also https://github.com/OpenTreeOfLife/opentree/issues/260)

      (2) In some areas of the tree, particularly on the branches that lead to humans, we have used alternative phylogenies culled mostly from single studies and grafted as replacements onto the OpenTree. We have done this so that we can produce dates for influential nodes, and also make informed decisions about resolving polytomies and about some contentious areas of the tree. As an example of the branches that lead to humans, almost all the mammals are taken from the Bininda-Emonds et al. 2007 paper, apart from the marsupials, the base of the afrothere/laurasiathere/xenarthra divergence, some stuff in the laurasiatheres (notorious for polytomies) and the primates (which are from the comprehensive Springer paper). Similarly, I have used bespoke hand-crafted backbones for some of the squamates, the sharks and rays (which are pretty messed up in OpenTree), among the Lophotrochozoa, and at the higher level at the base of the Eukaryotes. I have also gone with the (increasingly supported) ‘2 domain’ hypothesis which puts some Archaea as closer relatives of Eukaryotes than others. This is not yet something that has been incorporated into the OpenTree.

      Mostly, the bespoke studies used by OneZoom are represented in the OpenTree, but may conflict with other studies, so our choice to go with one particular phylogeny implies that we place more scientific trust in that study than in others. For example, there have been a number of studies which claim that ctenophores are the basal animal group, and this is reflected in the OpenTree. However, most experts in deep animal evolution still disagree with this (as do I, and as is also shown by some studies just published this year). So after consultation with various experts I have decided to ignore the studies which show the earliest animal divergence being between the ctenophores and everything else. This is purely a matter of which data you choose to believe (I think that the ctenophore studies suffer from extensive LBA artifacts).

      For more details, the (extensive) list of studies I have used to resolve OpenTree polytomies can be found by selecting "data sources" from within the OneZoom viewer.

      I’d be interested to know which areas of the tree you think are most divergent between OneZoom and the OpenTree - if you would like to point some out, I can explain why this might be in each case.

    • @opentreeapi you might want to comment on what OpenTree is likely to do about potential Archaeal paraphyly?

    • After a bit of email discussion, it seems like Aage is particularly interested in carnivores. So I'm wondering why the trees in https://tree.opentreeoflife.org/curator/study/view/ot_328/?tab=trees have not been included in synthesis.

    • I have pointed Aage at the carnivore super tree study, and that seemed to be satisfactory, so this can be closed