We are excited to publish the first draft of the Open Tree of Life in PNAS:
Scientists have used gene sequences and morphological data to construct tens of thousands of evolutionary trees that describe the evolutionary history of animals, plants, and microbes. This study is the first, to our knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life. This tree and the underlying data are available to browse and download from the Internet, facilitating subsequent analyses that require evolutionary trees. The tree can be easily updated with newly published data. Our analysis of coverage not only reveals gaps in sampling and naming biodiversity but also further demonstrates that most published phylogenies are not available in digital formats that can be summarized into a tree of life.
This is only a first draft, and there are plenty of places where the tree does not represent what we know about phylogenetic relationships. We can improve this tree through incorporation of new taxonomic and phylogenetic data. Our data store of trees (which contains many more trees than are included in the draft tree of life) is also a resource for other analyses. If you want to contribute a published tree for synthesis (or for analyses of coverage, conflict, etc), you can upload it through our curation interface.
Other pages and links:
- supplemental doc with details about methods
- Dryad data package when you can download the taxonomy and the tree
- infographics about the tree of life
- interactive tree browser
- roundup of news coverage
Many thanks to all of the people that provided data, discussion, review, curation, and code and of course to NSF Biology for funding this work!
Currently, OpenTree has two different types of node IDs. Taxonomy (OTT) IDs are assigned to named nodes when we construct a taxonomy release, and phylogenetic node IDs are assigned by the treemachine neo4j graph database for nodes that do not align to an OTT ID (i.e. nodes added due to phylogenetic resolution). The OTT IDs are fairly stable over time, but the neo4j node IDs are definitely not stable, and the same neo4j ID may point to a completely unrelated node in future versions of the graph.
This system is problematic because we expose both types of IDs in the APIs (and also in URLs for the tree browser). The lack of neo4j node stability therefore affects API calls that use nodeIDs, browser bookmarks to nodes in the synthetic tree, and feedback left by users about specific nodes in the tree (see feedback issue #63 and treemachine issue #183). The OTT IDs are problematic as well: it is not straightforward to document when we reuse an existing OTT ID, mint a new ID, or delete an existing ID, when going from one version of the taxonomy version to the next.
At our recent face-to-face meeting, we discussed a proposal for a node identifier registry and are looking for feedback. We don’t intend this system to be a universally-used set of node definitions (i.e. we aren’t trying making a PhyloCode registry). We want a lightweight system that prevents exposure of unstable nodeIDs through the APIs to clients (including our own web application) and provides some measure of predictability. Feeedback on this proposal would be greatly appreciated.
- be able to use the same node ID definitions across OTT and the synthetic tree
- transparency about when we re-use a nodeID from a previous version of tree or taxonomy (or not)
- users get an error when using a node ID from a previous version where there is no current node that fits that definition
- fixing errors (such as moving a snail found in a worm taxon to its proper location) should not involve massive numbers of ID changes
- generation of node definitions based on a given taxonomy must be automated and efficient
- application of node definitions to an existing tree / taxonomy must be automated and efficient
Develop a lightweight registry of node definitions based on the structure of the OpenTree taxonomy. For each new version of the taxonomy and synthetic tree, use the registry to decide when to re-use existing node IDs and when to register a new definition + ID.
Leaf nodes will be assigned IDs during creation of OTT based on name (together with enough taxonomic context to separate homonyms).
The definition of the ID for a non-leaf node will include a list of IDs for nodes that are descendents of the intended clade, a list that are excluded from being descendents, and (optionally) a taxonomic name.
Definitions would never be deleted from the registry, although not all definitions will be used in any given tree / taxonomy.
- How many descendant and excluded nodes to include in the definitions: The definition needs some specificity but also can’t assume a complete list due to future addition of new species. Perhaps, for example, four descendants and three exclusions would be a decent compromise between one and thousands?
- How to choose the specific nodes in the lists of descendants and exclusions: Should be ‘popular’ (should occur in as many sources as possible) and informative (if T has children T1 and T2 then at least one definition descendant should be taken from T1, and at least one from T2). Excluded nodes should be ‘near misses’ rather than arbitrarily chosen.
- What to do when >1 node meets the definition: Add an option of adding constraints to the registered definition in order to remove the ambiguity while preserving the ID.
- What to do when >1 definition matches a node: Ambiguous assignments can be resolved either by the addition of constraints, or by the creation of new ids.
- Modification / versioning of definitions: If we add constraints to a definition (for example, to resolve ambiguity), does this mint a new ID or version the existing definition?
The challenges to completing the Tree of Life and integrating data layers (NSF GoLife goals) are huge and vary across clades. Some groups have a nearly-complete tree but lack publicly available data layers, whereas other groups lack phylogenetic resolution or the resources to support tree / data integration. Partnering with Open Tree of Life and Arbor Workflows, FuturePhy will support a series of clade-based workshops to identify and solve specific challenges in tree of life synthesis and data layer integration.
RFP: 2 page proposals to fund small workshops and/or hackathons on completing the tree of life and integrating data layers for specific clades.
Proposal deadline: Nov. 1, 2015
Meeting dates: Feb 20-23
26-28, 2016 *note changed dates!*
Location: Gainesville, University of Florida
Participants per workshop: 10 maximum funded (virtual attendees possible)
Contacts: email@example.com (FuturePhy), firstname.lastname@example.org (OpenTree), email@example.com (Arbor)
The full call for participation and a link to a proposal template is available at the FuturePhy website.
Have questions about this or future workshops? Attend our webinar Thursday, September 17 at 1 pm EDT. See details on how to connect.