News
APG3 tree available, and APG3 derived megatree now the default base tree in the online phylomatic. Many thanks to Steve Hovick and Ken Whitney for coding and checking the subtrees.
Phylomatic 2
Over the years, the web-interface of phylomatic has seen a lot of use. However, I’m sure you have found it frustrating that within-family resolution is generally missing. Our goal with phylomatic, way back, was to keep on top of the literature and add clades to the megatree on a regular basis. This was clearly an unrealistic expectation. However, the need is still here for a tool for easily assembling phylogenies for communities and other lists of plants. I have now developed a work-plan that opens the assembly of the tree-of-trees database to users of phylomatic. If there are particular clades that are not yet well resolved in the database, please consider adding the newick version of a suitable published tree to the public database of trees. I know that several researchers have started with a backbone tree from phylomatic and then added better resolution for additional clades, and I suspect that there was much repetition of work because there was no way to share the refinements that users made to the megatree. Now we can all work together on making a usable, flexible hypothesis for the phylogeny of plants.
The components of `Phylomatic2′ are:
- A standardized protocol for encoding trees into newick. This includes the choice of a permanent name (within the domain of phylomatic) for key interior nodes. We would like to use, where possible, APG and/or PhyloCode-accepted names.
- An XML-format metadata file to accompany each newick tree.
-
An openly readable,
text-based data
repository for the trees, using
the Subversion
versioning system (to download the database, install an
SVN client and type
svn checkout http://svn.phylodiversity.net/tot/trees). If you are interested in contributing significantly and helping to fix errors in the database, please ask me for a SVN user account. - Submission of user-transcribed trees and metadata files via email (newick {AT} phylodiversity {DOT} net), or by direct SVN checkin, for registered users. Please note that it may take a few days to weeks for email-submitted trees to be incorporated into the data repository (depending on how busy the tree curators are). However, this does not stop the users incorporating their new trees into their local copy of the database immediately, to generate the megatree that they need.
- Once a local copy of the database has been downloaded, a configuration file permits selection of alternate clade representations that might coexist in the database.
- A simple GAWK script is then run to assemble a single megatree, based on configuration options. Alternatively, see the directory http://svn.phylodiversity.net/tot/megatrees/ for recently compiled trees.
-
This megatree is then ready for processing the taxon name
list the user supplies, with the
phylomaticprogram that comes in thephylocombundle.
Phylomatic2 and TreeBase If you contribute to this project, you will be concerned that your efforts in transcribing and describing trees are not lost at some point in the future. We have always considered phylomatic a pragmatic solution to a real need, but one whose functions will one day be included in a more sophisticated tool, the obvious choice being TreeBase. I have discussed the components of Phylomatic2 with Bill Piel, and, with a translation script, our PMMD metadata structure should be acceptable to the TreeBase database too, allowing dumping of appropriate trees from our tree database directly into TreeBase. What we can’t offer, obviously, is the original data matrices.
Phylomatic2 and APweb The ordinal-level trees in Phylomatic are those displayed in Peter Steven’s APweb, the foremost internet resource for plant systematic information. I am in discussion with Peter, Amy Zanne, and others, about possibly converting APweb from a `flat’ data store to a phylogenetically-structured database, that could link directly to Phylomatic2. Watch this space!
Additional tree coding If you are aware of a published phylogeny that will help resolve a clade you need for your research, but which you do not have time or desire to transcribe yourself, please feel free to request that we transcribe it for you. Thanks to funding from NESCent (see below), we have the capacity to speed up the transcription process with assistants. Please send a PDF of the paper containing the phylogeny, and an indication of which figure you need transcribed, to newick {AT} phylodiversity {DOT} net.
Go to:
Funding
Original funds for Phylomatic came from a Donnelley Fellowship of the Yale Institute of Biospheric Studies. Subsequently, I have been supported by the NSF (DEB-0212873), and am now gratefully employed by the Arnold Arboretum of Harvard University. A recent NESCent working group (co-sponsored by the ARC-NZ Research Network for Vegetation Function), permitted CW and Peter Stevens to meet and discuss APweb2. A subsequent small grant from NESCent is enabling the coding of phylogenies by a dedicated team of Indonesians.
Feedback
Please let me know what you think of this new development. Cam.