Every six months, we put together a set of summaries from various aspects of the project. The first status reports are from January 2013.

January 2013


SYNTHESIS: Started by creating an comprehensive taxonomy from multiple sources into a single graph structure, facilitated by the software Taxomachine. In parallel, developing methods to map input phylogenies onto a common structure, allowing for input tree conflict and tree tip labels at different taxonomic ranks. The Treemachine software packages implements storage in the graph as well as an initial method of synthesis that resolves conflict based on frequency of paths. Tests with simulated data, as well as phylogenies and taxonomies of all plants, indicate that we can efficiently produce synthetic trees with reasonable resolution. The software argus visualizes several trees simultaneously, highlighting dominant + conflicting trees.

DATA COLLECTION: Literature review of all fungal systematics literature, 250 studies uploaded to Open Tree. Nearly 300 studies and 750 angiosperm trees; started literature search in animal phylogeny and started to upload trees representing the main trunks of Metazoa and Arthropoda. Finally, we have an initial set of trees for Thermotogae and Ameobozoa. The web2py software Phylografter handles tree input and mapping input names to taxonomic names, and we tested this platform during a data curation sprint in November 2012.

EDUCATION: Designed a upper undergraduate / graduate course in tree thinking, to start at Clark University in spring 2013. Created a public overview of the tree, including approximately 200 species from the three domains of life.

OUTREACH: Developing an interactive visualization of this phylogeny, collaborating with EOL to provide information and images about each species. Active blog with updates about the project and requests for comment from the community.

Detailed status reports:

If you have any questions, you can ask on our public mailing list or email any of the project PIs.