Phylogenetic placement

Part of the submission is defining the phylogenetic position (node) of the fossil calibration.

##Design challenges

This was the most challenging part of the system to design. We wanted to use an existing taxonomy to standardize names, but taxonomies lack sufficient resolution for placing the calibration on a specific node. A comprehensive phylogeny does not yet exist, and the working group felt that authors may not have access to a tree file that contained the node of interest. Both taxonomies and phylogenies can change over time, so placements need to be robust to such changes.

##Defining placements

To enable search and browse, we use the NCBI taxonomy as a backbone. This structure is readily available and is more phylogenetically-informed than many other online taxonomies. To combat the lack of resolution in NCBI, we allow authors to define new nodes using NCBI taxon names. For example, if NCBI contains Genus A with (Species 1, Species 2, Species 3, Species 4), a user can define a new node with descendents (Species 1, Species 2, Species 4) and (Species 3).