Chronosynth methods overview

Chronosynth matches dates from input studies to nodes in the synthetic tree, using a phyloreferencing type approach.

E.g. for this dated tree from Dos Reis et al (2015)

we can see that this node

aligns to the taxon Echinozoa in the synthetic tree.

We can also make these node alignment statements between nodes in input trees and unnamed nodes in the synthetic tree. We use the otcetera conflict services to make these alignment statements (Redelings and Holder https://github.com/OpenTreeOfLife/otcetera).

Chronosynth iterates over every dated tree in Phylesystem, and links the node ages of internal nodes in published trees to the nodes each align to in the synthetic tree.

This information is directly available from the API either for single nodes via the call /dates/node_dates/{SYNTH_NODE_ID} or for every node using /dates/dated_node_dump.

As of Sept 29, 2022, 46573 synth nodes have dates, We have a total of 94430 node dates (some nodes have many dates, some have one, many have no dates) These dates are from 263 trees in 202 studies.

The dated tree API uses these dates, takes the mean date where there are multiple dates for a node, and uses BLADJ to smooth branch lengths.

If you run Chronosynth locally, you can get a better idea of uncertainty by sampling from the dates, and re-running the date smoothing.