The molecular time estimates were obtained from scientific literature.
Summary time estimates are calculated using a simple average and a weighted average based on the number of genes analyzed. The weighted average for each data type is calculated in addition to the overall weighted average.
When a valid pair of taxa is submitted through the search page, the TimeTree Database determines the most inclusive taxonomic groups for each query taxa. Such groups are one level lower in the taxonomic classification than the common taxon that includes both query taxa. Once these groups are determined, the TimeTree Database obtains all molecular time estimates in which a member of the most inclusive group for Taxon A is compared to a member of the most inclusive group for Taxon B.
Hedges SB, Dudley J, & Kumar S (2006). TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 22: 2971-2972.
The TimeTree Database data is currently not available for download. Methods for making these data available in the future are currently under discussion.
Errors and suggestions can be submitted to firstname.lastname@example.org
Yes, please click here to view a complete list of references.
Currently, the TimeTree Database is updated periodically, because each update requires changes to the large guide tree. In the future, updates will occur more frequently or continuously as new literature appears.
The TimeTree Database currently relies solely on published data and is not presently accepting unpublished time estimates.
The TimeTree Database was developed using the PostgreSQL database server. The web interface was developed with PHP.
Calibrations are important in timing but they are used in different ways by different investigators. For example they can be used as minimums, maximums, fixed points, and with different distributions (e.g., lognormal, exponential, uniform). Two studies with identical calibrations could present greatly different time estimates because of this complexity in methodology. If you have questions about such details, it is advisable to refer to the original studies.
There are many methods of time estimation and many options that can be used with each method. Two studies with identical data, calibrations, and using the same software, can yield different time estimates depending on how the software was used. If you have questions about such details, it is advisable to refer to the original studies.