Frequently Asked Questions

Q: How did you derive the molecular time estimates?

The molecular time estimates in Timetree represent a synthesis of published time estimates that were obtained from scientific literature. A detailed description of how the time estimates are derived is given in Hedges et al. (2015)

Q: How did you derive confidence intervals for molecular time estimates?

Our primary aim is to inform users about differences that exist among studies in estimated time through the presentation of "confidence intervals". This confidence interval is based on the Empirical Rule (95%) in statistics, which states that (assuming a normal distribution) approximately 95% of the times reported across studies will fall within two standard deviations of the mean time. That is, we use the 95% Empirical Rule for a population of studies, which has an interpretation similar to confidence intervals and hypothesis testing. Intuitively, we expect that the among-study variance, obtained based on study node times as single data points, to capture a variety of lower-level errors, including differences in calibrations and gene and taxon sampling. We present this confidence interval for nodes where times are available from 5 or more studies, otherwise a min-max range of time estimates is given. The Empirical Rule confidence interval is provided as a quick guide to the amount of variation among studies, and we strongly recommended that researchers review individual studies and their methodologies before using any time estimates in downstream research.

Q: Why do some time estimates have associated confidence intervals and other have min-max ranges?

For molecular time estimates derived from >= 5 time estimates from the scientific literature, a t-distribution is used to calculate a confidence interval for the molecular time estimate. When between 2 and 4 time estimates from the scientific literature are used to calculate a molecular time estimate, a range (min and max time estimates) is provided instead of a confidence interval. When only 1 time estimate from the scientific literature is available, no range or confidence interval is provided.

Q: How is topological incongruence among studies assessed?

Details about the acquisition of timetree data, their standardization, and the assembly of a global timetree (Timetree of Life, TTOL) based on individual timetrees are available in Hedges et al. (2015). In this method, timetrees and divergence data from individual studies are mapped onto a conservative guide tree available from the NCBI Taxonomy Browser, and these times are used to resolve polytomies and derive nodal times in the TTOL. This method also evaluates support for each resulting resolution by examining the number of timetree topologies in the database that are concordant with that resolution. When number of discordances are more than concordances, alternative topological configurations are tested for each resolution locally and the topology that minimizes the discordances is adopted. It is important to note that many nodes in the tree of life are poorly resolved and the robustness of this solution is limited by existing data. In particular, we recommend researchers to consult the most recent phylogenetic literature, some of which is not incorporated in the TimeTree because not all the phylogenetic studies include a timetree.

Q: How do you calculate the summary times?

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.

Q: What search method is employed to locate molecular time estimates for a pair of taxa?

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.

Q: How do I cite the TimeTree database?

Hedges SB, Marin J, Suleski M, Paymer M & Kumar S (2015) Tree of Life Reveals Clock-Like Speciation and Diversification. Mol Biol Evol 32: 835-845.

Kumar S & Hedges SB (2011) TimeTree2: species divergence times on the iPhone. Bioinformatics 27:2023-2024.

Hedges SB, Dudley J, & Kumar S (2006). TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 22: 2971-2972.

Q: Can I download the TimeTree Database data on to my computer?

The TimeTree Database data is currently not available for download. Methods for making these data available in the future are currently under discussion.

Q: I found an error on the TimeTree website. How can I report it?

Errors and suggestions can be submitted using the contact page.

Q: Can I get a list of the literature referenced by the TimeTree Database?

Yes, please click here to view a complete list of references.

Q: How often is the TimeTree Database updated?

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.

Q: Can I submit my own, unpublished, molecular time estimate to the TimeTree Database?

The TimeTree Database currently relies solely on published data and is not presently accepting unpublished time estimates.

Q: What software was used to create the TimeTree Database and Website?

The TimeTree Database was developed using the PostgreSQL database server. The web interface was developed with HTML, PHP, and Javascript.

Q: Why are the calibrations not listed for each study?

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.

Q: Why is the time estimation method not listed for each study?

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.

Q: In the timetrees, why do some nodes have open circles and others have solid circles?

Solid circles mark nodes that map directly to the NCBI Taxonomy and the open circles indicate nodes that were created during the polytomy resolution process which is described in Hedges et al. (2015).