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DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life
Luna L Sánchez Reyes1,2, Emily Jane McTavish1, Brian O'Meara2
1Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA.
Systematic Biology
|March 20, 2024
Summary
DateLife is a new software tool that simplifies the use of time-calibrated evolutionary trees (chronograms) for research. It helps researchers easily access and reanalyze existing chronogram data, improving the accuracy of evolutionary timing estimates.
Area of Science:
- Evolutionary biology
- Phylogenetics
- Computational biology
Background:
- Chronograms, phylogenies with time-calibrated branches, are crucial for understanding evolutionary events and informing conservation.
- Reconstructing high-quality chronograms is complex and data-intensive.
- Existing chronogram data is often scattered and difficult to access for reuse.
Purpose of the Study:
- To introduce DateLife, a novel software tool for efficient discovery, summary, reuse, and reanalysis of chronogram node age data.
- To provide a user-friendly platform for accessing and utilizing curated chronogram databases.
- To facilitate the dating of phylogenetic trees using secondary calibration data derived from existing chronograms.
Main Methods:
- DateLife processes user-provided taxon names, standardizes taxonomy, and queries a curated database of chronograms.
- It extracts relevant chronograms containing specified taxa and their metadata.
- Node ages are mapped to a target tree topology using the congruification algorithm and employed as secondary calibrations for phylogenetic dating methods (e.g., BLADJ, treePL).
Main Results:
- Cross-validation demonstrated that DateLife's node age estimates are consistent with original chronogram estimates, with variations mainly at deeper nodes.
- The software successfully uses secondary calibrations to date phylogenetic trees.
- DateLife facilitates the comparison of different chronogram hypotheses and their impact on downstream analyses.
Conclusions:
- DateLife offers an efficient and accessible framework for leveraging existing chronogram data in evolutionary research.
- The tool aids in understanding discrepancies between different evolutionary timing hypotheses.
- DateLife supports more informed interpretation of evolutionary results by providing a robust method for phylogenetic dating.
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