Journal
METHODS IN ECOLOGY AND EVOLUTION
Volume 4, Issue 7, Pages 688-691Publisher
WILEY
DOI: 10.1111/2041-210X.12051
Keywords
divergence time; geiger; phylogenetics; time scaling; tree of life
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Funding
- NSF [DEB 0919499, DEB 1208912, EF-0905606]
- Direct For Biological Sciences
- Division Of Environmental Biology [0919499] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [1208912] Funding Source: National Science Foundation
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1. Approaches for efficient statistical estimation of large phylogenies are now available (Bioinformatics, 2006, 22, 2688), and yet we lack adequate tools for synthesizing information from previous analyses into large timetrees. Here, we present a cross-platform r tool that integrates with tree of life efforts by mapping divergence times from an existing timetree (a reference') to another uncalibrated phylogeny (a target') that samples from the same lineage. Leveraging existing methods for rate-smoothing phylograms, this tool enables the rapid generation of very large timetrees where direct estimation of the timing of lineage diversification is either impracticable or impossible. 2. The primary output of the tool is to return divergence times for nodes resolved as concordant between the reference and target. Given the computed set of secondary calibrations, post hoc tree transformation can be accomplished using existing resources that assume either a strict or relaxed evolutionary clock. 3. Our software is provided open source in the geiger package (http://cran.r-project.org/package=geiger) and is thoroughly demonstrated in the Supporting Information.
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