Congruification: support for time scaling large phylogenetic trees
Article first published online: 29 APR 2013
© 2013 The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society
Methods in Ecology and Evolution
Volume 4, Issue 7, pages 688–691, July 2013
How to Cite
Eastman, J. M., Harmon, L. J., Tank, D. C. (2013), Congruification: support for time scaling large phylogenetic trees. Methods in Ecology and Evolution, 4: 688–691. doi: 10.1111/2041-210X.12051
- Issue published online: 2 JUL 2013
- Article first published online: 29 APR 2013
- Accepted manuscript online: 18 MAR 2013 02:59PM EST
- Manuscript Accepted: 4 MAR 2013
- Manuscript Received: 30 DEC 2012
- NSF DEB. Grant Number: 0919499
- DEB. Grant Number: 1208912
- NESCent working group
- NSF. Grant Number: #EF- 0905606
- divergence time;
- geiger ;
- time scaling;
- tree of life
- 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.
- 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.
- 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.