Projects per year
Abstract
Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori-calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori, appear to be less reliable than a priori calibrated, timescales.
Original language | English |
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Article number | evaa105 |
Pages (from-to) | 1087-1098 |
Number of pages | 12 |
Journal | Genome Biology and Evolution |
Volume | 12 |
Issue number | 7 |
DOIs | |
Publication status | Published - 22 May 2020 |
Keywords
- molecular clock
- Bayesian
- RelTime
- simulation
Fingerprint
Dive into the research topics of 'Performance of a priori and a posteriori calibration strategies in divergence time estimation'. Together they form a unique fingerprint.Projects
- 2 Finished
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Neoproterozoic - Phanerozoic transition
Donoghue, P. C. J. (Principal Investigator)
9/01/17 → 31/07/22
Project: Research
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Improving Bayesian methods for estimating divergence times integrating genomic and trait data
Donoghue, P. C. J. (Principal Investigator)
25/03/16 → 31/12/21
Project: Research
Datasets
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Data & Scripts from Beavan et al. (2020): Performance of a priori and a posteriori calibration strategies in divergence time estimation.
Pisani, D. (Creator), Beavan, A. (Contributor), Donoghue, P. (Contributor) & Beaumont, M. (Contributor), University of Bristol, 2 Jun 2020
DOI: 10.5523/bris.uopumskkuech206ueqdxpcrif, http://data.bris.ac.uk/data/dataset/uopumskkuech206ueqdxpcrif
Dataset
Equipment
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HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities
Alam, S. R. (Manager), Williams, D. A. G. (Manager), Eccleston, P. E. (Manager) & Greene, D. (Manager)
Facility/equipment: Facility