Local and relaxed clocks, the best of both worlds
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Abstract
Time-resolved phylogenetic methods use information about the time of sample collection to estimate the rate of evolution. Originally, the models used to estimate evolutionary rates were quite simple, assuming that all lineages evolve at the same rate, an assumption commonly known as the molecular clock. Richer and more complex models have since been introduced to capture the phenomenon of substitution rate variation among lineages. Two well known model extensions are the local clock, wherein all lineages in a clade share a common substitution rate, and the uncorrelated relaxed clock, wherein the substitution rate on each lineage is independent from other lineages while being constrained to fit some parametric distribution. We introduce a further model extension, called the flexible local clock (FLC), which provides a flexible framework to combine relaxed clock models with local clock models. We evaluate the flexible local clock on simulated and real datasets and show that it provides substantially improved fit to an influenza dataset. An implementation of the model is available for download from https://www.github.com/4ment/flc.
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2018. Local and relaxed clocks, the best of both worlds. PeerJ Preprints 6:e26744v1 https://doi.org/10.7287/peerj.preprints.26744v1Author comment
This is a submission to PeerJ for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Mathieu Fourment conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Aaron E Darling contributed reagents/materials/analysis tools, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
Funding
This work was supported by the Australian centre for genomic epidemiological microbiology (AusGEM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.