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Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach.
Open accessAbstract
Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.
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“The molecular clock assumption can be relaxed in a variety of ways [ 13– 15, 17, 49– 52].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [50]
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“Adopting this philosophy, Sanderson (1997Sanderson ( , 2002) ) proposed a nonparametric rate smoothing method and a semiparametric penalized likelihood approach, both of which operate by minimizing rate changes throughout the tree.”
From Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation (2005) · cites this paper as Sanderson 2002
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Metadata
- Authors
- Sanderson, M. J.
- Affiliations
- University of California, Davis (US)
- Corresponding author
- Sanderson, Michael J.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-01-01
- Volume
- 19
- Issue
- 1
- Pages
- 101-109
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W1982848324
- Cited by
- 1,977
- References
- 46
- Citations by year
- 2026: 23 · 2025: 38 · 2024: 36 · 2023: 35 · 2022: 47 · 2021: 64 · 2020: 58 · 2019: 70 · 2018: 64 · 2017: 54 · 2016: 68 · 2015: 67 · 2014: 94 · 2013: 72 · 2012: 106
- FWCI
- 28.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (9726856)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- molecular evolution rate, rate heterogeneity, divergence time estimation, penalized likelihood, phylogenetic tree, cross-validation, land plants
- MeSH terms
- Algorithms, Models, Genetic, Phylogeny, Plants, Time Factors, Genetic Variation, Reproducibility of Results, Models, Statistical, Likelihood Functions, Genes, Plant, Evolution, Molecular
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