Cited by 1,977Genomics and Phylogenetic StudiesEvolution and Genetic DynamicsPlant Diversity and Evolution

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Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach.

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Sanderson, Michael J.·2002·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a003974

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Abstract

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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Model Selection and Inference
Burnham, K. P., & Anderson, D. R. (1998) · doi:10.1007/978-1-4757-2917-7 · Cited by 3,387
The Theory of Stochastic Processes
Cox, D. R., Miller, H. D., Weiss, G., & Shuler, K. (1966) · Physics Today · doi:10.1063/1.3047872 · Cited by 3,324
The general stochastic model of nucleotide substitution
Rodríguez, F., Oliver, J. L. T., Marín, A., & Medina, J. R. (1990) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(05)80104-3 · Cited by 2,325
A molecular timescale for vertebrate evolution
Kumar, S., & Hedges, S. B. (1998) · Nature · doi:10.1038/31927 · Cited by 1,936
Nonparametric Regression and Generalized Linear Models
Green, P. J., & Silverman, B. W. (1994) · Springer eBooks · doi:10.1007/978-1-4899-4473-3 · Cited by 1,935
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · cited 3×
“The CV criterion proposed here provides an empirical method for comparing other recently proposed rate and time estimation procedures (Thorne, Kishino, and Painter 1998; Huelsenbeck, Larget, and Swofford 2000), which have mainly been evaluated on an absolute scale by simulation studies (Sanderson…”
BackgroundMethod
Smoothing Methods in Statistics
Yandell, B. S., & Simonoff, J. S. (1997) · Technometrics · doi:10.2307/1271147 · Cited by 1,306
Body size, metabolic rate, generation time, and the molecular clock.
Martin, A. P., & Palumbi, S. R. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.9.4087 · Cited by 1,239 · cited 1×
“…of rates have contributed to the development of ideas about modes of selection on different genomic elements, such as introns versus exons, and have permitted correlates of rate differences, such as generation time and metabolic rate, to be identified (Gillespie 1991; Martin and Palumbi 1993).”
Background
The causes of molecular evolution
Gillespie, J. H. (1992) · Choice Reviews Online · doi:10.5860/choice.30-2064 · Cited by 1,214
Among-site rate variation and its impact on phylogenetic analyses
Yang, Z. (1996) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(96)10041-0 · Cited by 1,202

Show all 46 references

Research works printed but not linked: 2

Gill P. E., W. Murray, M. H. Wright, 1981 Practical optimization Academic Press, New York
Press W. H., B. P. Flannery, S. A. Teukolsky, W. T. Vetterling, 1992 Numerical recipes in C. 2nd edition Cambridge University Press, New York

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Authors: Sanderson, M. J.
Affiliations: University of California, Davis (US)
Corresponding author: Sanderson, Michael J.
ORCID: 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
DOI: 10.1093/oxfordjournals.molbev.a003974
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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Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach.

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