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

Sanderson, Michael J.

doi:10.1093/oxfordjournals.molbev.a003974

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

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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The molecular clock assumption can be relaxed in a variety of ways.
“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]
Sanderson proposed a nonparametric rate smoothing method and a semiparametric penalized likelihood approach, both of which operate by minimizing rate changes throughout the tree.
“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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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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