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

By Michael J. Sanderson. Molecular biology and evolution, 2002

1,943 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0feca6705c1820d1fc9c4a2bb3affd39b5698c8f

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In Genetics

Citations in the corpus

As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates* (2009, background): “A potential way to bypass this arbitrary application of individual rates (yet allowing substitution rates to differ along a phylogeny) was developed by Sanderson in two key papers (Sanderson 1997, 2002).”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, methodology): “8a [57] and the GTR+Γ (-m GTRGAMMA) model of evolution and converted into ultrametric trees using penalized likelihood [58] as implemented in the ape package [59] in R.”
Molecular phylogeny and historical biogeography of the cosmopolitan parasitic wasp subfamily Doryctinae (Hymenoptera:Braconidae) (2008, methodology): “The PL method uses a combination of a parametric model with heterogeneous substitution rates on every branch and a nonparametric penalisation for the rapid rate changes among branches (Sanderson 2002).”
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. (2009, methodology): “A related method, penalized likelihood, was subsequently implemented in a maximum-likelihood framework (Sanderson 2002).”
Episodic radiations in the fly tree of life (2011, methodology): “Divergence time estimates were calculated for the ingroup-only combined dataset using the penalized likelihood method (43) in r8s, version 1.”
Freshwater bivalve (Unioniformes) diversity, systematics, and evolution: status and future directions (2008, methodology): “An additional benefit of such studies would be the ability to develop estimates of fossil-calibrated divergence times for lineages of mussels once the ancestors of modern taxa have been identified using the methods developed by Huelsenbeck et al. (2001), Sanderson (2002), and others.”
Phylogeny of Robinioid Legumes (Fabaceae) Revisited: Coursetia and Gliricidia Recircumscribed, and a Biogeographical Appraisal of the Caribbean Endemics (2009, methodology): “The program r8s (Sanderson 2001) was used to assess variance in evolutionary substitution rates for nucleotide sequences from the ITS region and the matK locus, and incorporate such variance into the estimation of ages of lineages (Sanderson 1997, 1998, 2001, 2002).”
PAML 4: phylogenetic analysis by maximum likelihood. (2007, neutral): “Sanderson MJ. 2002.”
The Pleasures and Perils of Darwinizing Culture (with Phylogenies) (2007, background): “In contrast, phylogenetic methods are capable of reliably estimating absolute divergence dates without assuming constant rates (Sanderson 2002).”
Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective (2007, methodology): “Additionally, we used both the clock-dependent Langley– Fitch (LF; Langley and Fitch 1974) method, which uses maximum likelihood to reconstruct divergence times and the clock-independent nonparametric rate smoothing (NPRS; Sanderson 1997) and penalized likelihood (PL; Sanderson 2002) methods as impl”