Performance of a divergence time estimation method under a probabilistic model of rate evolution.

By Hirohisa Kishino, Jeffrey L. Thorne, William J. Bruno. Molecular biology and evolution, 2001

629 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/48397bf1e84fab6c6249764bbae622005d5d071d

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Citations in the corpus

Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography (2010, methodology): “Molecular dating analyses were carried out using the paml/multidivtime package (Thorne et al., 1998; Kishino et al., 2001; Thorne & Kishino, 2002) following the instructions of Rutschmann (2005).”
A phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes : Marsupialia) based on nuclear DNA sequences (2008, methodology): “6 andMultidivtime, that allow for a relaxed molecular clock (Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002; Drummond et al. 2006; Drummond and Rambaut 2007).”
A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes (2008, methodology): “Woodburne et al. (2003) used the estbranches and divtime5b programs of Thorne et al. (1998) and Kishino et al. (2001) with hard constraints and amino acid sequences for two proteins (BRCA1 and IGF2) and obtained point estimates of 182–190 Ma for the split between marsupials and placentals.”
Molecular phylogenetics: principles and practice (2012, background): “Since the pioneering work of Thorne and colleagues 107,108 , models of evolutionary rate drift over time have been developed to relax the molecular clock 72,109 .”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, background): “This continuous-trait model produces autocorrelated preservation rates over the tree, where closely related fossils share similar rates, and is identical to the autocorrelated log-normal relaxed clock model described by Thorne and Kishino [11] (also see [3, 7, 10]).”
Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times (2006, methodology): “Method 10: Bayesian implementation of rate autocorrelation in MULTIDIVTIME (Thorne et al., 1998; Kishino et al., 2001; Thorne & Kishino, 2002) The Bayesian dating method implemented in (Thorne et al., 1998; Kishino et al., 2001; Thorne & Kishino, 2002) uses a fully probabilistic and high parametric”
PAML 4: phylogenetic analysis by maximum likelihood. (2007, methodology): “This is similar to the MULTIDIVTIME program (Thorne, Kishino, and Painter 1998; Kishino, Thorne, and Bruno 2001) and can be used to analyze data of multiple gene loci, incorporating multiple fossil calibrations and allowing the evolutionary rate to drift over time.”
Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. (2002, methodology): “More general, but still parametric, methods have been described (Thorne, Kishino, and Painter 1998; Huelsenbeck, Larget, and Swofford 2000; Kishino, Thorne, and Bruno 2001), which assume a specific model for rate variation from branch to branch.”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, methodology): “Bayesian (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002; Yang and Rannala, 2006) and likelihood (Yang and Yoder, 2003; Yang, 2004) methods have been developed and modified such that they can account for violations of the molecular clock and for uncertainties of the fossil…”
Phylogeny estimation: traditional and Bayesian approaches (2003, background): “In the model of Thorne et al.(37,38), the rate of molecular evolution evolves over the tree: species that are evolving quickly are expected to give rise to species with high, but not necessarily identical, rates of evolution.”
Estimating divergence times in large molecular phylogenies (2012, methodology): “For AR, we used autocorrelation parameter ν = 1 (39).”
Relaxed Phylogenetics and Dating with Confidence (2006, methodology): “To convert this tree from units of time to molecular evolutionary units, the rates are either assigned to branches [15,17] or to nodes [53,54].”
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) (2016, positive): “…to as relaxed or local molecular clocks, have been developed that allow the rate of evolution to vary (for whatever reason) among the branches of a phylogenetic tree (e.g., Huelsenbeck, Larget, and Swofford 2000; Kishino, Thorne, and Bruno 2001; Drummond et al. 2006; Drummond and Suchard 2010).”
The Lake Tanganyika cichlid species assemblage: recent advances in molecular phylogenetics (2008, methodology): “Especially, those methods that relax the assumption of a molecular clock (e.g., Thorne et al., 1998; Kishino et al., 2001; Sanderson, 2002; Britton, 2005) and combine molecular data with time constraints (upper and lower bounds), usually derived from fossils or geological data, have become…”
Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians (2005, methodology): “Recent Bayesian methods (Thorne et al., 1998; Kishino et al., 2001) that relax the clock were also used to estimate divergence times, using the computer software MULTIDIVTIME (available from J. Thorne, North Carolina State University).”