The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
A Compound Poisson Process for Relaxing the Molecular Clock
Abstract
The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.
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Cites
Equation of State Calculations by Fast Computing Machines
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953) · The Journal of Chemical Physics · doi:10.1063/1.1699114 · Cited by 37,192
Monte Carlo sampling methods using Markov chains and their applications.
Hastings, W. K. (1970) · Biometrika · doi:10.1093/biomet/57.1.97 · Cited by 15,195
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Evolutionary divergence and convergence in proteins.
ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
A molecular timescale for vertebrate evolution
Kumar, S., & Hedges, S. B. (1998) · Nature · doi:10.1038/31927 · Cited by 1,936
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
A nonparametric approach to estimating divergence times in the absence of rate constancy.
Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156
Research works printed but not linked: 16
- Arnason, 1997, Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenartha (Edentata) and Ferungulates, Mol. Biol. Evol., 14, 762, 10.1093/oxfordjournals.molbev.a025816 · DOI
- Geyer, 1999, Likelihood inference for spatial point processes, 79
- Gillespie, 1991, The Causes of Molecular Evolution
- Goodman, 1975, Darwinian evolution in the genealogy of hemoglobin, Nature, 253, 603, 10.1038/253603a0 · DOI · Paper page
- Green, 1995, Reversible jump Markov chain Monte Carlo computation and Bayesian model determination, Biometrika, 82, 711, 10.1093/biomet/82.4.711 · DOI · Paper page
- Hasegawa, 1984, A new molecular clock of mitochondrial DNA and the evolution of Hominoids, Proc. Japan Acad. Ser. B, 60, 95, 10.2183/pjab.60.95 · DOI
- Huelsenbeck, 1997, Statistical test of host-parasite cospeciation, Evolution, 51, 410, 10.1111/j.1558-5646.1997.tb02428.x · DOI
- Langley, 1973, The constancy of evolution: a statistical analysis of a and b haemoglobins, cytochrome c, and fibrinopeptide A, 246
- Langley, 1974, An estimation of the constancy of the rate of molecular evolution, J. Mol. Evol., 3, 161, 10.1007/BF01797451 · DOI · Paper page
- Sokal, 1958, A statistical method for evaluating systematic relationships, Univ. Kans. Sci. Bull., 28, 1409
- Swofford, 1998, Phylogenetic Analysis Using Parsimony (* and other Methods)
- Tierney, 1994, Markov chains for exploring posterior distributions, Ann. Stat., 22, 1701
- Wu, 1985, Evidence for higher rates of nucleotide substitution in rodents than in man, Proc. Natl. Acad. Sci. USA, 82, 1741, 10.1073/pnas.82.6.1741 · DOI · Paper page
- Yang, 1993, Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites, Mol. Biol. Evol., 10, 1396
- Yang, 1997, PAML: a program package for phylogenetic analysis by maximum likelihood, CABIOS, 15, 555
- Zuckerkandl, 1962, Molecular disease, evolution, and genetic heterogeneity, 189
Cited by
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys029 · Cited by 27,843
Self-citationPhylogenies and Community Ecology
Webb, C. O., Ackerly, D. D., McPeek, M. A., & Donoghue, M. J. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150448 · Cited by 4,609
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
Rambaut, A., Lam, T. T., Max Carvalho, L., & Pybus, O. G. (2016) · Virus Evolution · doi:10.1093/ve/vew007 · Cited by 2,063
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
Metadata
- Authors
- Huelsenbeck, J. P., Larget, B., & Swofford, D.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2000-04-01
- Volume
- 154
- Issue
- 4
- Pages
- 1879-1892
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W1944637642
- Cited by
- 351
- References
- 15
- FWCI
- 8.45
- Type
- journal article
- Language
- en
- Open access
- closed
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