The modern molecular clock

The discovery of the molecular clock — a relatively constant rate of molecular evolution — provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explained by assuming that most changes to genes are effectively neutral. Theory predicts several sources of variation in the rate of molecular evolution. However, even an approximate clock allows time estimates of events in evolutionary history, which provides a method for testing a wide range of biological hypotheses ranging from the origins of the animal kingdom to the emergence of new viral epidemics.

[1]  C. Darwin.  The Origin of Species by Means of Natural Selection, Or, The Preservation of Favoured Races in the Struggle for Life , 1859 .

[2]  M. Kasha.  Horizons in Biochemistry , 1962, The Yale Journal of Biology and Medicine.

[3]  J. L. King,et al.  Non-Darwinian evolution. , 1969, Science.

[4]  R B Setlow,et al.  Correlation between deoxyribonucleic acid excision-repair and life-span in a number of mammalian species. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[5]  L. Chao,et al.  COMPETITION BETWEEN HIGH AND LOW MUTATING STRAINS OF ESCHERICHIA COLI , 1983, Evolution; international journal of organic evolution.

[6]  M. Kimura.  The Neutral Theory of Molecular Evolution: Introduction , 1983 .

[7]  A. Wilson,et al.  Birds, behavior, and anatomical evolution. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[8]  W. Li,et al.  Evidence for higher rates of nucleotide substitution in rodents than in man. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Gillespie.  The causes of molecular evolution , 1991 .

[10]  W. Fitch,et al.  Positive Darwinian evolution in human influenza A viruses. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[11]  F. Tajima,et al.  Simple methods for testing the molecular evolutionary clock hypothesis. , 1993, Genetics.

[12]  Andrew P. Martin,et al.  Body size, metabolic rate, generation time, and the molecular clock. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[13]  P. Harvey,et al.  Metabolic rate, generation time, and the rate of molecular evolution in birds. , 1994, Molecular phylogenetics and evolution.

[14]  D. Rand.  Thermal habit, metabolic rate and the evolution of mitochondrial DNA. , 1994, Trends in ecology & evolution.

[15]  A P Martin,et al.  Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA. , 1995, Molecular biology and evolution.

[16]  A Rzhetsky,et al.  Phylogenetic test of the molecular clock and linearized trees. , 1995, Molecular biology and evolution.

[17]  N. Moran.  Accelerated evolution and Muller's rachet in endosymbiotic bacteria. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[18]  R. Doolittle,et al.  Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock , 1996, Science.

[19]  J Krushkal,et al.  Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. , 1996, Molecular phylogenetics and evolution.

[20]  N. Takahata.  Neutral theory of molecular evolution. , 1996, Current opinion in genetics & development.

[21]  Michael J. Sanderson,et al.  A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy , 1997 .

[22]  C. Mcintosh,et al.  Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K–Ar‐based ages of the Hawaiian Islands to estimate molecular evolutionary rates , 1998, Molecular ecology.

[23]  A. Rambaut,et al.  Estimating divergence dates from molecular sequences. , 1998, Molecular biology and evolution.

[24]  [Endogenous retroviruses in the human genome]. , 1998, Ugeskrift for laeger.

[25]  J. Schmitz,et al.  Sociality and the Rate of rDNA Sequence Evolution in Wasps (Vespidae) and Honeybees (Apis) , 1998, Journal of Molecular Evolution.

[26]  N. M. Brooke,et al.  A molecular timescale for vertebrate evolution , 1998, Nature.

[27]  J. Drake,et al.  Rates of spontaneous mutation. , 1998, Genetics.

[28]  S. Morris.  Early Metazoan Evolution: Reconciling Paleontology and Molecular Biology' , 1998 .

[29]  D. Penny,et al.  Testing the Cambrian explosion hypothesis by using a molecular dating technique. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[30]  J. W. Valentine,et al.  Fossils, molecules and embryos: new perspectives on the Cambrian explosion. , 1999, Development.

[31]  Archibald.  Molecular dates and the mammalian radiation. , 1999, Trends in ecology & evolution.

[32]  J. Margolick,et al.  Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection , 1999, Journal of Virology.

[33]  Phillips,et al.  Growing up with dinosaurs: molecular dates and the mammalian radiation. , 1999, Trends in ecology & evolution.

[34]  W Arber,et al.  Genomic evolution during a 10,000-generation experiment with bacteria. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Carroll,et al.  Towards a new evolutionary synthesis. , 2000, Trends in ecology & evolution.

[36]  M. Hendy,et al.  Can fast early rates reconcile molecular dates with the Cambrian explosion? , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[37]  A. Lapedes,et al.  Timing the ancestor of the HIV-1 pandemic strains. , 2000, Science.

[38]  Andrew Rambaut,et al.  Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies , 2000, Bioinform..

[39]  J. Bielas,et al.  Proliferation is necessary for both repair and mutation in transgenic mouse cells. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Michael D. Hendy,et al.  The Power of Relative Rates Tests Depends on the Data , 2000, Journal of Molecular Evolution.

[41]  Implications of Fluctuations in Substitution Rates: Impact on the Uncertainty of Branch Lengths and on Relative-Rate Tests , 2000, Journal of Molecular Evolution.

[42]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[43]  D. Cutler,et al.  Estimating divergence times in the presence of an overdispersed molecular clock. , 2000, Molecular biology and evolution.

[44]  M. Tristem.  Molecular Evolution — A Phylogenetic Approach. , 2000, Heredity.

[45]  Michael Tristem,et al.  Identification and Characterization of Novel Human Endogenous Retrovirus Families by Phylogenetic Screening of the Human Genome Mapping Project Database , 2000, Journal of Virology.

[46]  V. Savolainen,et al.  EVOLUTIONARY RATES AND SPECIES DIVERSITY IN FLOWERING PLANTS , 2001, Evolution; international journal of organic evolution.

[47]  J. Seger,et al.  Elevated rates of nonsynonymous substitution in island birds. , 2001, Molecular biology and evolution.

[48]  W. Bruno,et al.  Performance of a divergence time estimation method under a probabilistic model of rate evolution. , 2001, Molecular biology and evolution.

[49]  Diana J. Kao,et al.  Parallel adaptive radiations in two major clades of placental mammals , 2001, Nature.

[50]  Q Zheng,et al.  On the dispersion index of a Markovian molecular clock. , 2001, Mathematical biosciences.

[51]  C. Held.  No evidence for slow-down of molecular substitution rates at subzero temperatures in Antarctic serolid isopods (Crustacea, Isopoda, Serolidae) , 2001, Polar Biology.

[52]  Covarion Model of Molecular Evolution , 2001 .

[53]  T. Ohta.  Near-neutrality in evolution of genes and gene regulation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Jianzhi Zhang,et al.  Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey , 2002, Nature Genetics.

[55]  K. Peterson,et al.  Dating the Time of Origin of Major Clades: Molecular Clocks and the Fossil Record , 2002 .

[56]  L. Bromham.  Molecular clocks in reptiles: life history influences rate of molecular evolution. , 2002, Molecular biology and evolution.

[57]  A. Rambaut,et al.  TESTING THE RELATIONSHIP BETWEEN MORPHOLOGICAL AND MOLECULAR RATES OF CHANGE ALONG PHYLOGENIES , 2002, Evolution; international journal of organic evolution.

[58]  Stéphane Aris-Brosou,et al.  Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. , 2002, Systematic biology.

[59]  Masatoshi Nei,et al.  The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species. , 2002, The Journal of heredity.

[60]  B. Rannala.  Identi(cid:142)ability of Parameters in MCMC Bayesian Inference of Phylogeny , 2002 .

[61]  U. Bastolla,et al.  Lack of self-averaging in neutral evolution of proteins. , 2002, Physical review letters.

[62]  Adam Eyre-Walker,et al.  Adaptive protein evolution in Drosophila , 2002, Nature.

[63]  L. Bromham.  The human zoo: endogenous retroviruses in the human genome , 2002 .

[64]  L. Bromham,et al.  Testing the link between the latitudinal gradient in species richness and rates of molecular evolution , 2003, Journal of evolutionary biology.

[65]  Andrew Rambaut,et al.  Inferring the rate and time-scale of dengue virus evolution. , 2003, Molecular biology and evolution.

[66]  David Penny,et al.  Estimating Changes in Mutational Mechanisms of Evolution , 2003, Journal of Molecular Evolution.

[67]  Lindell Bromham,et al.  Molecular Clocks and Explosive Radiations , 2003, Journal of Molecular Evolution.

[68]  O. Pybus,et al.  Inference of viral evolutionary rates from molecular sequences. , 2003, Advances in parasitology.

[69]  T. Ohta,et al.  On the rate of molecular evolution , 2005, Journal of Molecular Evolution.

[70]  A. Rambaut,et al.  Determinants of rate variation in mammalian DNA sequence evolution , 1996, Journal of Molecular Evolution.

[71]  T. Ohta.  Very slightly deleterious mutations and the molecular clock , 2005, Journal of Molecular Evolution.

[72]  Richard E. Dickerson,et al.  The structure of cytochromec and the rates of molecular evolution , 2005, Journal of Molecular Evolution.

[73]  W. M. Fitch,et al.  Rate of change of concomitantly variable codons , 2005, Journal of Molecular Evolution.

[74]  T. Ohta,et al.  On the constancy of the evolutionary rate of cistrons , 2005, Journal of Molecular Evolution.

[75]  A. Wilson,et al.  Stomach lysozyme gene of the langur monkey: Tests for convergence and positive selection , 1991, Journal of Molecular Evolution.

[76]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.