Review Article | Published:

Bayesian molecular clock dating of species divergences in the genomics era

Nature Reviews Genetics volume 17, pages 7180 (2016) | Download Citation

Abstract

Five decades have passed since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species. This hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events. With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics and studying the macroevolutionary process of speciation and extinction to estimating a timescale for life on Earth.

Key points

  • Five decades have passed since Emile Zuckerkandl and Linus Pauling first proposed the molecular clock hypothesis. The molecular clock has become an essential tool in evolutionary biology, from tracking virus pandemics to estimating the timeline of evolution of life on Earth.

  • Early molecular clock dating studies made simplistic assumptions about the evolutionary process and proposed scenarios of species diversification that contradicted the fossil record.

  • Bayesian clock dating methodology has become the standard tool for integrating information from fossils and molecules to estimate the timeline of the Tree of Life.

  • Exciting developments in Bayesian clock dating include relaxed clock models, sophisticated fossil calibration curves and the joint analysis of morphology and sequence data.

  • Bayesian clock dating analysis of genome-scale data has resolved many iconic controversies between fossils and molecules, such as the pattern of diversification of mammals and birds relative to the end-Cretaceous mass extinction.

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References

  1. 1.

    & in Evolving Genes and Proteins (eds Bryson, V. & Vogel, H. J.) 97–166 (Academic Press, 1965). The seminal paper proposing the concept of a molecular evolutionary clock. Provides a justification for the clock based on the idea that most amino acid changes may not change the structure and function of the protein.

  2. 2.

    & in Horizons in Biochemistry (eds Kasha, M. & Pullman, B.) 189–225 (Academic Press, 1962). The earliest clock dating paper. Used the idea of approximate rate constancy to calculate the age of the alpha and beta globin duplication event.

  3. 3.

    Primary structure and evolution of cytochrome c. Proc. Natl Acad. Sci. USA 50, 672–679 (1963).

  4. 4.

    & Amino-acid sequence investigations of fibrinopeptides from various mammals: evolutionary implications. Nature 202, 147–152 (1964).

  5. 5.

    Emile Zuckerkandl, Linus Pauling, and the molecular evolutionary clock. J. Hist. Biol. 31, 155–178 (1998).

  6. 6.

    The Neutral Theory of Molecular Evolution (Cambridge Univ. Press, 1983). Authoritative book outlining the neutral theory. Chapter 4 has an extensive discussion of morphological versus molecular rates of evolution.

  7. 7.

    & The modern molecular clock. Nat. Rev. Genet. 4, 216–224 (2003).

  8. 8.

    Molecular clocks: four decades of evolution. Nat. Rev. Genet. 6, 654–662 (2005).

  9. 9.

    , , , & Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470–477 (1996).

  10. 10.

    & An examination of the constancy of the rate of molecular evolution. J. Mol. Evol. 3, 161–177 (1974).

  11. 11.

    Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376 (1981). Seminal paper describing how to calculate the likelihood for a molecular sequence alignment and describing a likelihood-ratio test of the clock.

  12. 12.

    , & A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23, 327–337 (2006).

  13. 13.

    The changing face of the molecular evolutionary clock. Trends Ecol. Evol. 29, 496–503 (2014).

  14. 14.

    , & Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12, 823–833 (1995).

  15. 15.

    & Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15, 442–448 (1998).

  16. 16.

    & Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17, 1081–1090 (2000).

  17. 17.

    et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369–1372 (2014).

  18. 18.

    et al. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science 346, 56–61 (2014).

  19. 19.

    et al. Dating the emergence of pandemic influenza viruses. Proc. Natl Acad. Sci. USA 106, 11709–11712 (2009).

  20. 20.

    , & Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus. J. Mol. Evol. 69, 333–345 (2009).

  21. 21.

    et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416–426 (2008).

  22. 22.

    et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).

  23. 23.

    & Revising the human mutation rate: implications for understanding human evolution. Nat. Rev. Genet. 13, 745–753 (2012).

  24. 24.

    et al. Phylogenomic data sets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. R. Soc. B. Biol. Sci. 279, 3491–3500 (2012). An example of using the molecular clock with genome-scale data sets to infer the timeline of diversification of modern mammals relative to the end-Cretaceous mass extinction.

  25. 25.

    et al. The delayed rise of present-day mammals. Nature 446, 507–512 (2007).

  26. 26.

    et al. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927–931 (2010).

  27. 27.

    et al. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89–92 (2014).

  28. 28.

    et al. Gibbon genome and the fast karyotype evolution of small apes. Nature 513, 195–201 (2014).

  29. 29.

    , & Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647–1657 (1998). Describes the first Bayesian molecular clock dating method. Introduces the geometric Brownian motion model of rate variation among species.

  30. 30.

    , , & Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).

  31. 31.

    & Inferring speciation times under an episodic molecular clock. Syst. Biol. 56, 453–466 (2007).

  32. 32.

    et al. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst. Biol. 60, 16–31 (2011). Develops a model of species origination, extinction and fossil preservation and discovery to construct time priors based on data of fossil occurrences.

  33. 33.

    Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst. Biol. 60, 466–481 (2011).

  34. 34.

    et al. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 61, 973–999 (2012). Develops a Bayesian 'total-evidence' dating method for the joint analysis of morphological and molecular data.

  35. 35.

    & A distance-based least-square method for dating speciation events. Mol. Phylogenet. Evol. 59, 342–353 (2011).

  36. 36.

    et al. Estimating divergence times in large molecular phylogenies. Proc. Natl Acad. Sci. USA 109, 19333–19338 (2012).

  37. 37.

    Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Mol. Phylogenet. Evol. 67, 436–444 (2013).

  38. 38.

    & Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evol. Biol. 14, 163 (2014).

  39. 39.

    & Molecular-clock methods for estimating evolutionary rates and timescales. Mol. Ecol. 23, 5947–5965 (2014).

  40. 40.

    & Immunological time scale for Hominoid evolution. Science 158, 1200–1203 (1967).

  41. 41.

    Man's immediate forerunners. Phil. Trans. R. Soc. 292, 21–41 (1981).

  42. 42.

    & Evolutionary explosions and the phylogenetic fuse. Trends Ecol. Evol. 13, 151–156 (1998).

  43. 43.

    & Dating the tree of life. Science 300, 1698–1700 (2003).

  44. 44.

    , & Molecular evidence for deep Precambrian divergences. Science 274, 568–573 (1996).

  45. 45.

    et al. Molecular evidence for the early colonization of land by fungi and plants. Science 293, 1129–1133 (2001).

  46. 46.

    , , & Continental breakup and the ordinal diversification of birds and mammals. Nature 381, 226–229 (1996).

  47. 47.

    & A molecular timescale for vertebrate evolution. Nature 392, 917–920 (1998).

  48. 48.

    & Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20, 80–86 (2004).

  49. 49.

    & Precision of molecular time estimates. Trends Genet. 20, 242–247 (2004).

  50. 50.

    et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331 (2014).

  51. 51.

    et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 346, 763–767 (2014).

  52. 52.

    , & Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352–361 (2001).

  53. 53.

    & Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51, 689–702 (2002).

  54. 54.

    & Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212–226 (2006). Develops a method to integrate the birth–death process to construct the time prior jointly with fossil calibrations with soft bounds. Introduces the limiting theory of uncertainty in divergence time estimates.

  55. 55.

    , , & A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24, 2669–2680 (2007).

  56. 56.

    , & The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc. Natl Acad. Sci. USA 111, E2957–E2966 (2014).

  57. 57.

    & Approximate likelihood calculation for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161–2172 (2011).

  58. 58.

    Bayesian estimation of divergence times from large sequence alignments. Mol. Biol. Evol. 27, 1768–1781 (2010).

  59. 59.

    Molecular Evolution: A Statistical Approach (Oxford Univ. Press, 2014).

  60. 60.

    & in Bayesian Phylogenetics: Methods, Algorithms, and Applications (eds Chen, M.-H, Kuo, L. & Lewis, P. O.) 277–318 (Chapman and Hall, 2014).

  61. 61.

    The molecular clock may be an episodic clock. Proc. Natl Acad. Sci. USA 81, 8009–8013 (1984). Proposes the idea of an episodic clock, modelling rate evolution through time and among lineages as a stochastic process.

  62. 62.

    & The unbearable uncertainty of Bayesian divergence time estimation. J. Syst. Evol. 51, 30–43 (2013).

  63. 63.

    , & Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci. Syst. Biol. 64, 267–280 (2015).

  64. 64.

    , & The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci. Syst. Biol. 63, 555–565 (2014).

  65. 65.

    , , , & Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc. Biol. Sci. 282, 20141013 (2015).

  66. 66.

    , & The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst. Biol. 59, 74–89 (2010).

  67. 67.

    A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14, 1218–1232 (1997).

  68. 68.

    & Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52, 705–716 (2003).

  69. 69.

    & Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa. Mol. Biol. Evol. 20, 1947–1954 (2003).

  70. 70.

    , & Molecular dates for the “cambrian explosion”: the influence of prior assumptions. Syst. Biol. 54, 672–678 (2005).

  71. 71.

    , & Dirichlet process prior for estimating lineage-specific substitution rates. Mol. Bio. Evol. 29, 939–955 (2012).

  72. 72.

    & Bayesian random local clocks, or one rate to rule them all. BMC Biol. 8, 114 (2010).

  73. 73.

    , & A compound Poisson process for relaxing the molecular clock. Genetics 154, 1879–1892 (2000).

  74. 74.

    & Rocks and clocks: calibrating the tree of life using fossils and molecules. Trends Ecol. Evol. 22, 424–431 (2007).

  75. 75.

    & Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 58, 367–380 (2009).

  76. 76.

    & The dating game: a reply to Heads. Zool. Scripta 39, 406–409 (2010).

  77. 77.

    On the Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life (John Murray, 1859).

  78. 78.

    et al. A new hominid from the upper Miocene of Chad, central Africa. Nature 418, 145–151 (2002).

  79. 79.

    et al. Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs. J. Hum. Evol. 79, 45–54 (2015).

  80. 80.

    & Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol. Ecol. 13, 757–773 (2004).

  81. 81.

    & Molecular timescales and the fossil record: a paleontological perspective. Trends Genet. 20, 237–241 (2004).

  82. 82.

    & Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24, 26–53 (2007).

  83. 83.

    , & Exploring uncertainty in the calibration of the molecular clock. Biol. Lett. 8, 156–159 (2012).

  84. 84.

    et al. Best practices for applying paleontological data to molecular divergence dating analyses. Syst. Biol. 61, 346–359 (2012). Sets out the criteria required for the establishment of fossil calibrations.

  85. 85.

    et al. The fossil calibration database – a new resource for divergence dating. Syst. Biol. 64, 853–859 (2015).

  86. 86.

    Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology 23, 165–173 (1997).

  87. 87.

    , , , & Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416, 726–729 (2002).

  88. 88.

    et al. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida). Syst. Biol. 63, 457–479 (2014).

  89. 89.

    & Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees. Sci. Rep. 3, 2545 (2013).

  90. 90.

    , , & Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Syst. Biol. 62, 264–284 (2013).

  91. 91.

    & A revised dated phylogeny of the arachnid order Opiliones. Front. Genet. 5, 255 (2014).

  92. 92.

    et al. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol. Phyl. Evol. 82, 131–145 (2015).

  93. 93.

    , , & Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Mol. Phyl. Evol. 69, 514–523 (2013).

  94. 94.

    , & Combining fossil and molecular data to date the diversification of New World Primates. J. Evol. Biol. 26, 2438–2446 (2013).

  95. 95.

    Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous–Palaeogene boundary. Meth. Ecol. Evol. 4, 734–744 (2013).

  96. 96.

    et al. Himalayan fossils of the oldest known pantherine establish ancient origin of big cats. Proc. Biol. Sci. 281, 20132686 (2014).

  97. 97.

    , & Dating tips for divergence–time estimation. Trends Genet. 31, 637–650 (2015).

  98. 98.

    A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913–925 (2001).

  99. 99.

    Sequencing technologies – the next generation. Nat. Rev. Genet. 11, 31–46 (2010).

  100. 100.

    10,000 genomes to come. Nature 462, 21 (2009).

  101. 101.

    , , , & How many species are there on Earth and in the ocean? PLoS Biol. 9, e1001127 (2011).

  102. 102.

    & Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology. Front. Genet. 5, 138 (2014).

  103. 103.

    et al. Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Curr. Biol. 25, 2939–2950 (2015).

  104. 104.

    & Are evolutionary rates really variable? J. Mol. Evol. 13, 27–34 (1979).

  105. 105.

    & The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times. Curr. Zool. 61, 874–885 (2015).

  106. 106.

    Evolutionary rate at the molecular level. Nature 217, 624–626 (1968).

  107. 107.

    & Non-Darwinian evolution. Science 164, 788–798 (1969).

  108. 108.

    Enzyme polymorphism in man. Proc. R. Soc. B. Biol. Sci. 164, 298–310 (1966).

  109. 109.

    & A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54, 595–609 (1966).

  110. 110.

    in Mathematical Proceedings of the Cambridge Philosophical Society 838–844 (Cambridge Univ Press, 1927).

  111. 111.

    Prepondence of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267, 275–276 (1977).

  112. 112.

    The Causes of Molecular Evolution (Oxford Univ. Press, 1991).

  113. 113.

    Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39, 105–111 (1994).

  114. 114.

    Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39, 306–314 (1994).

  115. 115.

    et al. Constraints on the timescale of animal evolutionary history. Palaeo. Electronica 18.1.1FC (2015).

  116. 116.

    , , , & Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution. Nature 453, 775–778 (2008).

  117. 117.

    Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25, 471–492 (1973).

  118. 118.

    Estimating the rate of molecular evolution: incorporating non-comptemporaneous sequences into maximum likelihood phylogenetics. Bioinformatics 16, 395–399 (2000).

  119. 119.

    , , , & Measurably evolving populations. Trends Ecol. Evol. 18, 481–488 (2003).

  120. 120.

    & Dating phylogenies with sequentially sampled tips. Syst. Biol. 62, 674–688 (2013).

  121. 121.

    , , & Fast dating using least-squares criteria and algorithms. Syst. Biol. syv068 (2015).

  122. 122.

    et al. Characterization of the 1918 influenza virus polymerase genes. Nature 437, 889–893 (2005).

  123. 123.

    , , & Charting the host adaptation of influenza viruses. Mol. Biol. Evol. 28, 1755–1767 (2011).

  124. 124.

    et al. Timing the ancestor of the HIV-1 pandemic strains. Science 288, 1789–1796 (2000).

  125. 125.

    et al. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 455, 661–664 (2008).

  126. 126.

    et al. Rise and fall of the Beringian steppe bison. Science 306, 1561–1565 (2004).

  127. 127.

    et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78 (2013).

  128. 128.

    et al. Mid-Pliocene warm-period deposits in the High Arctic yield insight into camel evolution. Nat. Commun. 4, 1550 (2013).

  129. 129.

    et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).

  130. 130.

    , & Reconstructing ancient genomes and epigenomes. Nat. Rev. Genet. 16, 395–408 (2015).

  131. 131.

    et al. Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324, 626–631 (2009).

  132. 132.

    et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comp. Biol. 10, e1003537 (2014).

  133. 133.

    A hierarchical Bayesian model for calibrating estimates of species divergence times. Syst. Biol. 61, 793–809 (2012).

  134. 134.

    PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).

  135. 135.

    et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).

  136. 136.

    , & PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288 (2009).

  137. 137.

    , , & PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).

  138. 138.

    & in Statistical Methods in Molecular Evolution (ed. Nielsen, R.) 233–256 (Springer-Verlag, 2005).

  139. 139.

    r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301–302 (2003).

  140. 140.

    & treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28, 2689–2690 (2012).

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Acknowledgements

This work was supported by Biotechnology and Biosciences Research Council (UK) grant BB/J009709/1. M.d.R. wishes to thank the National Evolutionary Synthesis Center, USA, National Science Foundation #EF-0905606, for its support during his research on morphological evolution.

Author information

Affiliations

  1. Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.

    • Mario dos Reis
    •  & Ziheng Yang
  2. School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.

    • Mario dos Reis
  3. School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.

    • Philip C. J. Donoghue

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Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Mario dos Reis or Ziheng Yang.

Glossary

Molecular clock

The hypothesis that the rate of molecular evolution is constant over time or among species. Thus, mutations accumulate at a uniform rate after species divergence, keeping time like a timepiece.

Tree of Life

The evolutionary tree depicting the relationships among all the living species of organisms, calibrated to the geological time.

Likelihood

The probability of the observed data given the model parameters viewed as a function of the parameters with the data fixed. In Bayesian clock dating, likelihood is calculated using the sequence data (and possibly morphological data) under a model of character evolution.

Fossil-age calibrations

Constraints on the timing of lineage divergence in molecular clock dating. They are established through fossil-based minimum and maximum constraints on clade ages (node calibrations) or through the inclusion of dated fossil species in the analysis (tip calibrations).

Clade

A group of species descended from a common ancestor.

Bayesian methods

Statistical inference methodologies in which statistical distributions are used to represent uncertainties in model parameters. In Bayesian clock dating, priors on times and rates are combined with the likelihood (the probability of the sequence data) to produce the posterior of times and rates.

Neutral theory

Also termed the neutral mutation-random drift theory; claims that evolution at the molecular level is mainly random fixation of mutations that have little fitness effect.

Neutral mutations

Mutations that do not affect the fitness (survival or reproduction) of the individual.

Advantageous mutations

Mutations that improve the fitness of the carrier and are favoured by natural selection.

Deleterious mutations

Mutations that reduce the fitness of the carrier and are removed from the population by negative selection.

Substitution

Mutations that spread into the population and become fixed, driven either by chance or by natural selection.

Relaxed clock models

Models of evolutionary rate drift over time or across lineages developed to relax the molecular clock hypothesis.

Prior probability distributions

Distributions assigned to parameters before the analysis of the data. In Bayesian clock dating, the prior on divergence times is specified using a branching model, possibly incorporating fossil calibration information, and the prior on evolutionary rates is specified using a model of rate drift (a relaxed-clock model).

Morphological characters

Discrete features or continuous measurements of different species that are informative about phylogenetic relationships.

Phylogeny

A tree structure representing the evolutionary relationship of the species.

Posterior probability distribution

The distribution of the parameters (or models) after analysis of the observed data. It combines the information in the prior and in the data (likelihood).

Likelihood-ratio test

A general hypothesis-testing method that uses the likelihood to compare two nested hypotheses, often using the χ2.

Markov Chain Monte Carlo algorithm

(MCMC algorithm). A Monte Carlo simulation algorithm that generates a sample from a target distribution (often a Bayesian posterior distribution).

Jukes–Cantor model

A model of nucleotide substitution in which the rate of substitution between any two nucleotides is the same.

Soft bounds

Minimum or maximum constraints on a node age with small error probabilities (such as 1% or 5%) used as bounds in clock dating.

Parsimony-informative characters

A discrete character is informative to the parsimony method of phylogenetic reconstruction if at least two states are observed among the species, each state at least twice.

Coalescent

The process of lineage joining when one traces the genealogical relationships of a sample backwards in time.

K-Pg boundary

The boundary between Cretaceous and Paleogene at 66 Ma. It coincides with a mass extinction, including that of the dinosaurs and many more species.

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https://doi.org/10.1038/nrg.2015.8

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