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Locating uncertainty in stochastic evolutionary models: divergence time estimation

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  1. Abrams Marshall, What determines biological fitness? The problem of the reference environment, 10.1007/s11229-007-9255-9
  2. Abrams Marshall, Measured, modeled, and causal conceptions of fitness, 10.3389/fgene.2012.00196
  3. Abrams Marshall, Mechanistic probability, 10.1007/s11229-010-9830-3
  4. Abrams Marshall, Probability and Manipulation: Evolution and Simulation in Applied Population Genetics, 10.1007/s10670-015-9784-4
  5. Ariew A., The Confusions of Fitness, 10.1093/bjps/55.2.347
  6. Baker Alan, Mathematical Spandrels, 10.1080/00048402.2016.1262881
  7. Beatty John, Desjardins Eric Cyr, Natural selection and history, 10.1007/s10539-008-9149-3
  8. Benton MJ, Donoghue PCJ, Asher RJ (2009) Calibrating and constraining molecular clocks. In: Hedges SB, Kumar S (eds) The timetree of life. Oxford University Press, Oxford, pp 35–86
  9. Brandon RN (1990) Adaptation and environment. Princeton University Press, Princeton
  10. Brandon Robert N., Ramsey Grant, What’s Wrong with the Emergentist Statistical Interpretation of Natural Selection and Random Drift?, The Cambridge Companion to the Philosophy of Biology ISBN:9781139001588 p.66-84, 10.1017/ccol9780521851282.004
  11. Desjardins Eric, Reflections on Path Dependence and Irreversibility: Lessons from Evolutionary Biology, 10.1086/662560
  12. Desjardins E (2016) Contingent evolution: not by chance alone. In: Ramsey G, Pence CH (eds) Chance in evolution. University of Chicago Press, Chicago, pp 223–243
  13. DOS REIS Mario, YANG Ziheng, The unbearable uncertainty of Bayesian divergence time estimation : Uncertainty in divergence time estimation, 10.1111/j.1759-6831.2012.00236.x
  14. Drouet Isabelle, Merlin Francesca, The Propensity Interpretation of Fitness and the Propensity Interpretation of Probability, 10.1007/s10670-014-9681-2
  15. Drummond Alexei J, Ho Simon Y. W, Phillips Matthew J, Rambaut Andrew, Relaxed Phylogenetics and Dating with Confidence, 10.1371/journal.pbio.0040088
  16. Earman J (2007) Aspects of determinism in modern physics. In: Butterfield J, Earman J (eds) Handbook of the philosophy of science: philosophy of physics. North-Holland, Amsterdam, pp 1369–1434
  17. Endler JA (1986) Natural selection in the wild. Princeton University Press, Princeton
  18. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland
  19. Foley A.M., Uncertainty in regional climate modelling: A review, 10.1177/0309133310375654
  20. Gillespie John H., MOLECULAR EVOLUTION OVER THE MUTATIONAL LANDSCAPE, 10.1111/j.1558-5646.1984.tb00380.x
  21. Gillespie JH (1991) The causes of molecular evolution. Oxford University Press, Oxford
  22. Graur Dan, Martin William, Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision, 10.1016/j.tig.2003.12.003
  23. Graves Leslie, Horan Barbara L., Rosenberg Alex, Is Indeterminism the Source of the Statistical Character of Evolutionary Theory?, 10.1086/392680
  24. Halpern A. L., Bruno W. J., Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies, 10.1093/oxfordjournals.molbev.a025995
  25. Hasegawa Masami, Kishino Hirohisa, Yano Taka-aki, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, 10.1007/bf02101694
  26. JUKES THOMAS H., CANTOR CHARLES R., Evolution of Protein Molecules, Mammalian Protein Metabolism (1969) ISBN:9781483232119 p.21-132, 10.1016/b978-1-4832-3211-9.50009-7
  27. Lenormand Thomas, Roze Denis, Rousset François, Stochasticity in evolution, 10.1016/j.tree.2008.09.014
  28. Lepage T., Bryant D., Philippe H., Lartillot N., A General Comparison of Relaxed Molecular Clock Models, 10.1093/molbev/msm193
  29. Linder Martin, Britton Tom, Sennblad Bengt, Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence, 10.1093/sysbio/syr009
  30. Matthen Mohan, Drift and “Statistically Abstractive Explanation”*, 10.1086/648063
  31. Matthen Mohan, Ariew André, , Two Ways of Thinking About Fitness and Natural Selection : , 10.2307/3655552
  32. Merlin F (2010) Evolutionary chance mutation: a defense of the modern synthesis’ consensus view. Philos Theory Biol 2:e103
  33. Merlin F (2016) Weak randomness at the origin of biological variation: the case of genetic mutations. In: Ramsey G, Pence CH (eds) Chance in evolution. University of Chicago Press, Chicago, pp 176–195
  34. Millstein Roberta L., Interpretations of Probability in Evolutionary Theory, 10.1086/377410
  35. Millstein Roberta L., Natural Selection as a Population-Level Causal Process, 10.1093/bjps/axl025
  36. Millstein Roberta L., Distinguishing Drift and Selection Empirically: “The Great Snail Debate” of the 1950s, 10.1007/s10739-007-9145-5
  37. Millstein Roberta L., Chances and causes in evolutionary biology: How many chances become one chance, Causality in the Sciences (2011) ISBN:9780199574131 p.425-444, 10.1093/acprof:oso/9780199574131.003.0020
  38. Millstein RL (2016) Probability in biology: the case of fitness. In: Hájek A, Hitchcock C (eds) The Oxford handbook of probability and philosophy. Oxford University Press, Oxford, pp 601–622
  39. Mulcahy Daniel G., Noonan Brice P., Moss Travis, Townsend Ted M., Reeder Tod W., Sites Jack W., Wiens John J., Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles, 10.1016/j.ympev.2012.08.018
  40. Nascimento Fabrícia F., Reis Mario dos, Yang Ziheng, A biologist’s guide to Bayesian phylogenetic analysis, 10.1038/s41559-017-0280-x
  41. Otsuka Jun, A critical review of the statisticalist debate, 10.1007/s10539-016-9528-0
  42. Pence Charles H., Is genetic drift a force?, 10.1007/s11229-016-1031-2
  43. Pence C. H., Ramsey G., A New Foundation for the Propensity Interpretation of Fitness, 10.1093/bjps/axs037
  44. Rannala Bruce, Yang Ziheng, Inferring Speciation Times under an Episodic Molecular Clock, 10.1080/10635150701420643
  45. Ronquist Fredrik, Klopfstein Seraina, Vilhelmsen Lars, Schulmeister Susanne, Murray Debra L., Rasnitsyn Alexandr P., A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera, 10.1093/sysbio/sys058
  46. Rosenberg A (1994) Instrumental biology, or the disunity of science. University of Chicago Press, Chicago
  47. Sanderson M. J., A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy, 10.1093/oxfordjournals.molbev.a025731
  48. Schwartz Jeffrey H., Maresca Bruno, Do Molecular Clocks Run at All? A Critique of Molecular Systematics, 10.1162/biot.2006.1.4.357
  49. Sober Elliott, A PrioriCausal Models of Natural Selection, 10.1080/00048402.2010.535006
  50. Stamos David N., Quantum Indeterminism and Evolutionary Biology, 10.1086/392871
  51. Strevens Michael, Probability out of Determinism, Probabilities in Physics (2011) ISBN:9780199577439 p.339-364, 10.1093/acprof:oso/9780199577439.003.0013
  52. Strevens Michael, Tychomancy : Inferring Probability from Causal Structure, ISBN:9780674075986, 10.4159/harvard.9780674075986
  53. Strevens M (2016) The reference class problem in evolutionary biology: distinguishing selection from drift. In: Ramsey G, Pence CH (eds) Chance in evolution. University of Chicago Press, Chicago, pp 145–175
  54. Thorne Jeffrey L., Kishino Hirohisa, Divergence Time and Evolutionary Rate Estimation with Multilocus Data, 10.1080/10635150290102456
  55. Thorne J. L., Kishino H., Painter I. S., Estimating the rate of evolution of the rate of molecular evolution, 10.1093/oxfordjournals.molbev.a025892
  56. Turner Derek, Local Underdetermination in Historical Science*, 10.1086/426851
  57. Walsh D. M., The Pomp of Superfluous Causes: The Interpretation of Evolutionary Theory*, 10.1086/520777
  58. Walsh Denis , Lewins Tim , Ariew André, The Trials of Life: Natural Selection and Random Drift*, 10.1086/342454
  59. Walsh DM, Ariew A, Matthen M (2017) Four pillars of statisticalism. Philos Theory Pract Biol 9:1
  60. Weisberg Michael, Understanding the Emergence of Population Behavior in Individual-Based Models, 10.1086/677405
  61. Werndl Charlotte, On choosing between deterministic and indeterministic models: underdetermination and indirect evidence, 10.1007/s11229-011-9966-9
  62. Wilkinson Richard D., Steiper Michael E., Soligo Christophe, Martin Robert D., Yang Ziheng, Tavaré Simon, Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data, 10.1093/sysbio/syq054
  63. Yang Ziheng, Rannala Bruce, Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds, 10.1093/molbev/msj024
  64. Zuckerkandl Emile, Pauling Linus, Molecules as documents of evolutionary history, 10.1016/0022-5193(65)90083-4
Bibliographic reference Pence, Charles H.. Locating uncertainty in stochastic evolutionary models: divergence time estimation. In: Biology & Philosophy, Vol. 34, no.2, p. 21 (2019)
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