Measured, modeled, and causal conceptions of fitness

Frontiers in Genetics

Volumn 3, Issue OCT, 2012, Pages

  Abrams, Marshall ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

Causality; Darwinian evolution; FST; Fitness; Natural; Probability; Selection; Simulations

Indexed keywords

EID: 84876155403     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00196     Document Type: Review

References (75)

1. Abrams, M. (2006). Infinite populations and counterfactual frequencies in evolutionary theory. Stud. Hist. Philos. Biol. Biomed. Sci. 37,256-268.
2. Abrams, M. (2007). Fitness and propensity's annulment? Biol. Philos. 22, 115-130.
3. Abrams, M. (2009a). Fitness "kinematics": altruism, biological function, and organism-environment histories. Biol. Philos. 24, 487-504.
4. Abrams, M. (2009b). The unity of fitness. Philos. Sci. 76, 750-761.
5. Abrams, M. (2009c). What determines fitness? The problem of the reference environment. Synthese 166, 21-40.
6. ST for the role of probability and causation in evolution. Philos. Sci. 79. (in press).
7. Abrams, M. (2012b). Mechanistic probability. Synthese 187, 343-375.
8. Abrams, M. (2012c). "Mechanistic social probability: how individual choices and varying circumstances produce stable social patterns," in Oxford Handbook of Philosophy of Social Science, ed H. Kincaid (Oxford, NY: Oxford University Press), 184-226.
9. Antonovics, J., Clay, K., and Schmitt, J. (1987). The measurement of small-scale environmental heterogeneity using clonal transplants of Anthoxanthum odoratum and Danthonia spicata. Oecologia 71, 601-607.
10. Ariew, A., and Ernst, Z. (2009). What fitness can't be. Erkenntnis 71, 289-301.
11. Ariew, A., and Lewontin, R. C. (2004). The confusions of fitness. Br. J. Philos. Sci. 55, 347-363.
12. Beatty, J., and Finsen, S. (1989). "Rethinking the propensity interpretation: a peek inside Pandora's box," in What the Philosophy of Biology is, ed M. Ruse (Dordrecht, the Netherlands: Kluwer Academic Publishers), 17-30.
13. Bouchard, F., and Rosenberg, A. (2004). Fitness, probability, and the principles of natural selection. Br. J. Philos. Sci. 55, 693-712.
14. Brandon, R. N. (1978). Adaptation and evolutionary theory. Stud. Hist. Philos. Sci. 9, 181-206.
15. Brandon, R. N. (1990). Adaptation and Environment. Princeton, NJ: Princeton University.
16. Byars, S. G., Ewbank, D., Govindaraju, D. R., and Stearns, S. C. (2010). Natural selection in a contemporary human population. Proc. Natl. Acad. Sci. U.S.A. 107(Suppl. 1), 1789-1792.
17. Byerly, H. C., and Michod, R. E. (1991). Fitness and evolutionary explanation. Biol. Philos. 6, 1-22.
18. Cooper, T. F., Rozen, D. E., and Lenski, R. E. (2003). Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 100, 1072-1077.
19. Darwin, C. (1964 [1859]). On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, 1st Edn. Cambridge, MA; London: Harvard University Press. With an introduction by Ernst Mayr.
20. de Jong, G. (1994). The fitness of fitness concepts and the description of natural selection. Q. Rev. Biol. 69, 3-29.
21. de Valpine, P. (2000). A new demographic function maximized by life-history evolution. Proc. R. Soc. Lond. B Biol. Sci. 267, 357-362.
22. Eagle, A. (2004). Twenty-one arguments against propensity analyses of probability. Erkenntnis 60, 371-416.
23. Endler, J. A. (1986). Natural Selection in the Wild. Princeton, NJ: Princeton University Press.
24. Elena, S. F., and Lenski, R. E. (2003). Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4, 457-469.
25. Ewens, W. J. (2004). Mathematical Population Genetics, I. Theoretical Introduction, 2nd Edn. New York, NY: Springer.
26. Gillespie, J. H. (2004). Population Genetics: A Concise Guide, 2nd Edn. Baltimore, London: The Johns Hopkins University Press.
27. Godfrey-Smith, P. (2009). Darwinian Populations and Natural Selection. Oxford, New York: Oxford University Press.
28. Hájek, A. (2010). "Interpretations of probability," in The Stanford Encyclopedia of Philosophy, Spring 2010 Edn, ed E. N. Zalta. Available online at: http://plato.stanford.edu/archives/spr2010/entries/probability-interpret/
29. Haug, M. C. (2007). Of mice and metaphysics: natural selection and realized population-level properties. Philos. Sci. 74,431-451.
30. Holsinger, K. E., and Weir, B. S. (2009). Genetics in geographically structure populations: defining, estimating and interpreting FST. Nat. Rev. Genet. 10, 639-650.
31. Huff, C. D., Witherspoon, D. J., Zhang, Y., Gatenbee, C., Denson, L. A., Kugathasan, S., et al. (2012). Crohn's disease and genetic hitchhiking at IBD5. Mol. Biol. Evol. 29, 101-111.
32. Hutchinson, G. E. (1957). Concluding remarks. Cold Spring Harb. Symp. Quant. Biol. 22,415-427.
33. Jablonka, E., and Lamb, M. J. (2006). Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge, MA; London: MIT Press.
34. Lenski, R. E., Rose, M. R., Simpson, S. C., and Tadler, S. C. (1991). Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am. Nat. 138, 1315-1341.
35. Lewontin, R. C. (1970). The units of selection. Annu. Rev. Ecol. Syst. 1, 1-18.
36. Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., et al. (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100-1104.
37. Lynch, M., and Walsh, B. (1998). Genetics and Analysis of Quantitative Traits. Sunderland, MA: Sinauer.
38. Matthen, M. (2009). Drift and 'statistically abstractive explanation'. Philos. Sci. 76, 464-487.
39. Matthen, M., and Ariew, A. (2009). Selection and causation. Philos. Sci. 76, 201-224.
40. Metz, J. A. J. (2008). "Fitness," in Encyclopedia of Ecology, Vol. 2, eds S. E. Jørgensen and B. D. Fath (Oxford: Elsevier), 1599-1612.
41. Michod, R. E. (1999). Darwinian Dynamics. Princeton, NJ: Princeton.
42. Mills, S., and Beatty, J. (1979). The propensity interpretation of fitness. Philos. Sci. 46, 263-286.
43. Millstein, R. L. (2003). Interpretations of probability in evolutionary theory. Philos. Sci. 70, 1317-1328.
44. Millstein, R. L., Skipper, R. A., and Dietrich, M. A. (2009). (Mis)interpreting mathematical models: drift as a physical process. Philos. Theory Biol. 1. Available online at: http://hdl. handle.net/2027/spo.6959004.0001. 002. [Accessed February 13, 2011].
45. Moreno-Estrada, A., Tang, K., Sikora, M., Marquès-Bonet, T., Casals, E, Navarro, A., et al. (2009). Interrogating 11 fast-evolving genes for signatures of recent positive selection in worldwide human populations. Mol. Biol. Evol. 26, 2285-2297.
46. Morris, J. J., Lenski, R. E., and Zinser, E. R. (2012). The black queen hypothesis: evolution of dependencies through adaptive gene loss. MBio 3, 1-7.
47. Nagylaki, T. (1992). Introduction to Theoretical Population Genetics. Berlin, Heidelberg, New York: Springer-Verlag.
48. Nei, M., and Kumar, S. (2000). Molecular Evolution and Phylogenetics. Oxford, New York: Oxford University Press.
49. Northcott, R. (2009). Walsh on causes and evolution. Philos. Sci. 77, 457-467.
50. Otsuka, J., Turner, T., Allen, C., and Lloyd, E. A. (2011). Why the causal view of fitness survives. Philos. Sci. 78, 209-224.
51. Pfennig, K. S. (2000). Female spadefoot toads compromise on mate quality to ensure conspecific matings. Behav.Ecol. 11,220-227.
52. Popper, K. R. (1959). The propensity interpretation of probability. Br. J. Philos. Sci. 10, 25-42.
53. Price, G. R. (1970). Selection and covariance. Nature 227, 520-521.
54. Ramsey, G. (2006). Block fitness. Stud. Hist. Philos. Biol. Biomed. Sci. 37, 484-498.
55. Reeve, H. K., and Sherman, P. W. (1993). Adaptation and the goals of evolutionary research. Q. Rev. Biol. 68, 1-32.
56. Reisman, K., and Forber, P. (2005). Manipulation and the causes of evolution. Philos. Sci. 72, 1113-1123.
57. Rice, S. H. (2004). Evolutionary Theory: Mathematical and Conceptual Foundations. Sunderland, MA: Sinauer Associates.
58. Rosenthal, J. (2010). "The natural-range conception of probability," in Time, Chance, and Reduction: Philosophical Aspects of Statistical Mechanics, eds G. Ernst and A. Hüttemann (Cambridge, UK; New York: Cambridge University Press), 71-90.
59. Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., et al. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature 449, 4913-919.
60. Scheinfeldt, L. B., Biswas, S., Madeoy, J., Connelly, C. F., and Akey, J. (2011). Clusters of adaptive evolution in the human genome. Front. Genet. 2:50. doi: 10.3389/fgene.2011.00050
61. Shapiro, L., and Sober, E. (2007). "Epiphenomenalism-the do's and the don'ts," in Thinking About Causes: From Greek Philosophy to Modern Physics, eds G. Wolters and P. Machamer (Pittsburgh, PA: University of Pittsburgh), 235-264.
62. Shaw, R. G., Geyer, C. J., Wagenius, S., Hangelbroek, H. H., and Etterson, J. R. (2008). Unifying life-history analyses for inference of fitness and population growth. Am. Nat. 172, E35-E47.
63. Sober, E. (1984). The Nature of Selection. Cambridge, MA; London: MIT Press.
64. Spitze, K. (1993). Population structure in Daphnia obtusa: quantitative genetic and allozymic variation. Genetics 135, 367-374.
65. Stearns, S. C. (1976). Life-history tactics: a review of the ideas. Q. Rev. Biol. 51,3-47.
66. Stearns, S. C. (1992). The Evolution of Life Histories. Oxford, New York: Oxford University Press.
67. Steiner, U. K., and Tuljapurkar, S. (2012). Neutral theory for life histories and individual variability in fitness components. Proc. Natl. Acad. Sci. U.S.A. 109, 4684-4689.
68. Strevens, M. (2011). "Probability out of determinism," in Probabilities in Physics, eds C. Beisbart and S. Hartmann (Cambridge, MA; London: Oxford University Press), 339-364.
69. Walsh, D. M. (2007). The pomp of superfluous causes: the interpretation of evolutionary theory. Philos. Sci. 74,281-303.
70. Walsh, D. M. (2010). Not a sure thing: fitness, probability, and causation. Philos. Sci. 77, 141-171.
71. Weir, B. S. (1996). Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sunderland, MA: Sinauer.
72. Weir, B. S., and Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370.
73. Weir, B. S., and Hill, W. G. (2002). Estimating F-statistics. Annu. Rev. Genet. 36,721-750.
74. Woodward, J. (2003). Making Things Happen. Oxford, New York: Oxford University Press.
75. Woodward, J. (2011). "Scientific explanation," in The Stanford Encyclopedia of Philosophy, Winter 2011 Edn, ed E. N. Zalta. Available online at: http://plato.stanford.edu/archives/win2011/entries/scientific-explanation/