Evolutionary Dynamics Bibliography (fledgling)

Caveat:

Don't see your papers here? Key reviews, classic papers, and new results missing?

Fine. What follows below is the beginning of a cooperative project to develop a bibliography for evolutionary dynamics.

Please send those essential missing books, reviews, papers, and web site URLs to Jim Crutchfield promptly and they will be added. Thanks!

Web Sites

• Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Austria.
• Department of Molecular Information Processing, IMB Jena.
• Santa Fe Institute Publications.
• University of Sussex Neutral Networks Bibliography.

Books

• Bell, G., Selection: The Mechanism of Evolution, Intl Thomson Publishing, New York (1997).
• Crow, J. F., and M. Kimura, An Introduction to Population Genetics Theory, Harper & Row, New York (1970).
• Darwin, C. Origin of Species, on-line version.
• Eigen, M., and R. Winkler, Laws of the Game: How the Principles of Nature Govern Chance, translated by Robert and Rita Kimber, Knopf, New York (1981).
• Gurney, W. S. C., and R. M. Nisnet, Ecological Dynamcis, Oxford University Press, New York (1998).
• Hofbauer, J., and K. Sigmund, The Theory of Evolution and Dynamical Systems, London Mat. Soc. Student Texts 7, Cambridge University Press, Cambridge, United Kingdom (1988).
• Kauffman, S. A., The Origins of Order---Self-Organization and Selection in Evolution, Oxford University Press, New York (1993).
• Keller, E. F, and E. A. Lloyd, Keywords in Evolutionary Biology, Harvard University Press, Cambridge, Massachusetts (1992).
• Kimura, M., The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge, United Kingdom (1983).
• Maynard-Smith, J., and E. Szathmary, The Major Transitions in Evolution, Oxford University Press, New York, (1995).
• Ohno, S., Evolution by Gene Duplication, Springer-Verlag, New York (1970).
• Royama, T., Analytical Population Dynamics, Population and Community Biology Series 10, Chapman and Hall, London (1992).
• Salthe, S. N., Development and Evolution---Complexity and Change in Biology, Bradford Books, MIT Press, Cambridge, Massachusetts (1993).
• Weibull, J. W., Evolutionary Game Theory, MIT Press, Cambridge, Massachusetts (1996).

Reviews

• Eigen, M., J. McCaskill, and P. Schuster, ``The Molecular Quasispecies'', Adv. Chem. Phys. 75 (1989) 149-263.
• Peliti, L., Fitness Landscapes and Evolution, NATO ASI on Physics of Biomaterials: Fluctuations, Self-Organization and Evolution, Geilo, Norway, March 27, April 6, 1995.
• Schuster, P., ``Landscapes and Molecular Evolution'', Physica D 107 (1997) 351-365.
• Schwarz, G., and A. Watts, Biophysical Chemistry 66, issues 2-3 (1997); a collection of reviews in honor of Manfred Eigen.

Papers

• Arthur, W. B., J. H. Holland, B. LeBaron, R. G. Palmer, P. J. Taylor, ``Asset Pricing under Endogenous Expectations in an Artificial Stock Market'', In: The Economy as an Evolving Complex System II, Santa Fe Institute Series in the Sciences of Complexity. Santa Fe Institute Preprint 96-12-093, Santa Fe, NM (1996).
• A. Babajide, I.L. Hofacker, M.J. Sippl and P.F. Stadler, ``Neutral Networks in Protein Space: A Computational Study Based on Knowledge-Based Potentials of Mean Force'', Folding and Design 2 (1997) 261-269. Santa Fe Institute Preprint 96-11-099, Santa Fe, NM (1996).
• Banzhaf, W., ``Genotype-Phenotype Mapping and Neutral Variation---A Case Study in Genetic Programming'', Proc. Parallel Problem Solving from Nature III, Y. Davidor, H.-P. Schwefel, and R. Männer (Eds.), Springer, Berlin (1994) 322-332.
• Barnett, L., Tangled Webs: Evolutionary Dynamics on Fitness Landscapes with Neutrality, MSc. in Evolutionary and Adaptive Systems, COGS, Sussex (1997), Gzip'd PostScript (771Kb).
• Baskaran, S., P. F. Stadler, and P. Schuster, ``Approximate Scaling Properties of RNA Free Energy Landscapes'', Santa Fe Institute Preprint 95-10-083, Santa Fe, NM (1995).
• Binmore, K. and L. Samuelson, ``Evolutionary Drift and Equilibrium Selection'', ELSE Working paper.
• Boerlijst, M. C., S. Bonhoeffer, and M. A. Nowak, ``Viral Quasispecies and Recombination'', Proc. R. Soc. Lond. B 263 (1996) 1577-1584.
• Bonhoeffer, S. and P. F. Stadler, ``Error Thresholds on Complex Landscapes'', J. Theo. Biol. 164 (1993) 359-372.
• Bornholdt, S., ``Genetic Algorithm Dynamics on a Rugged Fitness Landscape'', Phys. Rev. E 57 (1998) 3853. AIP Version.
• Bornholdt, S., and K. Sneppen, ``Neutral Mutations and Punctuated Equilibrium in Evolving Genetic Networks'', Phys. Rev. Lett. 81 (1998) 236. AIP Version.
• J. Cupal, C. Flamm, A. Renner, P.F. Stadler, ``Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule'', In: Proceedings of ISMB-97 , T. Gaasterland, P. Karp, K. Karplus, Ch. Ouzounis, Ch. Sander, A. Valencia (Eds.) AAAI Press (1997) 88-91. Santa Fe Institute Preprint 97-02-07, Santa Fe, NM (1997).
• Darley, V., and S.A. Kauffman, ``Natural Rationality'', In: The Economy as an Evolving Complex System II, Santa Fe Institute Series in the Sciences of Complexity. Santa Fe Institute Preprint 96-08-071, Santa Fe, NM (1996).
• Derrida, B. and L. Peliti, ``Evolution in a Flat Landscape'', Bull. Math. Biol. 53 (1991) 355-382.
• Fontana, W., and P. Schuster, ``Continuity in Evolution: On the Nature of Transitions'', Science 280 (1998) 1451-1455. Santa Fe Institute Preprint 98-04-030, Santa Fe, NM (1998).
• Forst, C. V., C. Reidys, and J. Weber, Evolutionary Dynamics and Optimization: Neutral Networks as Model-Landscapes for RNA Secondary-Structure Folding-Landscapes. Lecture Notes in Artificial Intelligence 929, Advances in Artificial Life, Morán, F., A. Moreno, J. J. Merelo, and Chacón, eds., Springer-Verlag, Berlin (1995); TBI Working Paper 95-10-14.
• R. Garcma-Pelayo and P. F. Stadler, ``Correlation Length, Isotropy, and Meta-stable States'', Physica D 107 (1997) 240-254. Santa Fe Institute Preprint 97-01-01, Santa Fe, NM (1997).
• Gavrilets, S., ``Evolution and Speciation on Holey Adaptive Landscapes'', Trends in Ecology and Evolution 12 (1997) 307-312.
• Gavrilets, S. and J. Gravner, ``Percolation on the Fitness Hypercube and the Evolution of Reproductive Isolation'', J. Theor. Biol. 184 (1996) 51-64.
• Gavrilets, S. and A. Hastings , ``Intermittency and Transient Chaos from Simple Frequency-Dependent Selection'', Proc. Roy. Soc Lond. Series B 261 (1995) 233-238.
• Gruener, W., R. Giegerich, D. Strothmann, C. Reidys, J. Weber, I. L. Hofacker, P. F. Stadler, and P. Schuster, ``Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration'', Part One: Neutral Networks, Monatsh. Chem. 127 (1996) 355-374 and Part Two: Structure of Neutral Networks and Shape Space Covering, Monatsh. Chem. 127 (1996) 375-389.
• Hordijk, W. and P. F. Stadler, ``Amplitude Spectra of Fitness Landscapes'', J. Complex Systems (1998) in press. Santa Fe Institute Preprint 98-03-002, Santa Fe, NM (1997).
• Huynen, M. A., ``Exploring Phenotype Space through Neutral Evolution'', Santa Fe Institute Working Paper 95-10-100, Santa Fe, NM (1995).
• Huynen, M. A., P. F. Stadler, and W. Fontana, ``Smoothness Within Ruggedness: The Role of Neutrality in Adaptation''. Proc. Natl. Acad. Sci. 93 (1996) 397-401.
• Kimura M., ``The neutral theory of molecular evolution'', Sci. Am. 241 (1979) 94-104.
• Newman, M. E. J., and R. Engelhardt, R., ``Effects of Neutral Selection on the Evolution of Molecular Species'', Proc. Roy. Soc. London Series B 265 (1998) 1333-1338. Santa Fe Institute Working Papers 98-01-001, Santa Fe, NM (1998)
• van Nimwegen, E., J. P. Crutchfield, and M. Mitchell, ``Statistical Dynamics of the Royal Road Genetic Algorithm'', Theo. Comp. Sci. (1998) in press. Santa Fe Institute Preprint 97-04-035, Santa Fe, NM, USA.
• van Nimwegen, E., J. P. Crutchfield, and M. Mitchell, ``Finite Populations Induce Metastability in Evolutionary Search'', Phys. Lett. A 229 (1997) 144-150. Santa Fe Institute Working Paper 96-08-054.
• Nowak, M. and P. Schuster, P., ``Error Thresholds of Replication in Finite Populations---Mutation Frequencies and the Onset of Muller's Ratchet'', J. Theor. Biol. 137 (1989) 375-395.
• Ohta, T., ``Slightly Deleterious Mutant Substitutions in Evolution'', Nature 246 (1973) 96-98.
• Ohta, T., ``Role of Very Slightly Deleterious Mutations in Molecular Evolution and Polymorphism'', Theo. Pop. Biol. 10 (1976) 254-275.
• Ohta, T. and J. H. Gillespie, ``Development of Neutral and Nearly Neutral Theories'', Theo. Pop. Biol. 49 (1996) 128-142.
• Reidys, C. M. and S. M Fraser, ``Evolution on Random Structures'', Santa Fe Institute Preprint 95-11-087, Santa Fe, NM (1995).
• Reidys, C. M., P. F. Stadler, and P. Schuster, P., ``Generic Properties of Combinatory Maps---Neutral Networks of RNA Secondary Structures'', Bull. Math. Biol. 59 (1997) 339-397. Santa Fe Institute Preprint 95-07-04, Santa Fe, NM (1995).
• Schuster, P., W. Fontana, P. F. Stadler, and I. L. Hofacker, ``From Sequences to Shapes and Back---A Case Study in RNA Secondary Structures'', Proc. Roy. Soc. London Series B 255 (1994) 279-284.
• Schuster, P., ``How Does Complexity Arise in Evolution?'', Complexity 2 (1996) 22-30. TBI Working paper 96-05-026.
• Stadler, P. F., ``Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers'', J. Mol. Struct. (THEOCHEM) (1998) in press. Santa Fe Institute Preprint 97-09-001, Santa Fe, NM (1997).
• Stadler, P. F., and R. Happel, ``Random Field Models for Fitness Landscapes'', J. Math. Bio. (1998) in press. Santa Fe Institute Preprint 95-07-09, Santa Fe, NM (1995).
• Stadler, P. F., and G. P. Wagner, ``The Algebraic Theory of Recombination Spaces'', Evol. Comp. 5 (1998) 241-275. Santa Fe Institute Preprint 97-11-082, Santa Fe, NM (1996).
• Stadler, P. F., ``Landscapes and their Correlation Functions'', J. Math. Chem. 20 (1996) 1-45. Santa Fe Institute Preprint 95-07-067, Santa Fe, NM (1995).
• Suzuki, H., ``The Optimum Recombination Rate that Realizes the Fastest Evolution of a Novel Functional Combination of Many Genes'', Theo. Pop. Bio. 51 (1997) 185-200.
• Wagner, G. P., and P. F. Stadler, ``Complex Adaptations and the Structure of Recombination Spaces'', In: Proceedings of the Conference on Semi-Groups and Algebraic Engineering University of Aizu, Japan (1998) in press. Santa Fe Institute Preprint 97-03-029, Santa Fe, NM (1997).
• Weinberger, E. D., ``Correlated and Uncorrelated Fitness Landscapes and How to Tell the Difference'', Biol. Cyber. 63 (1990) 325-336.
• Woodcock, G. and P. G. Higgs, P. G., ``Population Evolution in a Single Peak Fitness Landscape---How High are the Clouds?'', Lecture Notes in Artificial Intelligence 929, Advances in Artificial Life, Morán, F., A. Moreno, J. J. Merelo, and Chacón, eds., Springer-Verlag, Berlin (1995) 148-157.