TOWARDS A COMPREHENSIVE DYNAMICS OF EVOLUTION:
Exploring the Interplay of Selection,
Neutrality, Accident, and Function
5-9 October 1998, Santa Fe Institute,
Santa Fe,
New Mexico
Evolutionary Dynamics Bibliography
(Don't see your papers here? Key reviews, classic papers, and new results missing?
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
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.
Jim Crutchfield
Last modified: 7 October 1998