Population Genetics, Evolutionary Genetics

Last update: 11 Dec 2024 10:06
First version: 25 October 2024

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(I'm aware the two aren't quite synonyms, but c'mon.)

I'm including things like quasi-species models here, because close enough.

See also:
• Evolutionary Biology (in general)
• Evolutionary computation
• Evolutionary Game Theory
• Historical Genetics

Recommended, big picture:
• John H. Gillespie, Population Genetics: A Concise Guide
• Josef Hofbauer and Karl Sigmund, The Theory of Evolution and Dynamical Systems: Mathematical Aspects of Selection
• John Maynard Smith, Evolutionary Genetics [Review by Danny Yee]

Recommended, big picture, historical interest:
• R. A. Fisher, The Genetical Theory of Natural Selection
• J. B. S. Haldane, The Causes of Evolution

Recommended, close-ups:
• Armen A. Allahverdyan and Chin-Kun Hu, "Replicators in Fine-grained Environment: Adaptation and Polymorphism", arxiv:0905.3297 [A cute use of averaging techniques, though the particular one they employ will I think break down if the perturbations to fitness are not strictly periodic.]
• Carl T. Bergstrom and Michael Lachmann, "The fitness value of information", q-bio.PE/0510007
• R. C. Lewontin, The Genetic Basis of Evolutionary Change
• C. M. Newman, J. E. Cohen and C. Kipnis, "Neo-darwinian evolution implies punctuated equilibria", Nature 315 (1985): 400--401
• Martin Nilsson and Nigel Snoad, "Error Thresholds for Quasispecies on Dynamic Fitness Landscapes," Physical Review Letters 84 (2000): 191--194
• Olivier Rivoire and Stanislas Leibler, "The Value of Information for Populations in Varying Environments", arxiv:1010.5092
• Nigel Snoad, Limits to Evolvability in Changing Environments [Ph.D. thesis, Australian National University, 2000]
• Erik van Nimwegen, The Statistical Dynamics of Epochal Evolution [Ph.D. thesis, University of Utrecht, 1999]

To read:
• Stevan J. Arnold, Evolutionary Quantitative Genetics [2023]
• Ellen Baake and Wilfried Gabriel, "Biological Evolution through Mutation, Selection, and Drift: An Introductory Review," cond-mat/9907372
• Ellen Baake, Hans-Otto Georgii, "Mutation, selection, and ancestry in branching models: a variational approach", q-bio.PE/0611018
• Carl Boettiger, Jonathan Dushoff and Joshua S. Weitz, "Fluctuation Domains in Adaptive Evolution", Theoretical Population Biology 77 (2010): 6--13, arxiv:1004.4233
• R. A. Blythe and A. J. McKane, "Stochastic Models of Evolution in Genetics, Ecology and Linguistics", cond-mat/0703478
• Nicolas Champagnat, Régis Ferrière, Sylvie Méléar, "Individual-based probabilistic models of adaptive evolution and various scaling approximations", math.PR/0510453
• Nicolas Champagnat and Amaury Lambert, "Evolution of discrete populations and the canonical diffusion of adaptive dynamics", math.PR/0601643
• Freddy Bugge Christiansen, Theories of Population Variation in Genes and Genomes
• Jens Christian Claussen and Arne Traulsen, "Non-Gaussian fluctuations arising from finite populations: Exact results for the evolutionary Moran process", Physical Review E 71 (2005): 025101
• Elisheva Cohen, David A. Kessler and Herbert Levine, "Recombination dramatically speeds up evolution of finite populations", q-bio.PE/0410015
• Fabio Dercole and Sergio Rinaldi, Analysis of Evolutionary Processes: The Adaptive Dynamics Approach and Its Applications
• Peter Donnelly and Stephen Leslie, "The coalescent and its descendants", arxiv:1006.1514
• Rick Durrett and Jason Schweinsberg, "A coalescent model for the effect of advantageous mutations on the genealogy of a population", math.PR/0411071
• Bryan K. Epperson, Geographical Genetics
• A. Eriksson, B. Haubold, and B. Mehlig, "Statistics of selectively neutral genetic variation," physics/0111205
• Wendell H. Fleming and Michel Viot, "Some Measure-Valued Markov Processes in Population Genetics Theory", Indiana University Mathematics Journal 28 (1979): 817--843 [JSTOR]
• Steven A. Frank, "Wright's adaptive landscape versus Fisher's fundamental theorem", arxiv:1102.3709
• John H. Gillespie, The Causes of Molecular Evolution
• Dan Graur and William Martin, "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision", Trends in Genetics 20 (2004): 80--86 [PDF reprint]
• Joachim Hermisson, Oliver Redner, Holger Wagner and Ellen Baake, "Mutation-Selection Balance: Ancestry, Load, and Maximum Principle," cond-mat/0202432
• Kavita Jain and Joachim Krug, "Evolutionary trajectories in rugged fitness landscapes", q-bio.PE/0501028 = Journal of Statistical Mechanics: Theory and Experiment (2005): P04008
• P. D. Jarvis, J. D. Bashford and J. G. Sumner, "Path integral formulation of phylogenetic branching processes", q-bio.PE/0411047
• Stanislas Leibler and Edo Kussell, "Individual histories and selection in heterogeneous populations", Proceedings of the National Academy of Sciences (USA) 107 (2010): 13183--13188
• Mohan Matthen, "Drift and 'Statistically Abstractive Explanation'", Philosophy of Science 76 (2009): 464--487
• Mitton, Selection in Natural Populations
• Martin Nilsson, "Optimal Mutation Rates on Static Fitness Landscpes", physics/0005018
• Karen M. Page and Martin A. Nowak, "Unifying Evolutionary Dynamics", Journal of Theoretical Biology 219 (2002): 93--98 [Thanks to David Krakauer]
• Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander J. Tans, "Empirical fitness landscapes reveal accessible evolutionary paths", Nature 445 (2007): 383--386
• William B. Provine
  • The Origins of Theoretical Population Genetics
  • Sewall Wright and Evolutionary Biology
• Francois Rousset, Genetic Structure and Selection in Subdivided Populations
• Tor Schoenmeyr and Claus O. Wilke, "Finite genome size can halt Muller's ratchet," physics/0109058
• Sebastian J. Schreiber, Michel Benaïm, Kolawolé A. S. Atchadé, "Persistence in fluctuating environments", arxiv:1005.2580
• Mark Stegeman and Paul Rhode, "Stochastic Darwinian equilibria in small and large populations", Games and Economic Behavior 49 (2004): 171--214
• Simon Tavaré "Ancestral Inference in Population Genetics"
• Arne Traulsen, Jens Christian Claussen, and Christoph Hauert, "Coevolutionary Dynamics: From Finite to Infinite Populations", Physical Review Letters 95 (2005): 238701
• Arne Traulsen, Jorge M. Pacheco and Lorens A. Imhof, "Stochasticity and evolutionary stability", q-bio.PE/0609021 = Physical Review E 74 (2006): 021905
• Claus O. Wilke
  • "Adaptive evolution on neutral networks," physics/0101021
  • "Selection for Fitness vs. Selection for Robustness in RNA Secondary Structure Folding," physics/0103022
• Claus O. Wilke and D. Allan Drummond, "Population genetics of translational robustness", q-bio.PE/0509031
• Claus O. Wilke, Christopher Ronnewinkel and Thomas Martinetz, "Dynamic Fitness Landscapes in Molecular Evolution," physics/9912012