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Guidelines

Week 1

Preliminary reading

• Introduction to Evolution: Mechanisms, Microevolution, and the big issues, from Understanding Evolution by the University of California Museum of Paleontology.

Models in Biology

• Levins R (1966) The strategy of model builidng in population biology. Am Sci 54(3):421–431.
• Plutynski A (2007) Strategies of Model Building in Population Genetics. Philos Sci 73(5):755–764.
• Gunawardena J (2013) Biology is more theoretical than physics. Mol Biol Cell 24(12):1827–1829.

Week 2

Preliminary reading

• Lynch M (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci 104(Suppl 1):8597–604. doi:10.1073/pnas.0702207104.

Mutational load

• Kimura, M. and Maruyama, T. (1966) The mutational load with epistatic gene interactions in fitness. Genetics 54(6), 1337–51

Week 3

Preliminary reading

• None

Evolution of dominance

• Fisher RA (1930) The Genetical Theory of Natural Selection (Clarendon Press, Oxford).
• Haldane JBS (1939) The theory of the evolution of dominance. J Genet 37(2):365–374.

Week 4

Preliminary reading

• Wiser MJ, Lenski RE (2017) Evolutionary Theory and Experiments With Microorganisms. Ref Modul Life Sci (August 2016):1–14. doi:10.1016/B978-0-12-809633-8.13042-0

Serial transfer experiments

• Hegreness M, Shoresh N, Hartl DL, Kishony R (2006) An equivalence principle for the incorporation of favorable mutations in asexual populations. Science (80- ) 311(5767):1615–7. doi:10.1126/science.1122469
• Barrick JE, Kauth MR, Strelioff CC, Lenski RE (2010) Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol 27(6):1338–1347. doi:10.1093/molbev/msq024
• Moura De Sousa JA, Campos PRAA, Gordo I (2013) An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations. Genome Biol Evol 5(5):794–806. doi:10.1093/gbe/evt045

Week 5

Preliminary reading

• Friedman J, Gore J (2017) Ecological systems biology: The dynamics of interacting populations. Curr Opin Syst Biol 1:114–121.

Community ecology of the microbiome

• David LA, et al. (2014) Host lifestyle affects human microbiota on daily timescales. Genome Biol 15(7):R89.

Week 6

Preliminary reading

• Grassly NC, Fraser C (2008) Mathematical models of infectious disease transmission. Nat Rev Microbiol 6. doi:10.1038/nrmicro1845.

Big-data epidemiology

• Ginsberg, Jeremy, et al. “Detecting influenza epidemics using search engine query data.” Nature457.7232 (2009): 1012.

Week 7

Preliminary reading

• Flanagan SP (2018) Quantitative Genetics of Behavior. Encycl Anim Behav 2nd Ed. doi:10.1016/B978-0-12-809633-8.90044-X.

Polygenic risk scores

• De Vlaming R, Groenen PJF (2015) The current and future use of ridge regression for prediction in quantitative genetics. Biomed Res Int 2015. doi:10.1155/2015/143712.
• Dudbridge F (2013) Power and Predictive Accuracy of Polygenic Risk Scores. PLoS Genet 9(3). doi:10.1371/journal.pgen.1003348.
• Kong A, et al. (2018) The nature of nurture: Effects of parental genotypes. Science (80- ) 359(6374):424–428.

Week 8

Preliminary reading

• Introduction to cell biology, Diamantina Institute, The University Of Queensland

Cellular microscopy image enhancement with deep learning

• Weigert M, et al. (2018) Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat Methods 15(12):1090–1097.

Week 9

Preliminary reading

• None

Reduction principle

• Altenberg L, Liberman U, Feldman MW (2017) Unified reduction principle for the evolution of mutation, migration, and recombination. Proc Natl Acad Sci USA 114:E2392– E2400.

Adaptive evolution

• Taddei F, et al. (1997) Role of mutator alleles in adaptive evolution. Nature 387(6634):700–2.
• Sniegowski PD, et al. (1997) Evolution of High Mutation Rates in Experimental Populations of E. Coli. Nature 387(6634):703–5.
• Wielgoss S, et al. (2012) Mutation Rate Dynamics in a Bacterial Population Reflect Tension between Adaptation and Genetic Load. Proceedings of the National Academy of Sciences 110(1):222–27.

Week 10

Preliminary reading

• Creanza N, Kolodny O, Feldman MW (2017) Cultural evolutionary theory: How culture evolves and why it matters. Proc Natl Acad Sci 114(30):7782–7789. doi:10.1073/pnas.1620732114

Cultural evolution

• Aoki K, Wakano JY, Feldman MW (2005) The emergence of social learning in a temporally changing environment: a theoretical model. Curr Anthropol 46(2):334–340.
• McElreath R, Strimling P (2008) When Natural Selection Favors Imitation of Parents. Curr Anthropol 49(2):307–316.

Language evolution

• Simon Kirby (2001) Spontaneous Evolution of Linguistic Structure. An Iterated Learning Model of the Emergence of Regularity and Irregularity.
• Michael Cogswell, Jiasen L, et al. (2019) Emergence of Compositional Language with Deep Generational Transmission.
• Satwik Kottur, José M.F. Moura et al. (2017) Natural Language Does Not Emerge ‘Naturally’ in Multi-Agent Dialog.
• Raviv, Limor, Meyer, Antje, and Lev-Ari, Shiri. Compositional structure can emerge without generational transmission. Cognition, 182:151–164, 2018.

Week 11

Preliminary reading

• None

Analysis of spatial structure

• Novembre J, et al. (2008) Genes mirror geography within Europe. Nature 456(7218):98–101.
• Yang W-Y, Novembre J, Eskin E, Halperin E (2012) A model-based approach for analysis of spatial structure in genetic data. Nat Genet 44(6):725–731.
• Carja O, et al. (2017) Worldwide patterns of human epigenetic variation. Nat Ecol Evol:0–1.