The following references provide some pointers to important work in evolutionary systems biology. For a more comprehensive overview of existing work and a mechanistic framework that details, how various approaches can be combined in principle to obtain causal insights for understanding Landscapes of Incomplete Fitness Traits (LIFTs), see the most recent integrative review (Loewe 2016), which substantially increased the clarity and precision of Loewe (2009).

References:

Borenstein E, Kupiec M, Feldman MW & Ruppin E (2008) Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc. Natl. Acad. Sci. USA 105:14482-14487. PubMed

Dean, A. M. & Thornton, J. W. (2007) Mechanistic approaches to the study of evolution: the functional synthesis. Nat. Rev. Genet. 8, 675-88. PubMed

Dekel E, Alon U (2005) "Optimality and evolutionary tuning of the expression level of a protein." Nature 436:588-92. PubMed

Fong SS, Nanchen A, Palsson BO, Sauer U (2006) "Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes." J Biol Chem 281:8024-33. PubMed

Gillespie, D. T. (2007) Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 58, 35-55. PubMed

Harrison R, Papp B, Pál C, Oliver SG, Delneri D (2007) "Plasticity of genetic interactions in metabolic networks of yeast." Proc Natl Acad Sci U S A 104:2307-12. PubMed

Ibarra, R. U., Edwards, J. S., & Palsson, B. O. (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186-9. PubMed

Lande, R. (2008) Adaptive topography of fluctuating selection in a Mendelian population. J. Evol. Biol. 21, 1096-1105. PubMed

Loewe L (2009) A framework for evolutionary systems biology. BMC Systems Biology 3:27. Journal link

Loewe, L (2015): EvoSysBio in 10 Slides. Figshare 1427128 http://dx.doi.org/10.6084/m9.figshare.1427128

Loewe (2016) Systems in Evolutionary Systems Biology, pp 297–318, vol 4 in: Kliman (ed) Encyclopedia of Evolutionary Biology, Academic Press, Oxford, UK.

Lynch M (2007) "The evolution of genetic networks by non-adaptive processes." Nat Rev Genet 8:803-813. PubMed

MacLean C & Gudelj I (2006) Resource competition and social conflict in experimental populations of yeast. Nature 441:498-501. PubMed

MacLean C & Buckling A (2009) The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa. PLoS Genet 5: e1000406. Journal link

Michel JB, Yeh PJ, Chait R, Moellering RC Jr, Kishony R (2008) "Drug interactions modulate the potential for evolution of resistance." Proc Natl Acad Sci U S A 105:14918-23. PubMed

Pál C, Papp B, Lercher MJ, Csermely P, Oliver SG, Hurst LD (2006) "Chance and necessity in the evolution of minimal metabolic networks." Nature 440:667-70. PubMed

Papp, B., Pal, C., & Hurst, L. D. (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429, 661-4. PubMed

Schuetz R, Kuepfer L, Sauer U (2007) "Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli." Mol Syst Biol 3:119. PubMed

Segrè D, Deluna A, Church GM, Kishony R (2005) "Modular epistasis in yeast metabolism." Nat Genet 37:77-83. PubMed

Soyer O.S. (editor, 2012). Evolutionary Systems Biology. Book series: Advances in Experimental Medicine and Biology. Springer. Contents

Wagner A (2008) "Neutralism and selectionism: a network-based reconciliation.", Nat Rev Genet 9:965-74. PubMed

Weinreich DM, Delaney NF, Depristo MA, Hartl DL (2006) "Darwinian evolution can follow only very few mutational paths to fitter proteins." Science 312:111-4. PubMed

You L, Yin J (2002) "Dependence of Epistasis on Environment and Mutation Severity as Revealed by in Silico Mutagenesis of Phage T7" Genetics 160:1273-1281. PubMed

Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U (2004) "Just-in-time transcription program in metabolic pathways." Nat Genet 36:486-91. PubMed