Evolvability workshop readings

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Friday (April 28) – Invited Experts

(I) Jeremy Draghi

  • Essential Reading
  1. Draghi, J.A., and M.C. Whitlock. 2015. Overdominance interacts with linkage to determine the rate of adaptation to a new optimum. Journal of Evolutionary Biology 28:95–104.
  2. Draghi, J.A., T.L. Parsons, G.P. Wagner, and J.B. Plotkin. 2010. Mutational robustness can facilitate adaptation. Nature 463:353–355.
  • Background Papers
  1. Whitlock, M.C. 1996. The red queen beats the jack-of-all trades: limitations on the evolution of phenotypic plasticity and niche breadth. The American Naturalist 148:S65–S77.
  2. Stiffler, M.A., D.R. Hekstra, and R. Ranganathan. 2015. Evolvability as a function of purifying selection in TEM-1 β-lactamase. Cell 160:882–892.

 (II) Elena Alvarez-Buylla

  • Essential Reading
  1. Álvarez-Buylla, E.R., Á. Chaos, M. Aldana, M. Benítez, Y. Cortes-Poza, C. Espinosa-Soto, D.A. Hartasánchez2,3, R.B. Lotto, D. Malkin, G.J. Escalera Santos, and P. Padilla-Longoria. 2008. Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape. PLoS ONE 3(11):e3626.
  2. Barrio, R.Á., A. Hernández-Machado, C. Varea, J.R. Romero-Arias, and E.R. Álvarez-Buylla (2010) Flower development as an interplay between dynamical physical fields and genetic networks. PLoS ONE 5(10): e13523.
  • Background Papers
  1. Villarreal, C., P. Padilla-Longoria, and E.R. Álvarez-Buylla. 2012. General theory of genotype to phenotype mapping: derivation of epigenetic landscapes from N-node complex gene regulatory networks. Physical Review Letters 109:118102.
  2. Álvarez-Buylla, E.R., J. Dávila-Velderrain, and J.C. Martínez-García. 2016. Systems biology approaches to development beyond bioinformatics: nonlinear mechanistic models using plant systems. BioScience 66:371–383.

 (III) Joanna Masel

  • Essential Reading
  1. Masel, J. and M.V. Trotter. 2010. Robustness and evolvability. Trends in Genetics 26:406–414.
  2. Rajon, E. and J. Masel. 2011. Evolution of molecular error rates and the consequences for evolvability. Proceedings of the National Academy of Sciences USA 8:286–292.
  • Background Papers
  1. Wilson, B.A., S.G. Foy, R. Neme, and J. Masel. 2017. Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth. Nature Ecology & Evolution 1:0146.
  2. Bertram, J., K. Gomez, and J. Masel. 2017. Predicting patterns of long-term adaptation and extinction with population genetics. Evolution 71:204–214.

 (IV) David Houle

  • Essential Reading
  1. Hansen, T.F., and D. Houle. 2008. Measuring and comparing evolvability and constraint in multivariate characters. Journal of Evolutionary Biology 21:1201–1219.
  2. Hansen, T.F., C. Pelabon, and D. Houle. 2011. Heritability is not evolvability. Evolutionary Biology 38:258–277.
  • Background Papers
  1. Wagner, G.P., and L. Altenberg. 1996. Perspective: complex adaptations and the evolution of evolvability. Evolution 50:967-976.
  2. Houle, D., B. Morikawa, and M. Lynch. 1996. Comparing mutational variabilities. Genetics 143:1467-1483.

 Saturday (April 28) – Topics and Themes

(1) Brett Calcott – Engineering and Information

  • Background Papers
  1. Calcott, B. 2014a. Engineering and evolvability. Biology & Philosophy 29:293–313.
  2. Calcott, B. 2014b. The creation and reuse of information in gene regulatory networks. Philosophy of Science 81: 879–90.
  3. Dubuis, J.O., G. Tkačik, E.F. Wieschaus, T. Gregor, and W. Bialek. 2013. Positional information in bits. Proceedings of the National Academy of Sciences USA 110:16301–8.

 (2) Michael Travisano – Experimental Evolution

  • Background Papers
  1. Díaz Arenas, C., and T.F. Cooper. 2013. Mechanisms and selection of evolvability: experimental evidence. FEMS Microbiology Reviews 37:572–582.
  2. Libby, E., W.C. Ratcliff, M. Travisano, and B. Kerr. 2014. Geometry shapes evolution of early multicellularity. PLoS Computational Biology 10:e1003803.
  3. Ratcliff, W.C., J.D. Fankhauser, D.W. Rogers, D. Greig, and M. Travisano. 2015. Origins of multicellular evolvability in snowflake yeast. Nature Communications 6:6102.

 (3) Robustness, Criticality, Modularity

  • Background Papers
  1. Esteve-Altava, B., R. Diogo, C. Smith, J.C. Boughner, and D. Rasskin-Gutman. 2015. Anatomical networks reveal the musculoskeletal modularity of the human head. Scientific Reports 5:8298.
  2. Felix, M.-A., and M. Barkoulas. 2015. Pervasive robustness in biological systems. Nature Reviews Genetics 16:483-496.
  3. Friedlander, T., A.E. Mayo, T. Tlusty, and U. Alon. 2013. Mutation rules and the evolution of sparseness and modularity in biological systems. PLoS ONE 8:e70444.
  4. Torres-Sosa, C., S. Huang, and M. Aldana. 2012. Criticality is an emergent property of genetic networks that exhibit evolvability. PLoS Computational Biology 8:e1002669.
  5. Wagner, A. 2012. The role of robustness in phenotypic adaptation and innovation. Proceedings of the Royal Society B: Biological Sciences 279:1249–1258.

 (4) Networks and Proteins

  • Background Papers
  1. Garfield, D.A., D.E. Runcie, C.C. Babbitt, R. Haygood, W.J. Nielsen, and G.A. Wray. 2013. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biology 11:e1001696.
  2. Jiménez, A. J. Cotterell, A. Munteanu, and J. Sharpe. 2015. Dynamics of gene circuits shapes evolvability. Proceedings of the National Academy of Sciences USA 112:2103–2108.
  3. Landry, C.R., B. Lemos, S.A. Rifkin, W.J. Dickinson, and D.L. Hartl. 2007. Genetic properties influencing the evolvability of gene expression. Science 317:118–121.
  4. Niklas, K.J., S.E. Bondos, A.K. Dunker, and S.A. Newman. 2015. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications. Frontiers in Cell and Developmental Biology 3:8.
  5. Payne, J.L., and A. Wagner. 2014. The robustness and evolvability of transcription factor binding sites. Science 343:875–877.
  6. Yanagida, H., A. Gispan, N. Kadouri, S. Rozen, M. Sharon, N. Barkai, and D.S. Tawfik. 2015. The evolutionary potential of phenotypic mutations. PLoS Genetics 11: e1005445.

  (5) Paleobiology – History of Life

  • Background Papers
  1. Chirat, R., D.E. Moulton, and A. Goriely. 2013. Mechanical basis of morphogenesis and convergent evolution of spiny seashells. Proceedings of the National Academy of Sciences USA 110:6015–6020.
  2. Erwin, D.H. 2008. Macroevolution of ecosystem engineering, niche construction and diversity. Trends in Ecology & Evolution 23:304–310.
  3. Herringshaw, L.G., R.H.T. Callow, and D. McIlroy. 2017. Engineering the Cambrian explosion: the earliest bioturbators as ecosystem engineers. In: Brasier, A.T., D. McIlroy, and N. McLoughlin (eds) Earth System Evolution and Early Life. Geological Society, London, Special Publications, 448.18.
  4. Jablonski, D. 1987. Heritability at the species level: analysis of geographic ranges of Cretaceous mollusks. Science 238:360–363.
  5. Young, N.M., G.P. Wagner, and B. Hallgrímsson. 2010. Development and the evolvability of human limbs. Proceedings of the National Academy of Sciences USA 107:3400–3405.

 Sunday (April 30) – Conceptual Reflections

(1) Conceptual Issues: Extrinsicality

  • Background Papers
  1. Love, A.C. 2003. Evolvability, dispositions, and intrinsicality. Philosophy of Science 70:1015-1027.
  2. Cantalapiedra, J.L., J.L. Prado, M. Hernández Fernández, and M.T. Alberdi. 2017. Decoupled ecomorphological evolution and diversification in Neogene-Quaternary horses. Science 355:627-630.
  3. Zaman, L., J.R. Meyer, S. Devangam, D.M. Bryson, R.E. Lenski, and C. Ofria. 2014. Coevolution drives the emergence of complex traits and promotes evolvability. PLoS Biology 12:e1002023.

 (2) The Meaning of Evolvability

  • Background Paper
  1. Brookfield, J.F.Y. 2009. Evolution and evolvability: celebrating Darwin 200. Biology Letters 5:44–46.
  2. Brown, R.L. 2014. What evolvability really is. The British Journal for the Philosophy of Science 65:549–572.
  3. Pigliucci, M. 2008. Is evolvability evolvable? Nature Reviews Genetics 9:75–82.
  4. Wimsatt, W.C. 2013. Evolution and the stability of functional architectures. In P. Huneman (ed.), Functions: Selection and Mechanisms. New York: Springer, 19–41. 
  • General Background Papers
  1. Kirschner, M., and J. Gerhart. 1998. Evolvability. Proceedings of the National Academy of Sciences USA 95:8420–8427.
  2. Huynen, M.A., P.F. Stadler, and W. Fontana. 1996. Smoothness within ruggedness: the role of neutrality in adaptation. Proceedings of the National Academy of Sciences USA 93:397–401.
  3. Livnat, A., C. Papadimitriou, J. Dushoff, and M.W. Feldman. 2008. A mixability theory for the role of sex in evolution. Proceedings of the National Academy of Sciences USA 105:19803–19808.
  4. Prud’homme, B., N. Gompel, and S.B. Carroll. 2007. Emerging principles of regulatory evolution. Proceedings of the National Academy of Sciences USA 104:8605–12.
  5. Wagner, G., and J. Zhang. 2011. The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nature Reviews Genetics 12:204–213.
  6. Yampolsky, L.Y. and A. Stoltzfus. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evolution & Development 3:73–83.