The evolution of phenotypic correlations and "developmental memory"

Evolution

Volumn 68, Issue 4, 2014, Pages 1124-1138

  Watson, Richard A ^a   Wagner, Günter P ^b   Pavlicev, Mihaela ^c   Weinreich, Daniel M ^d   Mills, Rob ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF VIENNA   (Austria)

^d BROWN UNIVERSITY   (United States)

Author keywords

Adaptation; Associative learning; Evo devo; Evolvability

Indexed keywords

ADAPTATION; ADULT; EVOLUTION; GENE EXPRESSION; LEARNING; MEMORY; NATURAL SELECTION; PHENOTYPE;

BIOLOGICAL MODEL; EVOLUTION; GENE REGULATORY NETWORK; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GROWTH, DEVELOPMENT AND AGING; PHENOTYPE;

BIOLOGICAL EVOLUTION; GENE REGULATORY NETWORKS; GENETIC VARIATION; GROWTH AND DEVELOPMENT; MODELS, GENETIC; PHENOTYPE; SELECTION, GENETIC;

EID: 84897577914     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12337     Document Type: Article

References (73)

1. Ackley, D. H., G. E. Hinton, and T. J. Sejnowski 1985. A learning algorithm for Boltzmann machines, Cogn. Sci. 9:147-169.
2. Brigandt, I. 2007. Typology now: homology and developmental constraints explain evolvability. Biol. Philos. 22:709-725.
3. Cheverud, J. M., T. H. Ehrich, T. T. Vaughn, S. F. Koreishi, R. B. Linsey, and L. S. Pletscher 2004. Pleiotropic effects on mandibular morphology II: differential epistasis and genetic variation in morphological integration. J. Exp. Zool. Part B: Mol. Dev. Evol. 302:424-435.
4. Chevillon, C., D. Bourget, F. Rousset, N. Pasteur, and M. Raymon 1997. Pleiotropy of adaptive changes in populations: comparisons among insecticide resistance genes in Culex pipiens. Genet. Res. 70:195-204.
5. Clune, J., J. B. Mouret, and H. Lipson 2013. The evolutionary origins of modularity. Proc. R. Soc. B 280:20122863.
6. Coolen, A. C. C. 1991. On the relation between stability parameters and sizes of domains of attraction in attractor neural networks. Europhys. Lett. 16:73.
7. Crombach, A., and P. Hogeweg 2008. Evolution of evolvability in gene regulatory networks. PLoS Comput. Biol. 4:e1000112.
8. Davidson, E. H. 2010. Emerging properties of animal gene regulatory networks. Nature 468:911-920.
9. Davies, A. P., R. A. Watson, R. Mills, C. L. Buckley, and J. Noble (2010) If you can't be with the one you love, love the one you're with: how individual habituation of agent interactions improves global utility. Artif. Life 17:167-181.
10. Delph, L. F., J. C. Steven, I. A. Anderson, C. R. Herlihy, and E. D. Brodie, III 2011. Elimination of a genetic correlation between the sexes via artificial correlational selection. Evolution 65:2872-2880.
11. Draghi, J., and G. P. Wagner 2008. Evolution of evolvability in a developmental model. Evolution 62:301-315.
12. Draghi, J., and G. P. Wagner 2009. The evolutionary dynamics of evolvability in a gene network model. J. Evol. Biol. 22:599-611.
13. Draghi, J. A., T. L. Parsons, G. P. Wagner, and J. B. Plotkin 2010. Mutational robustness can facilitate adaptation. Nature 463:353-355.
14. Fernando, C., A. M. L. Liekens, L. E. H. Bingle, C. Beck, T. Lenser, D. J. Stekel, and J. E. Rowe 2008 Molecular circuits for associative learning in single-celled organisms. J. R. Soc. Interface 6:463-469.
15. Gillespie, J. H. 1984. Molecular evolution over the mutational landscape. Evolution 38:1116-1129.
16. Guillaume, F., and S. P. Otto 2012. Gene functional trade-offs and the evolution of Pleiotropy. Genetics 192:1389-1409.
17. Harnad, S. 2005. To cognize is to categorize: cognition is categorization. Pp. 19-43 in C. Lefebvre and H. Cohen Handbook of categorization in cognitive science. Elsevier Press, New York.
18. Hebb, D. O. 1949. The organization of behaviour. Wiley, New York.
19. Hendrikse, J. L., T. E. Parsons, and B. Hallgrímsson 2007. Evolvability as the proper focus of evolutionary developmental biology. Evol. Dev. 9:393-401.
20. Hopfield, J. J. 1982. Neural networks and physical systems with emergent collective computational abilities. Proc. Natl. Amer. Sci. USA 79:2554-2558.
21. Huang, S., G. Eichler, Y. Bar-Yam, and D. E. Ingber 2005. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys. Rev. Lett. 94:128701.
22. Izquierdo, E. J., and C. Fernando 2008. The evolution of evolvability in gene transcription networks. Pp. 265-273 in S. Bullock, J. Noble, R. Watson, and M. A. Bedau, eds. International conference on the simulation and synthesis of living system. MIT Press, Cambridge, MA.
23. Jones, A. G., S. J. Arnold, and R. Bürger 2007. The mutation matrix and the evolution of evolvability. Evolution 61:727-745.
24. Kashtan, N., and U. Alon 2005. Spontaneous evolution of modularity and network motifs. Proc. Natl. Amer. Sci. USA 102:13773-13778.
25. Kashtan, N., E. Noor, and U. Alon 2007. Varying environments can speed up evolution. Proc. Natl. Acad. Sci. USA 104:13711-13716.
26. Kashtan, N., A. Mayo, T. Kalisky, and U. Alon 2009. An analytically solvable model for rapid evolution of modular structure. PLoS Comput. Biol. 5:e1000355.
27. Kauffman, S. A. 1993. The origins of order. Oxford Univ. Press, New York.
28. Kim, H. S., J. Huh, and J. C. Fay 2009. Dissecting the pleiotropic consequences of a quantitative trait nucleotide. FEMS Yeast Res. 9:713-722.
29. Kirchner, M., and J. Gerhart 1998. Evolvability. Proc. Natl. Acad. Sci. USA 95:8420-8427.
30. Laland, K. N., K. Sterelny, J. Odling-Smee, W. Hoppitt, and T. Uller 2011. Cause and effect in biology revisited: is Mayr's proximate-ultimate dichotomy still useful? Science 334:1512-1516.
31. Lande, R., and S. J. Arnold 1983. The measurement of selection on correlated characters. Evolution 37:1210-1226.
32. Leamy, L. J., D. Pomp, and J. T. Lightfoot (2009). Genetic variation in the pleiotropic association between physical activity and body weight in mice. Genet. Sel. Evol. 41:41. Available from http://www.gsejournal.org/about#citingarticles.
33. Leclerc, R. D. 2008. Survival of the sparsest: robust gene networks are parsimonious. Mol. Syst. Biol. 4:213. doi:10.1038/msb.2008.52.
34. Lenski, R. E. 1988a. Experimental studies of Pleiotropy and epistasis in Escherichia coli. I. Variation in competitive fitness among mutants resistant to virus T4. Evolution 42:425-432.
35. Lenski, R. E. 1988b. Experimental studies of pleiotropy and epistasis in Escherichia coli. II. Compensation for maldaptive effects associated with resistance to virus T4. Evolution 42:433-440.
36. Lewis, M. 2009. An investigation into the evolution of relationships between species in an ecosystem. M.Sc. dissertation, ECS, University of Southampton, Southampton, U.K.
37. Lipson, H. 2007. Principles of modularity, regularity, and hierarchy for scalable systems. J. Biol. Phys. Chem. 7:125-128.
38. Lipson, H., J. B. Pollack, and N. P. Suh 2002 On the origin of modular variation. Evolution. 56:1549-1556.
39. McGregor, S., V. Vasas, P. Husbands, and C. Fernando 2012. Evolution of associative learning in chemical networks, PLoS Comput. Biol. 8:e1002739.
40. O'Reilly, R. C., and Y. Munakata 2000. Computational explorations in cognitive neuro-science: understanding the mind by simulating the brain. MIT Press, Cambridge, MA.
41. Parter, M., N. Kashtan, and U. Alon 2008. Facilitated variation: how evolution learns from past environments to generalize to new environments. PLoS Comput. Biol. 4:e1000206.
42. Pavlicev, M., and G. P. Wagner 2012. A model of developmental evolution: selection, pleiotropy and compensation. Trends Ecol. Evol. 27:316-322.
43. Pavlicev, M., J. P. Kenney-Hunt, E. A. Norgard, C. C. Roseman, J. B. Wolf, and J. M. Cheverud 2008. Genetic variation in pleiotropy: differential epistasis as a source of variation in the allometric relationship between long bone lengths and body weight. Evolution 62:199-213.
44. Pavlicev, M., J. M. Cheverud, G. P. Wagner 2011. Evolution of adaptive phenotypic variation patterns by direct selection for evolvability Proc. R. Soc. B: Biol. Sci. 278:1903-1912.
45. Raff, R. A. 2000. Evo-devo: the evolution of a new discipline. Nat. Rev. Genet. 1:74-79.
46. Riedl, R. 1978. Order in living organisms. Wiley, New York.
47. Rumelhart, D. E., L. James, and McClelland and the PDP Research Group. 1986. Parallel distributed processing. Vols. I and II. MIT Press, Cambridge, MA.
48. Sansom, R. 2011. Ingenious genes: how gene regulation networks evolve to control development. MIT Press, Cambridge, MA.
49. Schluter, D. 1996. Adaptive radiation along genetic lines of least resistance. Evolution 50:1766-1774.
50. Sniegowski, P. D., and H. A. Murphy 2006. Evolvability. Curr. Biol. 16:R831-R834.
51. Stewart, J. 1997. The evolution of genetic cognition. J. Social Evol. Syst. 20:53-73.
52. Toussaint, M., and W. von Seelen 2007. Complex adaptation and system structure. BioSystems 90:769-782.
53. Valiant, L. 2009. Evolvability. J. Assoc. Comput. Machinery 56:3:1-3:21.
54. Vohradsky, J. 2001a. Neural model of the genetic network. J. Biol. Chem. 276:36168-36173.
55. Vohradsky, J. 2001b. Neural network model of gene expression. FASEB J. 15:846-854.
56. Waddington, C. H., and E. Robertson 1966. Selection for developmental canalisation. Genet. Res. 7:303-312.
57. Wagner, G. P. 1989. Multivariate mutation-selection balance with constrained pleiotropic effects. Genetics 122:223-234.
58. Wagner, G. P., and L. Altenberg 1996. Complex adaptations and the evolution of evolvability. Evolution 50:967-976.
59. Wagner, G. P., and M. D. Laubichler 2004. Rupert Riedl and the re-synthesis of evolutionary and developmental biology: body plans and evolvability. J. Exp. Zool. B: Mol. Dev. Evol. 302B:92-102.
60. Wagner, G. P., M. Pavlicev, and J. M. Cheverud 2007. The road to modularity. Nat. Rev. Genet. 8:921-931.
61. Watson, R. A., C. L. Buckley, R. Mills, and A. P. Davies 2010a. Associative memory in gene regulation networks. Pp. 194-202 in H. Fellermann, M. Doerr, M. Hanczyc, L. L. Laursen, S. Maurer, D. Merkle, P.-A. Monnard, K. Støy, and S. Rasmussen, eds. Artificial life XII: proceedings of the twelfth international conference on the synthesis and simulation of living systems. MIT Press, Cambridge, MA.
62. Watson, R. A., R. Mills, C. L. Buckley, A. Penn, A. Davies, J. Noble, and S. Bullock 2010b Adaptation without natural selection. Pp. 80-81 in Artificial life XII: proceedings of the twelfth International Conference on the synthesis and simulation of living systems. MIT Press, Cambridge, MA.
63. Watson, R. A., C. L. Buckley, and R. Mills 2010c. Optimisation in 'self-modelling' complex adaptive systems. Complexity 16:17-26.
64. Watson, R. A., R. Mills, and C. L. Buckley 2010d. Global adaptation in networks of selfish components: emergent associative memory at the system scale. Artif. Life 17:147-166.
65. Watson, R. A., R. Mills, and C. L. Buckley 2011a. Transformations in the scale of behaviour and the global optimisation of constraints in adaptive networks. Adapt. Behav. 19:227-249.
66. Watson, R. A., D. M. Weinreich, and J. Wakeley 2011b. Genome structure and the benefit of sex. Evolution 65:523-536.
67. Watson, R. A., N. Palmius, R. Mills, S. T. Powers, and A. S. Penn 2011c. Can selfish symbioses effect higher-level selection? Pp. 27-36 in G. Kampis, I. Karsai, E. Szathmáry, eds. Advances in artificial life. Darwin Meets von Neumann. Springer, Berlin.
68. Watson, R. A., R. Mills R, C. L. Buckley, K. Kouvaris, A. Jackson, S. T. Powers, C. Cox, S. Tudge, P. Ryan, and A. Davies 2014. Evolutionary connectionism: how the principles of associative learning operate in the evolution of developmental interactions, the evolution of ecological relationships and the evolution of new levels of individuality. Technical Report, ECS, University of Southampton, Southampton, U.K.
69. Wessels, L., E. van Someren, and M. Reinders 2001. A comparison of genetic network models. Pacific Sympos. Biocomput. 6:508-519.
70. West-Eberhard, M.-J. 2003. Developmental plasticity and evolution. Oxford Univ. Press, New York.
71. Wimsatt, W. C. 2001. Generative entrenchment and the developmental systems approach to evolutionary processes. Pp. 219-237 in S. Oyama, P. E. Griffiths, and R. D. Gray, eds. Cycles of contingency: developmental systems and evolution. MIT Press, Cambridge, MA.
72. Young, N. M., and B. Hallgrímsson 2005. Serial homology and the evolution of mammalian limb covariation structure. Evolution, 59:2691-2704.
73. Young, N. M., G. P. Wagner, and B. Hallgrímsson 2010. Development and the evolvability of human limbs. Proc. Natl. Acad. Sci. 107:3400-3405.