Degeneracy: a design principle for achieving robustness and evolvability.

Robustness, the insensitivity of some of a biological system's functionalities to a set of distinct conditions, is intimately linked to fitness. Recent studies suggest that it may also play a vital role in enabling the evolution of species. Increasing robustness, so is proposed, can lead to the emergence of evolvability if evolution proceeds over a neutral network that extends far throughout the fitness landscape. Here, we show that the design principles used to achieve robustness dramatically influence whether robustness leads to evolvability. In simulation experiments, we find that purely redundant systems have remarkably low evolvability while degenerate, i.e. partially redundant, systems tend to be orders of magnitude more evolvable. Surprisingly, the magnitude of observed variation in evolvability can neither be explained by differences in the size nor the topology of the neutral networks. This suggests that degeneracy, a ubiquitous characteristic in biological systems, may be an important enabler of natural evolution. More generally, our study provides valuable new clues about the origin of innovations in complex adaptive systems.

[1]  A. Wagner Robustness and evolvability: a paradox resolved , 2008, Proceedings of the Royal Society B: Biological Sciences.

[2]  G Tononi,et al.  Measures of degeneracy and redundancy in biological networks. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[3]  A. Wagner Robustness against mutations in genetic networks of yeast , 2000, Nature Genetics.

[4]  A. Bergman,et al.  Waddington's canalization revisited: Developmental stability and evolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[5]  A. Bergman,et al.  Evolutionary capacitance as a general feature of complex gene networks , 2003, Nature.

[6]  G. Edelman,et al.  Degeneracy and complexity in biological systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[7]  G. Fink,et al.  A Saccharomyces gene family involved in invasive growth, cell-cell adhesion, and mating. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[8]  M Kimura,et al.  SOLUTION OF A PROCESS OF RANDOM GENETIC DRIFT WITH A CONTINUOUS MODEL. , 1955, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Stuart A. Kauffman,et al.  Requirements for evolvability in complex systems: orderly dynamics and frozen components , 1990 .

[10]  S. Kauffman,et al.  Robustness and evolvability in genetic regulatory networks. , 2007, Journal of theoretical biology.

[11]  M. Tyers,et al.  Still Stratus Not Altocumulus: Further Evidence against the Date/Party Hub Distinction , 2007, PLoS biology.

[12]  T. Ohta Near-neutrality in evolution of genes and gene regulation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[13]  An-Ping Zeng,et al.  The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks , 2003, Bioinform..

[14]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[15]  L. Altenberg,et al.  PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY , 1996, Evolution; international journal of organic evolution.

[16]  A. Wagner Distributed robustness versus redundancy as causes of mutational robustness. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[17]  John Doyle,et al.  Complexity and robustness , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[19]  U. Sauer,et al.  The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli* , 2004, Journal of Biological Chemistry.

[20]  Günter P. Wagner,et al.  Complex Adaptations and the Evolution of Evolvability , 2005 .

[21]  J. Stelling,et al.  Robustness of Cellular Functions , 2004, Cell.

[22]  Peer Bork,et al.  Shared components of protein complexes--versatile building blocks or biochemical artefacts? , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[23]  G. Wagner,et al.  EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS , 2003 .

[24]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[25]  Hiroaki Kitano,et al.  Biological robustness , 2008, Nature Reviews Genetics.

[26]  J M Carlson,et al.  Highly optimized tolerance: a mechanism for power laws in designed systems. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[27]  J. Doyle,et al.  Reverse Engineering of Biological Complexity , 2002, Science.

[28]  Lan V. Zhang,et al.  Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.

[29]  Andreas Wagner,et al.  Neutralism and selectionism: a network-based reconciliation , 2008, Nature Reviews Genetics.

[30]  A. Wagner,et al.  Innovation and robustness in complex regulatory gene networks , 2007, Proceedings of the National Academy of Sciences.

[31]  M. Tyers,et al.  Stratus Not Altocumulus: A New View of the Yeast Protein Interaction Network , 2006, PLoS biology.