Evolution in silico - From Neutral Networks to Multi-stable Molecules

Evolution in silico - From Neutral Networks to Multi-stable Molecules 

Two or more genotypes are neutral in evolution when the selection constraint is unable to distinguish between them. Early sequence comparison data [6] apparently confirmed Motoo Kimura s idea of neutral drift in population genetics [5]. Accordingly, many different genotypes could give rise to the same phenotype, and depending on the conditions, different phenotypes can share the same fitness value. Direct evidence for neutral evolution under controlled conditions came only two years ago Se- 

Formally, sequence-structure relations are considered as mappings from sequence space onto a discrete space of structures (for a review see [39])  

The equation expresses that the space of all genotypes, the sequence space I, is a discrete space with the Hamming distance as metric. It is mapped onto a discrete space of structures called shape space with the structure distance as metric (We use I rather than 4 in order to indicate different numbering schemes used for sequences and structures). The evolutionarily relevant quantity, the fitness value fk as shown in Fig. 2.3, is derived from the phenotype Sk through evaluation, which can be understood as another mapping, a map from shape space into the positive real numbers including zero, fk = f(Sk). Both maps need not be invertible in the sense that more than one phenotype may have the same fitness value, and more than one sequence may lead to the same structure. We shall study here neutrality induced by the first map, (// in Eq. (6). 

2) The idea to represent the phenotype in RNA evolution experiments by the RNA structure was formulated 

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