Fig. 1: The evotype and its key properties.
a The evotype visualised as a landscape surrounding the design type (red square), where fitneity (the combined function of fitness and utility) is plotted as a vertical axis against a 2D plane of sequence space with the probability of evolution exploring regions of sequence space overlaid in grey. The properties of this landscape are determined by the interaction of three components: variation, function and selection. b A variation probability distribution can be projected onto sequence space, which represents the likelihood of exploring a given sequence through genetic variation. Darker regions represent regions of higher probability. This is the sum of the distributions of the individual variation operators present in the system (variation operator set). For example, point mutation (bottom layer in set), recombination of homologous regions (middle layer in set), and slip-strand mutation (top layer in set). Red arrows in the middle and bottom layers represent algorithmic and point mutations, respectively. c How phenotypic functions are distributed in sequence space surrounding the design type is critical. Function space may be considered as discrete (top), where the space may have high genotypic robustness (left grid) or high variability (right grid). A continuous utility space (bottom) plotted against a 1D projection of sequence space. The colour under the curve represents the discrete function associated with that region of sequence space and the utility that each has as a continuous value. For example, if the goal is to produce blue-like functions, dark blue may have the highest utility, followed by lighter variants in the spectrum. The bioengineer must define a minimal threshold (dashed line), below which the design is deemed to be a failure (e.g., non-desired function is exhibited). d Sequences differ in their reproductive fitness. This is the driver of natural selection and can be plotted across sequence space as an adaptive landscape (red dotted line). Utility (blue dashed line) may or may not correlate with reproductive fitness across sequence space. The fitneity (grey solid line) is the combination of the fitness and utility. Bioengineers must optimise fitneity both for the design type and throughout the landscape.
