Optimal Evolution of the Standard Genetic Code

Abstract

The Standard Genetic Code (SGC) exists in every known organism on Earth. SGC evolution via early unique codon assignment, then later wobble, yields coding resembling the near-universal code. Below, later wobble is shown to also create an optimal route to accurate codon assignment. Time of optimal codon assignment matches the previously defined mean time for ordered coding, exhibiting ≥ 90% of SGC order. Accurate evolution is also accessible, sufficiently frequent to appear in populations of 10³ to 10⁴ codes. SGC-like coding capacity, code order, and accurate assignments therefore arise together, in one attainable evolutionary intermediate. Examples, which plausibly resemble coding at evolutionary domain separation, are characterized.

Keywords: Coding; Codon; Evolve; Triplet; Wobble.

Fig. 1

a Fraction of coding tables with coding capacity (≥ 20 encoded functions: left ordinate) or SGC-like assignments (0 mis, no misassignment; ≤ 1 mis, ≤ 1 misassignment; ≤ 2 mis, ≤ 2 misassignments: right ordinate), versus evolutionary time as passages. 100,000 Late wobble evolutions via Coevo_PR captures: coevolution (Wong ; Amirnovin ; Ronneberg et al. 2000) with chemical similarity (Freeland and Hurst ; Massey 2019) to direct amino acid choice. Probabilities per passage are P_mut = 0.04 for mutational capture, P_decay = 0.04 for assignment loss, P_init = 0.6 for initial triplet assignment, P_rand = 0.1 for random assignment (Yarus 2021). b Fraction of coding tables with coding capacity (≥ 20 encoded functions: left ordinate) or with both coding capacity and accurate assignment, versus evolutionary time as passages (labeling, history ,and parameters as in a); “order” indicates mean and s.e.m. for ≥ 20 functions with joint code order ≥ 0.9 of the SGC; “mean” indicates mean and sem for ≥ 20 encoded functions (Yarus 2021). c Fraction of coding tables with coding capacity (≥ 20 encoded functions: left ordinate) or number of independent codes examined to find a code with indicated accuracy half the time (right, logarithmic ordinate), versus evolutionary time as passages (labeling, history, and parameters as in a, b, save for numbered gray arrows at bottom, which mark their leftward eras for discussion)

Fig. 2

Evolved coding example from optimal time, with 20 encoded functions and no misassignments. Evolved for 115 passages using history and parameters as in Fig. 1a. More detail is in the text