The seven possible classes of viable genotypes. The dashed boxes for allelic classes 1 and 2 denote “absentee” loci in the single-copy background. Dark vertical lines denote the presence of a key amino acid change that is essential for the production of the novel two-residue function; their location at various positions is meant to remind the reader that various pairs of amino acid sites may participate in the production of the new protein.

The probability of neofunctionalization of a newly arisen duplicate gene scaled to the neutral expectation (θ), as a function of the effective population size (N), number of potentially participating amino acid sites in the new two-residue function (n), and the selective advantage of the new function (s). For the solid lines, s=0.01; for the dashed lines, s=0.0001. In all cases, the mutation rate to null alleles (μ) is 10⁻⁶, and the nonsynonymous mutation rate per codon (v₀) is 10⁻⁸. Each data point is derived from 10⁷ to 10¹⁰ stochastic simulations. The solid and dashed lines are the analytical approximations described in the text. The dotted line denotes the point at which the probability of neofunctionalization is equal to the fixation probability of a neutral mutation.

Average arrival times for a neofunctionalized allele destined for fixation. The curves are based on the theory described in the text, and assume a rate of gene duplication of 10⁻⁸ per gene copy per year.