Table 2 The list of symbols and definitions for parameters and variables, which are used and/or defined in Eqs. 1–11

Poisson rate of nucleotide mutations that interfere with transcription binding

u_b

1.0 × 10^–8–2.5 × 10^–8 nucleotide mutations per generation [70]

2.5 × 10^–8 nucleotide mutations per generation

Poisson rate of nucleotide mutations that interfere with production of a functional peptide sequence

u_h

1.0 × 10^–8–2.5 × 10^–8 nucleotide mutations per generation [70]

2.5 × 10^–8 nucleotide mutations per generation

Length of coding region

l_c

5.0 × 10⁴ nucleotides [71]

5.0 × 10⁴ nucleotides

Length of enhancer

l_r

50 bp to 1.5 kbp [72]

775 nucleotides

Subfunctionalization-Only Model poisson rate at which null mutations fix in the coding regions [59]

u_c

–

Equation 9, loss of function mutations per generation

Subfunctionalization-Only Model poisson rate at which null mutations are fixed in each of the z mutable regulatory regions for each gene [59]

u_r

–

Equation 10, loss of function mutations per generation

Number of regulatory regions/domains (promoters/enhancers/silencers)

z

 < 20 regulatory regions

4 regulatory regions

Effective population size

N_e

1.4 × 10⁴ individuals

1 × 10²–1.4 × 10⁶ individuals

Time in generations since duplication event

t

5.0 × 10³–1.4 × 10⁴generations

5.0 × 10³–1.0 × 10⁴generations

Equilibrium constant

K_eq

1.0 × 10⁶–1.0 × 10¹⁴ mol/mL [73, 74]

1.0 × 10⁴–1.0 × 10¹² mol/mL

Scalar on the relationship between the number of hydrophobic patches per cell and the corresponding fitness penalty

w

–

1.0

Heterodimer of interest

AB

–

Equation 1

Gene that codes for subunit A in heterodimer AB

G_A

–

–

Gene that codes for subunit B in heterodimer AB

G_B

–

–

Subunit of heterodimer of interest, gene product of G_A

A

–

Equation 1

Subunit of heterodimer of interest, gene product of G_B

B

–

Equation 1

Concentration of the heterodimer of interest that is in its bound form

[AB]

–

Total concentration of subunit A, likely to be estimated by transcription data

[A]_total

1 × 10^–6–1 × 10^–10 mol/mL

[75, 76]

2.5 × 10^–6 mol/mL

Total concentration of subunit B, gene product of G_B, likely to be estimated by transcription data

[B]_total

1 × 10^–6–1 × 10^–10 mol/mL

[75, 76]

2.5 × 10^–6 mol/mL

Concentration of subunit A in the unbound form

[A]_free

–

Equation 3, in mol/mL

Concentration of subunit B in the unbound form

[B]_free

–

Equation 4, in mol/mL

Concentration of exposed hydrophobic patches

[hp]

–

Equation 2, in mol/mL

Current state

i

–

–

Next possible state

j

–

–

Fitness of state

f

–

Equation 6

Fitness of current state

f_i

1.0

Equation 7

Fitness of next possible state

f_j

–

Equation 7

Probability of fixation of mutation

g

–

Equation 7 [66]

Subfunctionalization, an absorbing state

S

–

Equations 8 and 11

Pseudogenization/nonfunctionalization, an absorbing state

Y

–

Equations 8 and 11