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Fig. 1 | BMC Ecology and Evolution

Fig. 1

From: Dosage balance acts as a time-dependent selective barrier to subfunctionalization

Fig. 1Fig. 1

Markov model for the fate of retention of duplicate copies after gene duplication. In this example, the gene of interest (GOI A) has been duplicated into two copies, GOI A1 and GOI A2. Both copies of GOI A have been duplicated with all four of their regulatory domains upstream of the gene. Each regulatory domain acts as an enhancer for tissues 1–4. The state space includes the two copies with full redundancy (State 0), transient unresolved states (States 1–3), and absorbing states (States Y, S) indicated by neon colors. The absorbing states include nonfunctionalization of one of the gene copies (State Y) and subfunctionalization that leads to the retention of both copies (State S). The neon colors represent which copy is permanently retained and what function(s) it preforms. The light green parts indicate unresolved portions of the gene. The parts of the gene that are dark grey indicate that part being knocked-out through mutation. The parts of the gene that are light grey indicate parts of the gene that are no longer functional because of mutations that occurred in other parts of the gene. Note that for both part a and b, the rate equation for State 1 → State S is equal to the rate equation for State 1 → State 2 AND the rate equation for State 2 → State S is equal to the rate equation for State 2 → State 3. a Subfunctionalization + Dosage Model. The formulas for the rates between states are calculated using a fixation probability equation [66], which uses the relative fitness of the current state (fi) and the next state (fj), and the effective population size (Ne). The rates also incorporate the number of regulatory domains (z), the nucleotide length of the regulatory domains (lr), the nucleotide length of the coding region (lc), the loss of function nucleotide mutation rate (ub, uh). b Subfunctionalization-Only Model [59] for the fate of retention of duplicate copies after gene duplication. The formulas for the rates between states are calculated the effective population size (Ne), the number of regulatory domains (z), Poisson rate at which null mutations are fixed in each of the z mutable regulatory regions for each gene (ur, Eq. 10), and the Poisson rate at which null mutations fix in the coding regions (uc, Eq. 9)

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