Whole-Genome Duplication & Gene Fate Simulator (2D)

Duplication Parameters

Degeneration rate μ 0.06

Neofunctionalization rate 0.008

Gene pairs 60

Ancestral subfunctions N 3

Speed (gen/s) 4

Live Readouts

Generation

Still resolving — 60 Subfunctionalized (both kept) — 0 Nonfunctionalized (pseudogene) — 0 Neofunctionalized (new role) — 0

Both copies retained

60/60

Single copy retained

0/60

Pair Inspector

Click any pair in the grid to inspect its subfunction-by-subfunction state.

How it works

After a whole-genome duplication (WGD), every gene briefly exists as two identical paralogs. The Duplication-Degeneration-Complementation (DDC) model (Force et al. 1999) treats each ancestral gene as bundling several independent subfunctions (separate regulatory modules — e.g. distinct enhancers driving expression in different tissues or timepoints). Each generation, a shared subfunction can degrade in one random copy with probability μ:

P(subfunction k degrades in copy X this generation) = μ
Once asymmetric, that subfunction is under purifying
selection in whichever copy still carries it — locked.

Three outcomes compete as subfunctions resolve, one at a time, across the pair:

Nonfunctionalization (most common, ~92% in classic estimates) — one paralog loses every subfunction it started with and becomes a silenced pseudogene; the other reverts to carrying the full ancestral role alone.
Subfunctionalization — degeneration happens to different subfunctions in each copy, so neither copy alone reconstitutes the ancestral gene; both are now essential and permanently retained (the mechanism proposed to explain why duplicate genes survive far more often than simple redundancy predicts).
Neofunctionalization — before resolving, a copy that has already specialized acquires a genuinely new, beneficial role (rare — modelled here as an independent low-probability event per generation).

This is the same logic behind vertebrate 2R/teleost-3R whole-genome duplications, the hexaploid wheat genome, and yeast's post-WGD gene repertoire — most duplicate pairs are pruned back to one functional copy, and the survivors are usually the ones whose subfunctions split apart rather than the ones that stayed fully redundant.

Drag to pan · scroll to zoom · click a pair to inspect

Gen 0

Shared subfunction (both copies) Subfunctionalized pair Pseudogene / sole survivor Neofunctionalized copy

Population fate history (stacked, by generation)