Each gene node tracks a sequence-conservation score c ∈ [0,1] that drifts down from background mutation and is pulled back up by purifying selection. Genes are laid out on a circular genome map and linked by ortholog/synteny edges; when a gene's conservation collapses below the divergence threshold it is counted as a divergence event and its synteny links visibly weaken.
c(t+dt) = c(t) - mutationRate*dt + selection*e*(1-c(t))*dt
equilibrium: c* = 1 - mutationRate/(selection*e)
- Gene nodes — orthologous gene copies traced across the simulated genome map.
- Synteny connectivity — how many conserved gene-order (synteny) edges link nearby genes.
- Mutation rate — background rate of sequence change accumulating per unit time.
- Purifying selection — how strongly selection pulls conservation back toward 1; each gene also has a fixed essentiality factor e that scales its own selection strength.
When mutation rate exceeds a gene's effective selection strength, its equilibrium conservation collapses toward 0 — the gene diverges. When selection dominates, conservation holds near 1 — the classic signature comparative genomics uses to flag essential, highly conserved genes.