Generation-Establishment Tradeoffs Shape the Temporal Window of Recombinant Evolution

Abstract

Recent viral coinfection experiments show that recombinant genomes are generated readily and depend strongly on infection timing and order, yet only a small fraction give rise to persistent lineages. We develop a hybrid deterministic-stochastic framework that resolves this discrepancy by coupling density-dependent recombinant generation with stochastic establishment of rare lineages. The resulting hazard of successful lineage formation is generically non-monotonic, increasing with parental abundance through enhanced generation while decreasing under competitive suppression, and exhibits a unique interior maximum in parental-density space. As parental populations evolve, their trajectory across this hazard landscape defines a sharply localized temporal window of evolutionary opportunity. These results reveal a general principle: evolutionary success is determined not only by intrinsic fitness, but by when variants arise within a dynamically changing ecological context.