For stationary adaptation in a time-dependent fitness seascape, the upper bound Vdrive ≃ γL produces the estimate 2 NγL > 1 for the crossover from dilute to dense sweeps.
Data and model show large deviations from single-site theory, which demonstrate strong interference effects in the dense-sweep regime.
In summary, interference interactions in the dense-sweep mode produce the following selection classes of mutations and genomic sites.
We treat the dense-sweep regime by an approximation: each sweep is associated with a unique driver mutation, which is the strongest beneficial mutation in its cluster.
Our model predicts an important consequence of interference interactions: a substantial fraction of the genomic substitutions observed in laboratory or field data of dense-sweep processes are not driver mutations, but moderately beneficial or deleterious passenger mutations fixed by hitchhiking.
This fraction increases with increasing population size N or genome length L. Disentangling driver and passenger mutations in the dense-sweep regime poses a challenge for the inference of selection from such data.
Interference interactions in the dense-sweep regime may be complicated in their details, but their net effect is simple: genomic sites with selection coefficients σ smaller than a threshold σ ˜ have nearly random fixed alleles, and mutations at these sites fix with near-neutral rates.
However, we are primarily interested in adaptive processes under linkage in the dense-sweep regime at high rates of beneficial mutations, which generates strongly correlated clusters of fixed mutations nested in each other's background (the crossover between these regimes is further quantified below).
Hence, we obtain a self-consistent relation, (11) V drive = p drive G 0 U with (12) p drive = exp [ − τ fix ∫ σ ∞ V drive d ζ ] , which can be regarded as a partial summation of higher-order interference interactions characteristic of the dense-sweep regime (see the Appendix for details).
Idealized simulations have also found that fragmentation in the dense shell swept up by the SN remnant may occur (Salvaterra et al. 2004; Machida et al. 2005; Vasiliev et al. 2008; Nagakura et al. 2009; Chiaki et al. 2013b).
