Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele
Fig 2
Schematic of HAF score dynamics.
We consider HAF scores in 50 kb segments, examining n = 200 haplotypes sampled from a constant-sized (N = 20000 haploids) population, evolving with population-scaled mutation rate θ = 48 and selection coefficient s = 0.05. We do forward simulations, with time t = 0 at the onset of selection and t increasing towards the present time. Snapshots of generations are shown at specific times indicated at tick marks on the x-axis. Note that these times are increasing but neither consecutive nor regularly spaced. Each selected generation is depicted as a tall thin rectangle. The number in each rectangle is the frequency of the favored allele (carriers). A few rectangles are shown for each phase of a simulated population undergoing a selective sweep. Each point within a rectangle represents the 1-HAF score of a randomly chosen haplotype. Red points represent carriers of the favored allele and blue points represent non-carriers. Points are scattered randomly on the x-axis within each rectangle, but all points within the same rectangle represent the same generation at the time indicated by the tick mark on the x-axis, regardless of their horizontal position within the rectangle. Darker shades of red or blue indicate a higher density of points at that level. The dotted line represents the expected 1-HAF score in the neutral population. (A) Simulation of a non-recombining segment. (B) Simulation with population-scaled recombination rate ρ = 25 (see Methods).