Soft sweeps
From EESwiki
Soft Sweeps- Molecular Population Genetics of Adaptation from Standing Genetic Variation
J. Hermisson and P.S. Pennings,
Genetics (2005) 169 (4): 2335
Soft sweeps II - Molecular population genetics of adaptation from recurrent mutation or migration
P. S. Pennings and J. Hermisson
Mol. Biol. Evol. (2006) 23: 1076-1084.
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Soft selective sweep from recurrent mutation in a schematic Wright-Fisher model. Circles represent individuals, the different patterns indicate independent ancestral haplotypes. The beneficial allele B (dark grey individuals) substitutes the ancestral b allele (white). The B allele arises three times by independent mutation; individuals then change their color from white to grey, but keep their haplotype pattern. The "zoom" into a single time step shows how reproduction and mutation are separated. Directly after fixation (time 0), we take a sample of size three (K,L,M) that contains descendents from the first (L,M) and the second (K) mutational origin of B. The right panel shows DNA fragments of the sampled individuals. The vertical ticks represent neutral polymorphisms. Individuals L and M share a recent ancestor and are identical in this region of the genome. Individual K carries a different ancestral haplotype.
Soft sweeps III - The signature of positive selection from recurrent mutation
P. S. Pennings and J. Hermisson (2006)
PLoS Genetics (2006) 2(12): e186
The percentage of simulation runs that yielded a significant test statistic depending on the value of the beneficial mutation rate Theta_b, other parameters as standard. The x-axis shows the distance from the selected site. The y-axis shows the time since fixation of the B allele in units of N_e generations.
