Background selection: refers to a process in which weakly deleterious mutations drift up to low frequencies and are then purged from the population. This causes a reduction in diversity, especially around conserved regions. In some respects, the signals of background selection can mimic patterns produced by positive selection [ 29 McVicker G.

Gordon D.

Davis C.

Green P. Widespread genomic signatures of natural selection in hominid evolution. 32 Charlesworth B.

Morgan M.T.

Charlesworth D. The effect of deleterious mutations on neutral molecular variation. refers to a process in which weakly deleterious mutations drift up to low frequencies and are then purged from the population. This causes a reduction in diversity, especially around conserved regions. In some respects, the signals of background selection can mimic patterns produced by positive selection [].

F ST : a classical measure of the amount of allele frequency differentiation between two or more populations. F ST can take values between 0 and 1, with 0 corresponding to identical allele frequencies in both (all) populations, and 1 corresponding to a fixed difference: i.e., that the allele is absent in one population, and fixed in the other. High F ST values for particular SNPs may sometimes provide evidence that those SNPs are under selection.

Hard sweep: the classical selective sweep model in which a new advantageous mutation arises, and spreads quickly to fixation due to natural selection [ 40 Maynard Smith J.

Haigh J. The hitch-hiking effect of a favourable gene. 5 Sabeti P.C.

Schaffner S.F.

Fry B.

Lohmueller J.

Varilly P.

Shamovsky O.

Palma A.

Mikkelsen T.S.

Altshuler D.

Lander E.S. Positive natural selection in the human lineage. the classical selective sweep model in which a new advantageous mutation arises, and spreads quickly to fixation due to natural selection []. Under this model, neutral variation near to the favored site “hitch-hikes” along with the favored allele. This impacts patterns of variation around the selected site in ways that can be detected using a variety of tests of selection [].

Mutational target size: refers to the number of sites at a locus that, if appropriately mutated, could generate a particular favored phenotype. For example, it appears that several mutations in an upstream enhancer of lactase cause lifelong expression of the lactase gene [ 27 Tishkoff S.A.

Reed F.A.

Ranciaro A.

Voight B.F.

Babbitt C.C.

Silverman J.S.

Powell K.

Mortensen H.M.

Hirbo J.B.

Osman M.

et al. Convergent adaptation of human lactase persistence in Africa and Eur. 76 Enattah N.S.

Sahi T.

Savilahti E.

Terwilliger J.D.

Peltonen L.

Jarvela I. Identification of a variant associated with adult-type hypolactasia. refers to the number of sites at a locus that, if appropriately mutated, could generate a particular favored phenotype. For example, it appears that several mutations in an upstream enhancer of lactase cause lifelong expression of the lactase gene []. The size of the mutational target affects the probability that standing variation will be available to allow rapid evolution following an environmental change.

Polygenic adaptation: here, we use this term to describe a process in which adaptation occurs by simultaneous selection on variants at many loci (perhaps tens or hundreds or more). We envisage that a common scenario of polygenic adaptation would be that there is a shift in the optimal phenotype for a quantitative trait that is affected by hundreds of alleles of small effect. In this case, we can anticipate a response to selection that is due to small frequency shifts of many alleles. Polygenic adaptation might also occur from new mutations at many loci, following a shift in the optimal phenotype. This latter scenario would be most likely if the newly favored phenotype had previously been strongly disfavored.

Partial sweep: an event in which a favored allele increases rapidly from low frequency, but has not yet reached fixation (perhaps because the sweep is still in progress, or because the selective advantage of the favored allele has weakened).

Selective sweep: an event in which the frequency of a favored allele increases rapidly due to selection. This term is often understood to refer to complete hard sweeps, but may also refer to partial sweeps or soft sweeps (see below), depending on the context.

Soft sweep: this term was introduced to describe two slightly different scenarios that both contrast with the standard hard sweep model [ 41 Hermisson J.

Pennings P.S. Soft sweeps: molecular population genetics of adaptation from standing genetic variation. this term was introduced to describe two slightly different scenarios that both contrast with the standard hard sweep model []. In one scenario, due to a change in selection, an allele that is already segregating in the population (i.e., standing variation) becomes selectively favored, and sweeps up in frequency. It is usually assumed that the allele is neutral or mildly deleterious prior to the change in selection. In the second scenario, multiple independent mutations at a single locus are all favored and all increase in frequency simultaneously until the sum of the frequencies is 1. If the favored alleles are all similarly advantageous, then typically none of the favored mutations would fix during the selective event. Both scenarios tend to be more difficult than hard sweeps to detect using standard tests of selection.

Standing variation: variants that are polymorphic in a population. The term is used here in the context of a selective force that is turned on so that variants that had been drifting (nearly) neutrally suddenly become favored.