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Fig. 2. | BMC Biology

Fig. 2.

From: Detecting positive selection in the genome

Fig. 2.

The site frequency spectrum. The numbers of variants segregating at different frequencies in a population can be summarized as the site frequency spectrum (SFS). Consider the ten chromosome samples shown in a. Observations of a particular minor allele frequency are used to populate the folded SFS b. ‘Unfolding’ the SFS requires knowledge of whether alleles are ancestral or derived. Aligning sequenced data to an outgroup (the blue nucleotides in a) allows the inference of ancestral and derived states for polymorphic and diverged sites, by maximum parsimony. However, the parsimony approach makes a number of biologically unrealistic assumptions; for example, that there have been no mutations in the lineage leading to the outgroup. Because of these, a number of alternative approaches have been proposed that have been shown to be more accurate than parsimony (e.g. [15]). Various evolutionary processes can alter the SFS, including directional and balancing selection, gene conversion, population size change and migration. For example, purifying selection prevents harmful variants from rising in frequency, resulting in a skew in the SFS towards rare variants. Multiple statistics have been proposed to summarize both the folded and unfolded SFS, and these can shed light on the evolutionary process (reviewed in [4])

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