In population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum, is the distribution of the allele frequencies of a given set of loci (often SNPs) in a population or sample.[1][2][3][4] Because an allele frequency spectrum is often a summary of or compared to sequenced samples of the whole population, it is a histogram with size depending on the number of sequenced individual chromosomes. Each entry in the frequency spectrum records the total number of loci with the corresponding derived allele frequency. Loci contributing to the frequency spectrum are assumed to be independently changing in frequency. Furthermore, loci are assumed to be biallelic (that is, with exactly two alleles present), although extensions for multiallelic frequency spectra exist.[5]
Many summary statistics of observed genetic variation are themselves summaries of the allele frequency spectrum, including estimates of such as Watterson's and Tajima's , Tajima's D, Fay and Wu's H and the fixation index .[6]
^Fisher, Ronald A. (1930). "The distribution of gene ratios for rare mutations". Proceedings of the Royal Society of Edinburgh. 50: 205–220.
^Wright, Sewall (1938). "The distribution of gene frequencies under irreversible mutation". Proc. Natl. Acad. Sci. USA. 24 (7): 253–259. Bibcode:1938PNAS...24..253W. doi:10.1073/pnas.24.7.253. PMC 1077089. PMID 16577841.
^Kimura, Motoo (1964). "Diffusion models in population genetics". J. Appl. Probab. 1 (2): 177–232. doi:10.2307/3211856. JSTOR 3211856. S2CID 86705023.
^Evans, Steven N.; Shvets, Yelena; Slatkin, Montgomery (2007). "Non-equilibrium theory of the allele frequency spectrum". Theoretical Population Biology. 71 (1): 109–119. arXiv:q-bio/0604010. doi:10.1016/j.tpb.2006.06.005. PMID 16887160. S2CID 924340.
^Jenkins, Paul A.; Mueller, Jonas W.; Song, Yun S. (2014). "General triallelic frequency spectrum under demographic models with variable population size". Genetics. 196 (1): 295–311. arXiv:1310.3444. doi:10.1534/genetics.113.158584. PMC 3872192. PMID 24214345.
^Durrett, Rick (2008). Probability Models for DNA Sequence Evolution(PDF) (2 ed.).
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