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a selective sweep in that region (could be due to linkage too). The magnitude of the selective sweep will be decided by the strength of H. If the allele was the same, it means the sequence is experiencing negative selection and the ancestral state is maintained. On the other hand, an H close to 0 means that there is no evidence of deviation from
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Fay and Wu's H not only uses population polymorphism data but also data from an outgroup species. Due to the outgroup species, you can now tell what the ancestral state of the allele was before the two lineages split. If, for example, the ancestral allele was different, you can now say that there was
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A significantly positive Fay and Wu's H indicates a deficit of moderate- and high-frequency derived single nucleotide polymorphisms (SNPs) relative to equilibrium expectations, whereas a significant negative Fay and Wu's H indicates an excess of high-frequency derived SNPs.
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The sequence just experienced a bout of selective sweep (an allele rose to fixation/near fixation), so all alleles became homogenized. The rare polymorphisms you see are very recent, or
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88:, Tajima's D will show up negative and will tell you that the particular sequence was evolving non-randomly. However, you don't know whether this is because of some
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Imagine a DNA sequence which has very few polymorphisms in its alleles across different populations. This could arise due to at least three causes:
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The sequence is experiencing heavy negative selection, so any new mutation in the sequence is deleterious and is purged off immediately, or
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There was a population bottleneck, so all individuals in the population are derived from a small set (or one) common ancestor
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Now, when you calculate Tajima's D using all the alleles across all populations, because there is an excess of rare
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257:"A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selection"
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Sterken R, Kiekens R, Coppens E, Vercauteren I, Zabeau M, Inzé D, Flowers J, Vuylsteke M (October 2009).
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recently or due to population expansion/contraction. To know that, you calculate Fay and Wu's H.
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181:"Statistical method for testing the neutral mutation hypothesis by DNA polymorphism"
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evolving randomly ("neutrally") and one evolving under
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132:"Hitchhiking under positive Darwinian selection"
234:. Jones & Bartlett Learning. p. 436.
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308:Hartl, Daniel L.; Clark, Andrew G. (2007).
26:created by and named after two researchers
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16:Statistical test in population genetics
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312:(4th ed.). Sinauer Associates.
42:. This test is an advancement over
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451:Models of nucleotide substitution
310:Principles of Population Genetics
92:acting or whether there was some
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130:Fay, JC.; Wu, CI. (July 2000).
62:in their evolutionary history.
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655:. You can help Knowledge by
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228:Hedrick, Philip W. (2005).
148:10.1093/genetics/155.3.1405
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507:Nonsynonymous substitution
352:(Mac OS X, Linux, Windows)
346:(Mac OS X, Linux, Windows)
197:10.1093/genetics/123.3.585
179:Tajima F (November 1989).
732:Molecular biology stubs
502:Synonymous substitution
446:Models of DNA evolution
231:Genetics of Populations
537:-related article is a
273:10.1105/tpc.109.067017
425:Stabilizing selection
410:Directional selection
332:Computational tools:
48:directional selection
712:Statistical genetics
415:Disruptive selection
350:PopGenome R package
707:Molecular evolution
480:Molecular processes
405:Balancing selection
389:Molecular evolution
56:genetic hitchhiking
52:balancing selection
420:Negative selection
40:positive selection
717:Statistical tests
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649:molecular biology
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36:DNA sequence
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461:Ka/Ks ratio
696:Categories
535:statistics
466:Tajima's D
261:Plant Cell
117:References
102:neutrality
44:Tajima's D
32:Chung-I Wu
28:Justin Fay
344:Variscan
90:selection
592:genetics
291:19880799
185:Genetics
166:10880498
136:Genetics
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66:Concept
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30:and
702:DNA
277:PMC
269:doi
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.