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Tajima's D is a population genetic test statistic created by and named after the Japanese researcher Fumio Tajima. [1] Tajima's D is computed as the difference between two measures of genetic diversity: the mean number of pairwise differences and the number of segregating sites, each scaled so that they are expected to be the same in a neutrally evolving population of constant size.
Comparing the value of the Watterson's estimator, to nucleotide diversity is the basis of Tajima's D which allows inference of the evolutionary regime of a given locus.
Fumio Tajima was born in Ōkawa, in Japan's Fukuoka prefecture, in 1951. [1] [2] He graduated from high school in 1970, completed his undergraduate degree at Kyushu University in 1976, and received a Master's degree from the same institution in 1978. [3]
The allele frequency spectrum can be written as the vector = (,,,,), where is the number of observed sites with derived allele frequency .In this example, the observed allele frequency spectrum is (,,,,), due to four instances of a single observed derived allele at a particular SNP loci, two instances of two derived alleles, and so on.
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Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many sophisticated methods and tools for phylogenomics and phylomedicine .
Fay and Wu's H is a statistical test created by and named after two researchers Justin Fay and Chung-I Wu. [1] The purpose of the test is to distinguish between a DNA sequence evolving randomly ("neutrally") and one evolving under positive selection.
Tajima's D is based on the expectation that S = theta * x where x is the sum of 1/i for i from 1 to N. Thus, we turn this into a method to estimate theta by noting that theta = E(S)/x. The current version suggests that S/x part is a "normalized" version of segregating sites, and this leads to a mistake in the calculation of D in the example.