Tajima's D Track Settings
 
Tajima's D (from Human May 2004 assembly)   (All Variation and Repeats tracks)

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 Tajima's D AD  Tajima's D from African Descent (from Human May 2004 assembly)   Schema 
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 Tajima's D ED  Tajima's D from European Descent (from Human May 2004 assembly)   Schema 
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 Tajima's D XD  Tajima's D from Chinese Descent (from Human May 2004 assembly)   Schema 

Description

This track shows Tajima's D (Tajima, 1989), a measure of nucleotide diversity, estimated from the Perlegen data set (Hinds et al., 2005). Tajima's D is a statistic used to compare an observed nucleotide diversity against the expected diversity under the assumption that all polymorphisms are selectively neutral and constant population size. The track data were originally computed on the Human May 2004 assembly; their coordinates were transformed to this assembly using UCSC's liftOver program.

Methods

Tajima's D was estimated in 100 kbp sliding windows across the autosomal genome, reporting the Tajima's D measure at the central 10 kbp of the window and stepping by 10 kbp. Thus, the Tajima's D for the window chr1:100,001-200,000 is reported at coordinates chr1:145,001-155,000, the Tajima's D for the window chr1:110,001-210,000 is reported at coordinates chr1:155,001-165,000, and so forth.

The theoretical distribution of Tajima's D (95% c.i. between -2 and +2) assumes that polymorphism ascertainment is independent of allele frequency. High values of Tajima's D suggest an excess of common variation in a region, which can be consistent with balancing selection, population contraction. Negative values of Tajima's D, on the other hand, indicate an excess of rare variation, consistent with population growth, or positive selection. Population admixture can lead to either high or low Tajima's D values in theory. Demographic parameters would be expected to affect the genome more evenly than selective pressures, so previous analyses have suggested that using the empiric distribution of Tajima's D from a collection of regions across the genome provides advantages in assessing whether selection or demography might explain an observed deviation from expectation. Because of the ascertainment bias toward common polymorphism in the Perlegen data set, positive Tajima's D values are difficult to interpret, and modeling ascertainment is difficult. However, given that the ascertainment bias raises the mean of the distribution, extreme negative values in extended regions can be useful in qualitatively identifying interesting regions for full resequencing and more rigorous theoretical analysis of nucleotide diversity. For further discussion, see Carlson et al. (2005).

In full display mode, this track shows the nucleotide diversity across three human populations: 23 individuals of African American Descent (AD), 24 individuals of European Descent (ED) and 24 individuals of Chinese Descent (XD), as well as the polymorphic sites within each population used to estimate nucleotide diversity. Only SNPs observed to be polymorphic within each subpopulation were used in the Tajima's D calculation. Nucleotide diversity is shown in dense display mode using a grayscale density gradient, with light colors indicating low diversity.

Credits

This track was created at the University of Washington using gfetch from the Nickerson Laboratory and the R statistical software package.

References

Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989 Nov;123(3):585-95.

Carlson CS, Thomas DJ, Eberle M, Livingston R, Rieder M, Nickerson DA. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 2005 Nov;15(11):1553-65.