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