What does a positive Tajima's D suggest about the allele frequency spectrum?

• A. Excess intermediate-frequency alleles, possibly balancing selection or population structure or bottlenecks.
• B. Excess rare alleles.
• C. Population expansion.
• D. Directional selection only.

Answer: (B)

A positive Tajima's D indicates the allele frequency spectrum has relatively more intermediate-frequency variants than expected under neutrality. This happens when alleles are maintained at moderate frequencies rather than being common at very low frequencies or rising to fixation. The pattern can arise from balancing selection, where multiple alleles are kept due to selective advantages, or from population structure (subpopulations with different allele frequencies) or a past bottleneck followed by recovery, which can inflate the number of alleles at intermediate frequencies. In this scenario, the average pairwise differences (pi) exceed what the number of segregating sites (theta_w) would predict, pushing D above zero.

If the spectrum were dominated by many rare alleles, Tajima's D would be negative, reflecting pi being less than theta_w. Populations that have recently expanded or are under strong purifying selection tend to show that negative signal. Directional selection alone doesn’t uniquely explain a positive D; the key clue is the surplus of intermediate-frequency variants relative to the neutral expectation.