What does a negative Tajima's D indicate about the allele frequency spectrum?

• A. Excess rare alleles, suggesting population expansion or purifying selection.
• B. Excess intermediate-frequency alleles, balancing selection.
• C. No evidence for selection or demography.
• D. Bottleneck without recovery.

Answer: (C)

Negative Tajima's D shows that the allele frequency spectrum has more rare alleles than expected under neutrality with a constant population size. In other words, there’s an excess of low-frequency variants (singletons and very rare alleles) compared with the neutral expectation. This pattern can arise from recent population growth, where new mutations start at low frequencies, or from purifying selection removing deleterious variants, or from a recent selective sweep that reduces overall diversity and leaves many new variants at low frequencies. So, the key takeaway is that a negative value signals a skew toward rare alleles in the spectrum, rather than a neutral or uninformative pattern.