Selection Sweep (Tajima's D)
Also known as: Tajima's D test, Selective sweep analysis, Neutrality test
Tajima's D is a statistical test designed to detect selective sweeps—recent, rapid fixation of advantageous mutations—from patterns of genetic variation in DNA sequences. Developed by Fumio Tajima in 1989, this test measures deviations from neutrality by comparing different measures of DNA sequence diversity. A significant Tajima's D value indicates departure from neutral evolution, suggesting positive selection, population structure, or demographic events.
Key highlights
- Simple calculation requiring only sequence alignment data
- Does not require specification of a selection model or fitness landscape
- Computationally efficient and widely implemented in population genetics software
- Sensitive to recent selective sweeps and demographic events
- Provides intuitive interpretation of deviation from neutrality
Intuition
This section is available to Pro members. Upgrade to Pro
How it works
This section is available to Pro members. Upgrade to Pro
When to use it
Use Tajima's D when investigating whether a genomic region shows evidence of recent selection or demographic events. It is most powerful for detecting recent, hard selective sweeps in moderately-sized populations. Avoid applying it when demographic history is complex or unknown, as population expansion or subdivision can produce D values mimicking selection. It is particularly useful as a screening test before deeper phylogenetic or population structure analysis.
Strengths & limitations
- Simple calculation requiring only sequence alignment data
- Does not require specification of a selection model or fitness landscape
- Computationally efficient and widely implemented in population genetics software
- Sensitive to recent selective sweeps and demographic events
- Provides intuitive interpretation of deviation from neutrality
- Cannot distinguish between positive selection and population expansion, which produce similar D signatures
- Limited power with small sample sizes or short genomic regions
- Sensitive to recombination, which can break the characteristic selection sweep signature
- Assumes a single, well-mixed population; population structure inflates false positive rates
- Does not identify the target of selection or the mechanism of selective advantage
Common pitfalls
This section is available to Pro members. Upgrade to Pro
Applications
This section is available to Pro members. Upgrade to Pro
Frequently asked
What does a negative Tajima's D value indicate?
Negative D suggests an excess of rare alleles relative to intermediate-frequency variants. This is consistent with recent positive selection (a sweep) or recent population expansion, both of which increase the proportion of rare, newly-arising mutations.
Can Tajima's D distinguish between selection and demographic change?
Not definitively. Both recent selection and population expansion produce negative D values. Distinguishing them requires additional tests (e.g., Fu's Fs test) or demographic modeling. Multiple neutrality tests applied jointly provide stronger inference.
How many sequences are needed for a reliable Tajima's D test?
A minimum of 20–30 sequences is recommended for adequate statistical power. Smaller sample sizes reduce power dramatically. The test's power also depends on the genomic region's length and the intensity of selection.
Does recombination affect the interpretation of Tajima's D?
Yes. Recombination breaks linkage and decays the selective sweep signature over time. A region under strong recent selection may show reduced signal if recombination has shuffled alleles since the sweep occurred.
Sources
- 1.Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3), 585–595.
- 2.Braverman, J. M., Hudson, R. R., Kaplan, N. L., Langley, C. H., & Stephan, W. (1995). The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics, 140(2), 783–796.
- 3.Fay, J. C., & Wu, C. I. (2000). Hitchhiking under positive Darwinian selection. Genetics, 155(3), 1405–1413.
You have read it. What now?
Cite this page
ScholarGate. (2026, June 3). Selection Sweep (Tajima's D). ScholarGate. https://scholargate.app/genetics/selection-sweep