Trajectories Nobody Noticed: Allele Statistics Under Strong Selection ✎

Original: "How deterministic trajectories and their fluctuations underlie allele-frequency statistics in the strong-selection regime"
· David Waxman
arXiv:2609.14549v1 · 2026-09-13 · arXiv non-exclusive · independent analysis · 2 min
Even strong selection doesn't cancel out randomness: allele loss makes a contribution you can't afford to ignore.

A fast-flowing river scours its banks, yet part of the water slips away into a side channel. Evolution works the same way: even when selection pushes an allele hard toward fixation, randomness can steer it into the dead end of loss. For a long time researchers watched only the main channel, the deterministic trajectory along which the allele frequency climbs. The side channel, where the allele vanishes, was written off as irrelevant. That was a big mistake: for the variance of the frequency, the error reached 100%.

The author of the study proposes watching both channels. He writes the statistic of the allele frequency as the sum of two conditional expectations: one conditioned on the allele fixing, the other on it being lost. Each of them is rewritten in terms of a modified process with altered selection. Then comes an expansion in a small parameter, the inverse of the selection strength. The result is explicit expressions for the mean and the variance of the frequency at any point in time.

The mean is approximated by a sum of weighted deterministic trajectories plus a correction of order 1/R. The variance contains a term from the difference between the two trajectories and a term from fluctuations.

A numerical comparison with exact results from the Wright-Fisher model shows that the new method sharply reduces errors. At selection strength R=50 and an initial frequency of 0.001, the error in the mean drops from 10.6% to 3.2%, and the error in the variance from 12.6% to 4.9%. The fluctuation contribution matters most at early times, when the deterministic variance is nearly zero.

At R=50 and an initial frequency y=0.001, the deterministic contribution to the variance is essentially zero up to time τ≈5, whereas the fluctuation contribution describes the actual variance accurately.

Researchers now have a tool for seeing both channels of the river. The method applies to the analysis of time series of allele frequencies in experimental evolution, viral populations, and artificial selection programs. It helps estimate selection strength more accurately and predict the fate of beneficial alleles in small populations. The river of evolution has become more transparent.

Even under strong selection, when the deterministic force is large, the variance of the allele frequency can be almost entirely determined by random fluctuations for a long time. For example, at R=50 and initial frequency y=0.001, the deterministic contribution to the variance is essentially zero up to time τ≈5, whereas the fluctuation contribution accurately describes the actual variance.

R = 2 N_e |s|
R shows how many times the deterministic change in allele frequency due to selection exceeds random changes due to drift. When R >> 1, selection is strong.
Q(\tau) \simeq Q_0(\tau) + \frac{1}{R} Q_1(\tau)
The statistic Q (e.g., mean or variance) is expanded in the small parameter 1/R. Q0 is the contribution of the two deterministic trajectories, and Q1/R is the contribution of fluctuations.
\pi^{(1)}(y) = \frac{1 - e^{-2 \sigma R y}}{1 - e^{-2 \sigma R}}
The probability that an allele with initial frequency y eventually fixes (reaches frequency 1). This is Kimura's formula, depending on R and the sign of selection σ.
Concepts
Wright–Fisher model Fisher's fundamental theorem of natural selection statistical method trials factor transcription factor Percentile stochastic gene expression regime shift random walk average diagnostic accuracy