Site frequency spectrum: why most variants are rare

Sample

Effective size Ne

Sets the time scale: one coalescent unit is 2 Ne generations.

Sample size (chromosomes)

Theta = 4 Ne mu

Expected number of singletons in the sample, and expected pairwise differences.

Spectrum

Unfolded needs to know which allele is ancestral; folded counts the minor allele.

Log scale on the count axis

Replicate genealogies

The spectrum shown is the average; Tajima's D is summarised across them.

Demography

History

Bottleneck severity

Size during the small phase as a fraction of Ne.

Generations since the event

Trajectories tab

New mutations

Generations followed

Selection s

Fitness advantage of the new allele per copy. Acts on the trajectories; the spectrum tabs are neutral.

Seed

Spectrum

Segregating sites-

Singletons-

Singleton fraction-

Watterson theta-

Pi-