The probability of hypothetical and published DNA polymorphism surveys under the neutral model

LocusSample sizeVariable sitesθWθπθHdP(BM)No. of occurrences of each derived variantP(D)P(H)
Example1031.060.605.400.0100.004[9 9 9]0.1280.002
Example1031.060.603.620.0100.004[1 9 9]0.1280.018
Example1031.060.601.840.0100.004[1 1 9]0.1280.090
Example1031.060.600.070.0100.004[1 1 1]0.1280.665
achaete14730.540.873.850.0620.084[84, 120, 141]0.8630.027
asense662.632.204.600.0380.014[1, 1, 1, 4, 5, 5]0.2150.077
Pgd13144.515.446.060.0690.026[1(2), 3(3), 4(3), 5(3), 10(2), 11]0.8250.298
vermilion4561.370.812.550.0220.008[1(3), 3, 24, 44]0.1600.070
Acp26Aa1015410.418.0717.970.1170.044See Figure 40.0830.043
  • d is divergence to the outgroup. P(BM) is the probability of a backmutation (materials and methods). P(D) and P(H) are the probability of observing a more negative D and H value under neutrality (α = 0.05, one sided), respectively. Numbers in parentheses indicate the number of sites where the derived variant is observed; i.e., Pgd has two singletons. For Acp26Aa, 4Nc/bp = 0.0725 was used to generate the expected distribution of D and H values. At two of the three polymorphic sites at the achaete locus, the derived variant was inferred to be a loss of a restriction site.