TABLE 4

Ne estimates and confidence intervals for data simulated with true Ne = 10, 20, or 50 for one or five generations (T)

f-statistic basedLikelihood based
LAFNeFk (SE)Embedded Image Summary of CIsNeLB (SE)Embedded Image Summary of CIs
Ne = 10, T = 1
5A11.1 (500)7071.62.8–∞8.4 (2.5)34.32.9–463
5aA10.0 (0.3)4.43.0–49.47.3 (0.3)4.22.8–57.7
10A9.7 (0.6)8.43.9–49.17.8 (0.3)4.33.6–130.6
10C11.2 (1209)17323.52.9–∞12.7 (6.6)93.52.1–475.3
20A10.4 (0.2)2.55.0–26.47.8 (0.1)2.64.4–21.2
Ne = 20, T = 5
5C23.8 (1683)24491.41.9–∞19.3 (8.1)119.93.6–478.2
5aA25.1 (0.6)10.48.3–86.317.3 (0.5)6.37.8–57.0
5B20.8 (0.6)8.77.1–79.419.4 (0.6)9.38.9–124.9
5aB19.6 (0.5)6.76.7–66.818.3 (0.5)6.88.4–62
5A26.3 (1.1)177.6–124.418.1 (0.5)7.76.3–105.6
10A26.9 (0.5)10.611.3–74.718.4 (0.4)5.49.7–53.9
20A25.9 (0.3)7.814.0–52.017.7 (0.3)3.910.6–35.3
5F24.5 (0.7)12.37.4–103.218.8 (0.6)8.16.9–117.3
Ne = 50, T = 5
10aA55.7 (1.3)2022.2–181.247.4 (1.0)17.323.3–136.7
10A56.9 (2.6)39.419.6–475.149.9 (2.1)30.020.4–435.5
20A57.6 (1.6)26.026.6–193.749.5 (1.3)18.426.4–183.0
  • The point estimates distributions obtained with 200 replicates are described for each parameter set in the columns NeFk and NeLB (i.e., mode of the likelihood curve for NeLB) by the median of the 200 point estimates and the standard error (SE) in parentheses. The square root of the mean squared error is also given in the following column (Embedded Image ) as a measure of accuracy. NeLB estimates were computed using NeMAX = 500. The spreads of the confidence and credible intervals (CIs) are summarized by the 5th percentile of the lower limits and the 95th percentile of the upper limits obtained from 200 simulation replicates. For example, x–y means 95% of the 200 lower limits independently obtained were above x, and 95% of the 200 upper limits independently obtained were below y. L, number of loci used; T, number of generations between samples; AF, allele frequencies array used to simulate populations (see Table 2).

  • a 60 individuals sampled (all other simulations have 30).