Table 4 The sensitivity of NI to sampling
Sample1 African1 African1 African19 African-American30 African-American
1 European1 European1 European20 European-Americanc30 European-Americanc
1 Japanesea1 Japaneseb1 Japaneseb
NIdZ*NIZ*NIZ*NIZ*NIZ*
ATPase2.27−0.372.78−0.442.84−0.451.62−0.221.65−0.22
COI12.50-1.086.89−0.8810.33-1.033.61-0.563.68-0.56
COII3.33−0.525.80−0.823.28−0.520.86−0.130.64−0.01
COIII2.36−0.531.38−0.141.60−0.391.38−0.230.95−0.08
Cyt-b3.78-0.573.64−0.553.64−0.552.29−0.363.23*-0.50
ND11.58−0.282.51−0.432.63−0.451.49−0.201.49−0.19
ND25.86-0.765.86-0.767.73-0.863.59−0.552.95-0.46
ND32.83−0.526.80−0.772.83−0.521.33−0.281.52−0.25
ND40.93−0.090.520.050.520.050.130.600.110.70
ND4L2.20−0.342.63−0.422.63−0.425.00−0.624.00−0.54
ND52.00−0.322.38−0.392.23−0.371.20−0.091.44−0.16
ND630.71*-1.225.50−0.741.79−0.251.30−0.201.17−0.16
All coding2.88*-0.462.50*-0.402.41*-0.391.46-0.171.55-0.19
NITG (C.I.)e2.85 (1.83, 4.99)2.60 (1.65, 3.91)2.56 (1.59, 3.81)1.48 (0.90, 2.24)1.59 (0.93, 2.36)
  • NI, neutrality index; ATPase, ATP synthase; CO, cytochrome c oxidase; Cyt-b, Cytochrome B; ND, NADH dehydrogenase; C.I., confidence interval; MK, McDonald-Kreitman.

  • a MK table counts from Nachman et al. (1996).

  • b MK table counts as mentioned previously, but substituting two different, randomly chosen Japanese samples.

  • c MK table counts from African-American and European-American sequences sampled from (Just et al. 2008) and (Rubino et al. 2012) with the chimpanzee mitochondrial reference genome as an outgroup (Horai et al. 1995).

  • d A count of 1 was added to each cell when calculating NI for any locus with a zero count in any cell. Values in bold indicate P ≤ 0.05; * indicates significant sample-wise Bonferroni-corrected P-value of less than 0.004 for Fisher’s exact test of the MK table.

  • e Calculated as in Table 3. No sample rejected Woolf’s test of homogeneity (P > 0.19 for all samples). Values in bold indicate that the confidence intervals do not overlap the neutral expectation of 1.