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Table 3 Standard diversity indices and mismatch distribution analyses obtained from d-loop sequence of 855 birds belonging to 13 populations. Coturnix japonica that was used as an outgroup is not included.

From: Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken

  India Indonesia Japan Misc.* China murghi gallus spadiceus Bankiva G. jabouillei G. Varius G. lafayettei G. sonneratii
Group→ G. gallus domesticus (Domestic chicken) G. gallus (RJF) Other species of Gallus
Sample size 43 12 104 4 551 56 21 41 6 3 4 3 6
Haplotypes 23 6 26 - 82 42 15 12 6 - - - 5
Haplotype diversity (Hd) 0.932 0.836 0.925 - 0.934 0.948 0.971 0.789 1.000 - - - 0.933
Sum of square freqs. 0.023 0.083 0.010 0 0.002 0.018 0.048 0.024 0.167 0 0.250 0.333 0.167
Number of observed transitions 30 16 30 17 49 45 31 23 8 14 7 4 33
Number of observed transversions 20 0 3 0 9 47 3 4 0 1 3 1 2
Number of substitutions 50 16 33 17 58 92 34 27 8 15 10 5 35
Number of polymorphic sites 55 16 37 17 55 113 36 29 10 15 75 5 39
Nucleotide diversity Standard deviation (±) 0.018 0.009 0.015 0.008 0.021 0.011 0.024 0.016 0.018 0.009 0.029 0.015 0.022 0.011 0.023 0.011 0.012 0.008 0.025 0.019 0.082 0.054 0.007 0.006 0.034 0.020
Mismatch observed mean 7.409 6.000 8.670 9.500 7.354 12.436 8.800 9.229 5.000 10.000 38.000 3.333 16.000
Harpending's Raggedness index 0.021 0.236 0.012 0.167 0.009 0.001 0.029 0.136    0.750 1.000 0.289
P (Sim. Rag. > = Obs. Rag.) 0.310 0.000 0.230 0.960 0.310 1.000 0.300 0.000    0.120 0.860 0.160
Tajima's D -1.406 0.571 0.835 0.250 -0.148 -1.923 -0.352 1.518 0.947 0 -0.222 0 -0.357
P(D random < D obs) 0.075 -0.293 -0.204 -0.321 0.470 0.015 0.383 -0.073 -0.204 0 0.540 0 0.420
Fs -24.995 -7.215 -24.627 0.273 NC -24.401 -14.732 -24.738 -2.160 1.139 1.798 -0.077 -0.284
Prob(sim_Fs < = obs_Fs) 0 0.001 0 0.319 - 0 0 0 0.049 0.46 0.496 0.239 0.233
  1. * Misc. represents birds from Iran, UK and Vietnam. NC – not calculated.