|
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. |
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| Group→ |
G. gallus domesticus (Domestic chicken) |
G. gallus (RJF) |
Other species of Gallus |
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|
|
|
|
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| India |
Indonesia |
Japan |
Misc.* |
China |
murghi |
gallus |
spadiceus |
Bankiva |
G. jabouillei |
G. Varius |
G. lafayettei |
G. sonneratii |
|
|
|
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| 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 |
|
* Misc. represents birds from Iran, UK and Vietnam. NC – not calculated. | |||||||||||||
Kanginakudru et al. BMC Evolutionary Biology 2008 8:174 doi:10.1186/1471-2148-8-174 |
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