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

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.

	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

ISSN: 2730-7182