Table 2. mtDNA diversity in the Chad Basin.

		HVS-I						mtSNP						HVS-I plus mtSNP
	n	k	k/n	S	h	Π	M	k	k/n	S	h	π	M	k	k/n	S	h	π	M
Ethnic group
Hide	47	38	0.81	51	0.991±0.006	0.025±0.002	8.60	25	0.53	70	0.963±0.013	0.051±0.003	11.61	38	0.81	121	0.991±0.006	0.036±0.002	20.21
Kotoko	62	33	0.53	51	0.961±0.014	0.020±0.002	6.91	29	0.47	72	0.947±0.016	0.051±0.003	11.61	40	0.65	123	0.977±0.010	0.033±0.002	18.52
Mafa	57	37	0.65	62	0.980±0.008	0.023±0.002	7.80	32	0.56	71	0.961±0.012	0.047±0.012	10.52	42	0.74	133	0.985±0.007	0.032±0.002	18.32
Masa	41	35	0.85	43	0.991±0.008	0.022±0.002	7.34	26	0.63	67	0.971±0.012	0.049±0.003	11.01	36	0.88	110	0.993±0.008	0.032±0.002	18.35
Buduma	30	22	0.73	43	0.968±0.021	0.023±0.002	7.74	18	0.60	57	0.954±0.021	0.041±0.003	9.34	22	0.73	100	0.968±0.021	0.030±0.002	17.09
Chad Arabs	27	20	0.74	36	0.963±0.023	0.020±0.002	6.78	19	0.70	54	0.969±0.018	0.046±0.003	10.52	22	0.81	90	0.980±0.017	0.030±0.001	17.30
Shuwa Arabs	39	29	0.74	44	0.980±0.011	0.018±0.001	6.04	23	0.59	54	0.968±0.012	0.042±0.002	9.57	31	0.79	98	0.987±0.009	0.027±0.001	15.61
Fali	40	23	0.58	44	0.962±0.014	0.022±0.002	7.43	22	0.55	55	0.953±0.017	0.050±0003	11.32	26	0.65	99	0.971±0.013	0.033±0.002	18.75
Bongor Fulani	50	27	0.54	35	0.937±0.023	0.020±0.001	6.87	24	0.48	50	0.937±0.023	0.045±0.002	10.19	32	0.64	85	0.954±0.021	0.030±0.001	17.05
Tcheboua Fulani	40	21	0.53	42	0.953±0.016	0.021±0.002	7.31	19	1.30	52	0.942±0.017	0.043±0.002	9.87	27	0.68	94	0.971±0.014	0.030±0.002	17.19
Kanembu	50	38	0.76	57	0.989±0.006	0.026±0.002	8.80	31	0.62	68	0.978±0.008	0.049±0.003	10.99	42	0.84	125	0.993±0.006	0.035±0.002	19.79
Kanuri	59	47	0.80	55	0.990±0.006	0.022±±0.002	7.44	35	0.59	82	0.976±0.008	0.047±0.003	10.74	51	0.86	137	0.994±0.005	0.032±0.002	18.18
TOTAL	542	248	0.46	117	0.991±0.001	0.022±0.001	7.44	143	0.26	136	0.977±0.002	0.049±0.001	11.08	315	0.58	253	0.995±0.001	0.033±0.000	18.53
Lifestyle
Sedentary	386	195	0.51	107	0.990±0.001	0.022±0.001	7.57	112	0.29	128	0.975±0.002	0.050±0.001	11.22	237	0.61	235	0.994±0.001	0.033±0.001	18.79
Nomadic	156	83	0.53	73	0.979±0.005	0.021±0.001	7.01	59	0.38	91	0.969±0.0006	0.046±0.001	10.45	101	0.65	164	0.987±0.004	0.031±0.001	17.46
Language Family
Niger-Congo	130	60	0.46	61	0.964±0.007	0.021±0.001	7.28	45	0.35	80	0.956±0.009	0.047±0.001	10.56	75	0.58	141	0.980±0.006	0.031±0.001	17.85
Nilo-Saharan	109	80	0.73	74	0.993±0.002	0.024±0.001	8.25	55	0.50	96	0.978±0.005	0.050±0.002	11.25	88	0.81	170	0.995±0.002	0.034±0.001	19.49
Afro-Asiatic	303	151	0.50	105	0.990±0.001	0.021±0.001	7.23	101	0.33	119	0.977±0.003	0.049±0.001	10.98	192	0.63	217	0.995±0.001	0.032±0.001	18.21
Geographical region
North	267	143	0.54	98	0.990±0.002	0.021±0.001	7.26	96	0.36	117	0.978±0.003	0.049±0.001	11.00	1789	6.70	215	0.994±0.001	0.032±0.001	18.26
South	275	143	0.52	87	0.987±0.002	0.023±0.001	7.76	83	0.30	112	0.970±0.004	0.049±0.001	10.96	170	0.62	199	0.993±0.001	0.033±0.001	18.72

NOTE: n  =  sample size; k  =  number of different sequences; S  =  number of segregating sites; h  =  haplotype diversity; π  =  nucleotide diversity; M  =  average number of pairwise differences (mismatch observed mean). For all of the samples, the common segment of the HVS-I region analyzed ranges from position 16030 to 16370 (with the exception of samples #Fa108 and #Hi14 that present sequence ranges outside 16030–16370 and were therefore eliminated from the analysis; see Table S2).