Table 1.

Analysis of Nonsynonymous (A) and Synonymous (S) Haplogroup-Associated and Private Polymorphisms^[Note]

	No. of Haplogroup-Associated Substitutions			No. of PrivateSubstitutions
mtDNAGene	A	S	A/S	A	S	A/S	Pa	NIb
ND1	9	26	.35	23	40	.58	NS	1.66
ND2	12	31	.39	15	44	.34	NS	.88
CO1	3	54	.06	28	49	.57	<.0001	10.29
CO2	4	13	.31	10	29	.35	NS	1.12
AT8	3	5	.60	13	12	1.08	NS	1.81
AT6	14	17	.82	34	21	1.62	NS	1.97
CO3	3	17	.18	18	33	.55	∼.05	3.09
ND3	3	9	.33	3	20	.15	NS	0.45
ND4L	1	8	.13	5	8	.63	NS	5.00
ND4	2	41	.05	25	53	.47	<.0004	9.67
ND5	18	51	.35	33	88	.38	NS	1.06
ND6	3	22	.14	17	21	.81	<.0116	5.94
CYb	14	36	.39	33	55	.60	NS	1.54
Total	89	330	.27	257	473	.54	≪.0001	2.02

Note.— Both types of polymorphisms are described in greater detail in the “Methods” section (see also Herrnstadt et al. [2002]).

^aP values were determined with Fisher’s exact test. “NS” indicates that the difference between the Ka/Ks ratios was not statistically significant (P>.05).

^bWe calculated an intraspecies neutrality index (NI) that is based on the interspecies index developed and used by Rand and Kann (1996). NI is a ratio of ratios and is calculated as (A-private/A-haplo)/(S-private/S-haplo). The value will be 1.0 under strict neutrality.