Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes

Table 1 Polymorphism within the mtDNA control region (CR) and ATPase regions

Clade	Number of sites analyzed	Sample size (n)	Number of haplotypes (h)	Number of variable sites (%)	Nucleotide diversity (Pi) per site	Pi SD
CR
All_CR	335	83	29	49 (14.6)	0.04257	0.00214
NW_CRall	337	56	20	30 (8.9)	0.01718	0.00223
NW_CR1ew	341	9	2	4 (1.2)	0.01173	0.00587
NW_{CR2coyI+CR3coyII}	337	47	18	25 (7.4)	0.01424	0.00161
NW_CR2coyI	338	16	7	15 (4.4)	0.0155	0.00259
NW_CR3coyII	339	31	11	14 (4.1)	0.01019	0.0016
OW_CRall	345	24	7	11 (3.2)	0.01408	0.00176
OW_CR4gwNA	345	20	3	2 (0.6)	0.00386	0.00129
OW_CR5gwEU	345	4	4	7 (2.0)	0.01208	0.00227
ATPase
All_ATP	1067	89	26	104 (9.7)	0.02596	0.00177
NW_ATPall	1067	61	18	42 (3.9)	0.00543	0.00076
NW_ATP1ew	1067	12	2	5 (0.5)	0.00469	0.00234
NW_{ATP2coyI+ATP3coyII}	1067	49	16	33 (3.1)	0.00441	0.00056
NW_ATP2coyI	1067	37	10	16 (1.5)	0.003	0.00059
NW_ATP3coyII	1067	12	6	17 (1.6)	0.00594	0.00073
OW_ATPall	1067	27	7	19 (1.8)	0.00643	0.00157
OW_ATP4gwNA	1067	22	2	1 (0.09)	0.00094	0.00047
OW_ATP4gwEU	1067	5	5	17 (1.6)	0.00731	0.00164
ATPase6
All_ATP	681	89	23	65 (9.5)	0.02513	0.00016
NW_ATPall	681	61	16	28 (4.1)	0.00592	0.00079
NW_ATP1ew	681	12	2	5 (0.7)	0.00734	0.00367
NW_{ATP2coyI+ATP3coyII}	681	49	14	22 (3.2)	0.00495	0.00064
OW_ATPall	681	27	7	16 (2.3)	0.00839	0.00133
OW_ATP4gwNA	681	22	2	1 (0.1)	0.00147	0.00073
OW_ATP4gwEU	681	5	5	14 (2.1)	0.00881	0.00142
ATPase8
All_ATP	204	89	14	23 (11.3)	0.03507	0.00629
NW_ATPall	204	61	10	10 (4.9)	0.0111	0.00143
OW_ATPall	204	27	4	4 (2.0)	0.01062	0.00311

Analysis was conducted in DnaSP v. 5.10 with nucleotide diversity calculated according to [60]. Gaps were excluded in the analysis. The full 1067 bp of the ATPase region is section 7729 - 8795 in the Canis complete mtDNA genome (Genbank Accession DQ480510) and includes gene regions ATPase8 (204 bp), ATPase6 (681 bp), plus flanking regions that overlap with COX2 and COX3 genes. Subscripts refer to clade designations in Figures 2a and 2b. CR = control region; SD=standard deviation.

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