Table 2. Summary of canid samples studied and the results of their genetic analyses.

Sequences and mutational positions are relative to the dog mtDNA reference sequence (U96639; [34]). Only haplotypes of sequences spanning nps 15459–15691 are reported here. Number of samples identified as coyotes are indicated, regardless of the span of the sequences used for the identification. See S2 Table for full results.

Unit of Comparison	Site	Site Name/ Component	Date (CE)	n	Dog haplotypes of sequences spanning nps 15459–15691							Dog Partial Sequence	Coyote	No DNA
					15484G, 15627G, 15639A	15627G, 15639A	15484G, 15567A, 15627G, 15639A	15484G, 15627G, 15639A, 15727T	15484G, 15522C, 15523C, 15627G, 15639A	15625C, 15627G, 15639A	15484G, 15553G, 15627G, 15639A
CMV Pre-1280 CE	5MT123	Albert Porter Pueblo	1060–1260	13	4	1	0	0	0	0	0	1	1	4
	5MT23	Grass Mesa Village	725–980	24	13	0	1	0	0	0	0	2	0	8
	5MT3807	Shields Pueblo	1060–1260	26	5	0	0	1	0	0	0	1	5	14
	5MT3936	Lillian's Site	1180–1225	1	1	0	0	0	0	0	0	0	0	0
	5MT4475	McPhee Pueblo	725–980	31	16	0	0	0	2	0	0	2	2	10
	5MT5	Yellow Jacket Pueblo	1020–1280	1	0	0	0	0	0	1	0	0	0	0
	5MT765	Sand Canyon Pueblo	1225–1280	2	0	0	0	0	0	0	0	0	0	2
	TOTAL			98	39	1	1	1	2	1	0	6	8	38
NRG Pre-1280 CE	LA265	No name	800–950	5	2	0	0	0	0	0	2	0	0	1
	LA3333	No name	1170–1230	5	5	0	0	0	0	0	0	0	0	0
	LA391	No name	1000–1100	1	0	0	0	0	0	0	0	0	0	1
	LA6169	No name	1200–1280	2	2	0	0	0	0	0	0	0	0	0
	TOTAL			13	9	0	0	0	0	0	2	0	0	2
NRG Post-1280 CE	LA275	Abiquiu Pueblo	1350–1450	4	0	0	0	0	0	0	0	0	4	0
	LA12	Arroyo Hondo, component I	1310–1345	10	0	0	0	0	0	0	0	0	5	5
	LA12	Arroyo Hondo, component II	1310–1345	2	0	0	0	0	0	0	0	0	1	1
	LA908	Tsama Pueblo	1425–1625	1	0	0	0	0	0	0	0	0	1	0
	TOTAL			17	0	0	0	0	0	0	0	0	11	6