Table 2.

Genome-wide local ancestry assignment values from PCAdmix.

		Reference populations
		Sardinian mouflon	Corsican mouflon	Domestic sheep	PP < 0.95
Focal population	Mouflon
	MSar1	26.3 ± 0.40	20.4 ± 3.26	10.8 ± 1.74	42.6 ± 1.84
	*MSar3	16.5 ± 0.59	11.5 ± 2.24	30.6 ± 3.49	41.4 ± 0.75
	MSpa	16.8 ± 2.19	48.3 ± 5.50	4.0 ± 0.29	30.9 ± 3.21
	Domestic sheep
	ALT	1.5 ± 0.85	2.6 ± 2.69	82.3 ± 11.43	13.6 ± 7.89
	CHI	1.4 ± 1.16	2.2 ± 2.87	85.8 ± 12.47	10.6 ± 8.45
	CHU	1.7 ± 1.01	2.8 ± 3.03	82 ± 12.68	13.5 ± 8.68
	COM	1.7 ± 0.92	2.5 ± 2.69	82.3 ± 11.47	13.5 ± 7.91
	CFT	1.0 ± 0.73	2.3 ± 3.17	87.7 ± 11.06	9.0 ± 7.16
	RAK	1.3 ± 0.60	2.3 ± 2.82	86.2 ± 10.74	10.2 ± 7.35
	SAR	1.5 ± 0.67	2.1 ± 2.21	85.5 ± 8.22	11.0 ± 5.34
	SBF	1.6 ± 0.84	3.3 ± 3.61	80.8 ± 12.86	14.3 ± 8.42
	SOA	2.3 ± 0.63	4.1 ± 3.37	80.0 ± 10.24	13.6 ± 6.26
	SPW	1.7 ± 1.05	3.3 ± 3.62	81.0 ± 12.76	14.1 ± 8.10
	VBN	1.5 ± 0.88	2.6 ± 3.17	84.4 ± 12.07	11.5 ± 8.03

Shown is the average proportion of genome assigned by PCAdmix with posterior probability ≥ 0.95 to Sardinian mouflon, Corsican mouflon and domestic sheep, respectively. PP < 0.95 denotes the cumulative genome proportion remaining unassigned with posterior probability < 0.95. Averages were calculated across four reference sets (detailed in S5 Table), each comprising the same mouflon references (MSar2 and MHun for Sardinian and Corsican mouflon, respectively) and four different domestic sheep breeds (CAS, ASM, LAC and SAB_p). An asterisk highlights the mouflon population (MSar3) that presents a higher sheep genetic component than mouflon. For population abbreviations see Table 1.