Table 2.

Significant ABBA-BABA Test for Four Populations (P1, P2, P3, O).

P1	P2	P3	aABBA sites	aBABA sites	D (±SE)	bZ-score
Gene Flow with japonica
O. nivara	ausDJ123	japonica	65702	27461	0.41 ± 0.07	6.15
O. nivara	ausKasalath	japonica	60243	24190	0.43 ± 0.05	8.28
O. nivara	indicaIR64	japonica	71212	36520	0.32 ± 0.05	5.86
O. nivara	indica93-11	japonica	79451	32779	0.42 ± 0.05	9.14
Gene Flow with indica
O. rufipogon	japonica	indicaIR64	55955	31426	0.28 ± 0.05	5.80
O. rufipogon	japonica	indica93-11	58892	30055	0.32 ± 0.04	7.66
Gene Flow with aus
O. rufipogon	japonica	ausKasalath	52744	29107	0.29 ± 0.05	6.38
O. rufipogon	japonica	ausDJ123	55873	31422	0.28 ± 0.05	5.43
Gene Flow with O. rufipogon
O. nivara	ausDJ123	O. rufipogon	54327	32606	0.25 ± 0.05	4.71
O. nivara	ausKasalath	O. rufipogon	50974	29685	0.26 ± 0.06	4.52
O. nivara	indica93-11	O. rufipogon	65547	39474	0.25 ± 0.05	5.00

Note.—The ABBA-BABA test examines possible admixture between P3 lineage and P1 or P2 lineage. The O. punctata genome was used as the outgroup genome (O).

^aNumber of sites with allele conformations ABBA or BABA for 4 populations in order of P1, P2, P3, and O.

^bZ-score higher then 3.9 (P < 0.0001) are shown.