Table 4. Significant inter-chromosomal epistasis for non-Mendelian ratios in F₂ hybrid T. californicus, showing proportions of two-locus allelic classes relative to expected frequency for combinations of sex and mitochondrial background, after accounting for the main effect of single locus genotype frequency.

	Chr1	Chr2	M1	M2	A1A2	A1B2	A1H2	B1A2	B1B2	B1H2	H1A2	H1B2	H1H2	χ 2	P=
All	1	Mit	2	—	1.15	0.85	—	0.23	1.76	—	1.12	0.89	—	134.55	3 × 10−27
	4	7	5	1	1.05	1.05	0.95	0.092	1.22	1.25	1.28	0.90	0.93	74.34	7 × 10−13
F	1	Mit	2	—	1.16	0.84	—	0.26	1.74	—	1.19	0.81	—	99.10	8 × 10−20
	4	7	5	1	0.98	1.00	1.00	0.14	1.21	1.28	1.31	0.91	0.90	38.90	5 × 10−6
M	1	Mit	2	—	1.14	0.86	—	0.15	1.83	—	1.03	0.97	—	42.20	5 × 10−8
	2	Mit	2	—	1.27	0.70	—	0.64	1.37	—	1.04	0.95	—	32.72	4 × 10−6
	9	Mit	3	—	1.30	0.66	—	0.80	1.20	—	0.90	1.10	—	25.54	0.0001
	4	7	4	5	1.13	1.08	0.93	0.04	1.25	1.22	1.26	0.88	0.95	36.58	1 × 10−5
	4	6	1	1	1.56	0.77	0.74	0.84	1.24	0.98	0.84	0.98	1.09	27.97	0.00048
SCmit	4	7	5	1	1.16	0.97	0.95	0.17	1.22	1.22	1.23	0.93	0.94	32.22	8.5 × 10−5
SDmit	4	7	5	1	0.93	1.13	0.96	0.04	1.22	1.28	1.34	0.86	0.91	44.96	4 × 10−7
	4	6	1	1	1.62	0.85	0.72	0.80	1.14	1.02	0.78	0.99	1.10	32.40	7.9 × 10−5
SCmitF	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—
SCmitM	6	8	2	2	0.98	0.32	1.10	0.91	2.08	0.63	1.03	0.85	1.02	30.87	0.00015
SDmitF	—	—	—	—	—	—	—	—	—	—	—	—	—	—	—
SDmitM	4	6	1	1	2.04	0.76	0.56	0.78	1.15	1.01	0.61	1.02	1.16	41.00	2 × 10−6

Significantly interacting chromosomes are shown, with the most significantly interacting pair of markers M1 and M2 (numbered by position from 0 cM on each chromosomal linkage map). Here A equals the SC homozygote, B equals the SD homozygote and H equals the heterozygote at locus 1 or 2. The proportion of the observed frequency of each marker class relative to the random expectation is shown, with model χ² and P-value. The Bonferroni threshold is P<1.74 × 10⁻⁴, assuming 288 independent tests for All, F and M; P<1.89 × 10⁻⁴ assuming 264 tests for all other groups where there are no mitochondrial interactions.