Table 3. Summary of MK tests using intraspecific polymorphism within S. conica relative to interspecific divergence between S. conica and S. latifolia.

	Gene	Ps	Pn	Ds	Dn	NI	DoS	P-Value
Plastid CLP	CLPP3	8	3	16	83	0.07	0.57	0.000
	CLPP4	18	0	31	51	0.00	0.62	0.000
	CLPP5a	5	2	4	19	0.08	0.54	0.006
	CLPP5b	0	0	11	25	–	–	–
	CLPP6	0	2	11	59	–	−0.16	0.543
	CLPR1	1	1	22	144	0.15	0.37	0.256
	CLPR3	3	2	48	120	0.27	0.31	0.128
	CLPR4	1	1	22	80	0.28	0.28	0.337
	CLPC	4	1	55	50	0.28	0.28	0.226
	CLPT1	4	0	10	34	0.00	0.77	0.001
	CLPT2	7	1	19	39	0.07	0.55	0.002
	CLPS	3	0	11	2	0.00	0.15	0.467
	Concatenated	54	13	260	706	0.09 (0.11)	0.54	0.000
ACC	ACCA	13	7	42	111	0.20	0.38	0.001
	ACCB1	0	1	14	11	–	−0.56	0.270
	ACCB2	4	3	10	7	1.07	−0.02	0.939
	ACCC	10	3	22	18	0.37	0.22	0.160
	Concatenated	27	14	88	147	0.31 (0.31)	0.28	0.001
Photosystem I	LHCA2	4	0	19	6	0.00	0.24	0.271
	LHCA3	13	1	28	9	0.24	0.17	0.167
	PSAK	1	0	13	7	0.00	0.35	0.468
	PSAL	5	0	15	5	0.00	0.25	0.211
	PSAN	11	2	18	10	0.33	0.20	0.183
	Concatenated	34	3	93	37	0.22 (0.20)	0.20	0.011
mtCLP	CLPP2	1	1	21	4	5.25	−0.34	0.233
	CLPX2	4	5	26	23	1.41	−0.09	0.634
	CLPX3	9	3	12	8	0.50	0.15	0.387
	Concatenated	14	9	59	35	1.08 (1.05)	−0.02	0.866
Random	Concatenated	368	178	1297	570	1.10 (1.07)	−0.02	0.371

For each gene, the NI and the DoS were calculated, with NI values < 1 and DoS values > 0 indicative of positive selection (i.e., an excess of nonsynonymous divergence). For concatenations of genes within each complex, NI_TG (an unbiased estimator of NI) is reported in parentheses. Only concatenated results are reported for the set of random genes. Individual gene results for this random set are available in Table S6. MK, McDonald–Kreitman test; P_s, synonymous polymorphisms; P_n, nonsynonymous polymorphisms; D_s, synonymous divergence; D_n, nonsynonymous divergence; NI, neutrality index; DoS, direction of selection; CLP, caseinolytic protease; ACC, acetyl-coA carboxylase; mtCLP, mitochondrial-targeted CLP protease.