Table 3. Results for the 51 genes for the monocot/eudicot chloroplast dataset, and with the ancestral sequences (a_x and a_y) inferred independently.

Gene	Gene length(amino acids)	Ancestral alignmentscore	Number of higher alignment scores	Proportion of higher alignment scores	Chi-squared term
atpA	503	440.6	8	0.0076	9.7656
atpB	433	390.7	58	0.0549	5.8036
atpF	178	159.9	2	0.0019	12.5382
atpH	81	72.5	364	0.3447	2.1302
atpI	241	263.2	10	0.0095	9.3193
ccsA	150	200.8	16	0.0152	8.3793
cemA	155	158.0	30	0.0284	7.1221
clpP	186	129.5	80	0.0758	5.1604
matK	380	338.8	1	0.0009	13.9245
petA	313	306.2	1	0.0009	13.9245
petB	213	245.6	611	0.5786	1.0943
petD	157	179.2	850	0.8049	0.4340
petG	37	36.8	665	0.6297	0.9249
petL	30	26.4	15	0.0142	8.5084
petN	29	38.1	741	0.7017	0.7085
psaA	748	926.2	35	0.0331	6.8138
psaB	733	952.9	45	0.0426	6.3112
psaC	81	107.1	338	0.3201	2.2784
psaI	24	20.8	35	0.0331	6.8138
psaJ	22	26.5	589	0.5578	1.1676
psbA	319	383.6	208	0.1970	3.2494
psbB	506	639.2	33	0.0313	6.9315
psbC	460	581.6	181	0.1714	3.5275
psbD	345	439.3	274	0.2595	2.6982
psbE	80	90.5	419	0.3968	1.8488
psbF	39	43.8	387	0.3665	2.0076
psbH	71	71.5	7	0.0066	10.0327
psbJ	30	36.6	119	0.1127	4.3662
psbK	57	56.2	436	0.4129	1.7692
psbL	38	41.3	998	0.9451	0.1130
psbM	34	29.2	211	0.1998	3.2208
psbN	43	41.0	778	0.7367	0.6110
psbT	30	30.9	782	0.7405	0.6008
psbZ	16	12.1	469	0.4441	1.6233
rbcL	443	490.1	728	0.6894	0.7439
rpl14	122	112.4	66	0.0625	5.5452
rpl16	126	142.4	8	0.0076	9.7656
rpl2	201	210.9	13	0.0123	8.7946
rpoA	256	246.2	0	0.0009	13.9245
rpoB	824	837.7	0	0.0009	13.9245
rpoC1	270	281.3	253	0.2396	2.8577
rpoC2	1168	1138.0	0	0.0009	13.9245
rps11	131	133.6	20	0.0189	7.9330
rps12	113	114.2	175	0.1657	3.5949
rps15	57	54.7	2	0.0019	12.5382
rps2	234	247.6	117	0.1108	4.4001
rps3	207	190.2	90	0.0852	4.9249
rps4	105	98.0	22	0.0208	7.7424
rps7	155	143.2	274	0.2595	2.6982
rps8	125	107.6	47	0.0445	6.2242
ycf3	157	170.3	158	0.1496	3.7993
Av/Sum	224.6	239.9	230.8	0.2186	289.0582