Table 2.

Branch-site tests for positive selection on lineage-specific expansion foreground branches

Clades	na	dbS	lnL		2Δlc (df = 1)	P value (without Bonferroni Correction)	P value (with Bonferroni Correction)
			Null model	Alternative model
9-exon1 $1 Aech & Acep	11 (6)	0.17	−7178.30	−7177.54	1.52	0.218	3.045
9-exon2 $1 Aech & Acep	20 (6)	0.11	−10419.64	−10408.81	21.65	3.27E-6**	4.57E-5**
$2 Pbar	20 (5)	0.11	−10426.11	−10422.62	6.98	8.26E-3*	0.116
9-exon3 $1 Aech & Acep	34 (32)	0.07	−12015.98	−11995.80	40.36	2.11E-10**	2.96E-09**
9-exon4 $1 Aech & Acep	23 (14)	0.11	−10103.70	−10099.98	7.43	6.42E-3*	0.089
A1 $1 Hsal	10 (5)	0.21	−8010.95	−8010.95	3.95	1	1
H1 $1 Aech & Acep	8 (6)	0.12	−3976.99	−3976.99	0.00	1	1
L1 $1 Aech & Acep	15 (7)	0.16	−8415.00	−8415.00	0.00	1	1
L2 $1 Aech & Acep	11 (9)	0.12	−5629.05	−5629.05	0.00	1	1
L3 $1 Aech & Acep	24 (20)	0.10	−11115.08	−11115.08	0.00	1	1
U1 $1 Aech & Acep	43 (16)	0.13	−22254.33	−22254.33	0.00	1	1
$2 Cflo	43 (6)	0.17	−22277.77	−22277.77	0.64	1	1
$3 Lhum	43 (10)	0.11	−22256.65	−22256.33	1.52	0.4233	1

^aNumber of sequences in the data set with number of sequences in the foreground branch in the parentheses

^bMean d_S for all branches estimated under M0 model

^cLog Likelihood ratios; 2x(lnL_H1 − lnL_H0)

** Significant at the 0.1 % level

* Significant at the 5 % level