TABLE 1.

LRT for the molecular clock hypothesis of HCV^a

Cluster	Donor or recipient	No. of strains	−ln ML	−ln MLK	Δl	P value
1	d	12	−401.94	−406.91	9.95	0.44
	r1	10	−394.22	−397.45	6.46	0.60
	r2	11	−426.17	−431.93	11.51	0.24
2	d	12	−462.00	−469.32	14.65	0.15
	r1	10	−475.88	−480.10	8.45	0.39
	r2	10	−431.01	−436.14	10.26	0.25
3	d	12	−437.37	−441.35	7.96	0.63
	r1	10	−447.43	−452.12	9.38	0.31
4	d	9	−439.42	−443.82	8.81	0.27
	r1	8	−430.99	−436.11	10.23	0.12
5	d	5	−396.05	−397.43	2.77	0.43
	r1	6	−474.37	−478.09	7.43	0.11
	r2	6	−498.87	−502.38	7.03	0.13
6	d	7	−403.67	−405.67	3.99	0.55
	r1	10	−577.45	−581.94	8.97	0.34

^aThe alignments used for testing the clock hypothesis were those described in Materials and Methods. Calculations were performed by PUZZLE (42), assuming the HKY85 model with uniform substitution rate across sites, except for r1 in cluster 2 and r1 in cluster 6, where γ-distributed rates across sites were assumed (see Results). ML and MLK are the likelihoods with and without the clock, respectively. Δl is the likelihood ratio statistic; if Δl is not significant (P > 0.05 in a χ² test with n − 2 df), the clock hypothesis cannot be rejected. Strains with identical sequences were removed from the alignment.