Population genetic processes affecting the mode of selective sweeps and effective population size in influenza virus H3N2

Table 1 Effect of s _d on nonsynonymous-to-synonymous substitution ratios for internal (ω_i) versus external (ω_e) branches and on π_s and f _soft

Dataset or model^a	Description	L	s	s _d	ω_i ^a	ω_e ^a	ω_e/ω_i ^a	π_s	f _soft	L _b	N
Fitch et al. 1997 [37]					0.28	0.40	1.44	6.2	0
Data from 1987 ~ 1996					0.27	0.35	1.28	6.2	0
B1	Equal s _d for all nonsynonymous non-beneficial sites	1,000	0.05	0.02	0.55	0.73	1.36	6.15	0.03	30	2 × 10³
				0.05	0.15	0.46	3.11	5.95	0.02	30
				0.1	0.10	0.26	2.75	6.32	0.04	30
			0.1	0.02	0.58	0.69	1.21	5.96	0.13	6	10⁴
				0.05	0.15	0.37	2.50	5.87	0.13	6
				0.1	0.09	0.19	2.13	5.94	0.16	6
			0.2	0.02	0.56	0.67	1.23	5.89	0.72	2	5 × 10⁴
				0.05	0.16	0.35	2.31	5.53	0.61	2
				0.1	0.09	0.19	2.25	5.98	0.72	2
		2,000	0.05	0.02	0.50	0.69	1.41	6.26	0.02	30	10⁴
				0.05	0.11	0.41	3.68	5.75	0.02	35
				0.1	0.04	0.20	5.42	7.15	0.04	20
			0.1	0.02	0.51	0.66	1.31	6.18	0.13	6	5 × 10⁴
				0.05	0.12	0.35	3.09	5.77	0.1	7
				0.1	0.04	0.17	4.22	6.40	0.19	5
B2	s _d is either 0.01, 0.02, 0.05, 0.1, or 0.2 (20 % of sites each)	1,000	0.1	0.01 ~ 0.2	0.37	0.44	1.22	6.03	0.14	6	10⁴
B2		2,000	0.1	0.01 ~ 0.2	0.29	0.41	1.44	6.52	0.16	5	5 × 10⁴
B3	25 % of nonsynonymous non-beneficial sites are neutral (s _d = 0), another 25 % lethal (s _d = 1), and the rest with a given value of s _d	1,000	0.1	0.02	0.56	0.59	1.07	6.35	0.19	5	10⁴
				0.05	0.38	0.43	1.16	6.01	0.15	6
				0.1	0.34	0.35	1.05	6.30	0.21	5
		2,000	0.1	0.02	0.53	0.59	1.13	6.25	0.17	6	2 × 10⁴
				0.05	0.33	0.42	1.32	5.93	0.14	6
				0.1	0.29	0.34	1.17	6.31	0.19	5

^aFor each parameter combination, simulation results were obtained as averages over 300 replicates and their standard errors are within 5 % of the values

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