The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host

Table 3 Neutrality tests and test of positive selection for the H1N1 host-switch events.

	Model	p-MKT	p _D	np	ln L	p-value	ω	p_ω;	sites (95%)
PB2	H ₀			108	-10489.86		0.037	0.964	na
	H ₁	nfd	0.864	109	-10489.86	1.000	1.000	0.000	none
PB1	H ₀			116	-10150.60		0.022	0.960	na
	H ₁	nfd	0.528	117	-10150.60	1.000	0.022	0.960	none
PA	H ₀			110	-9736.96		0.032	0.955	na
	H ₁	nfd	0.940	111	-9736.96	1.000	1.000	0.000	none
HA	H ₀			158	-10294.27		0.067	0.862	na
	H ₁	nfd	0.066	159	-10288.97	0.001	2.190	0.003	D144T; G172N
NP	H ₀			110	-6402.15		0.037	0.948	na
	H ₁	nfd	0.965	111	-6402.15	1.000	1.000	0.001	none
NA	H ₀			154	-8083.65		0.075	0.728	na
	H ₁	nfd	0.611	155	-8078.72	0.002	8.469	0.002	V80K; Q250A; F351Y
M2	H ₀			224	-1700.43		0.136	0.611	na
	H ₁	nfd	0.824	225	-1697.33	0.013	34.479	0.010	none
M1	H ₀			142	-3173.37		0.021	0.941	na
	H ₁	nfd	0.569	143	-3173.37	1.000	1.000	0.001	(1 site)
NS2	H ₀			286	-2341.50		0.082	0.865	na
	H ₁	nfd	0.230	287	-2341.50	0.981	1.000	0.000	none
NS1	H ₀			182	-4142.63		0.125	0.699	na
	H ₁	nfd	0.334	183	-4142.63	1.000	1.000	0.000	none

Results of the McDonald-Kreitman test (MKT; p-value), Tajima's D test (p_D), as well as log-likelihood values (ln L), parameter estimates and p-values for the ten standard protein-coding genes of 2009 H1N1 Influenza A genomes. H₀ is the null branch-site codon model, without positive selection; H₁ is the alternative model that allows for positive selection at sites in the foreground branches. The p-values are derived from a $χ_{1}^{2}$ distribution (see Methods). Parameter estimates for ω and its proportion of sites p_ωare for rate categories ω < 1 under H₀, and ω ≥ 1 under H₁.
Notes--na: not applicable; nfd: no fixed differences. Sites in boldface are those for which the LRT rejects H₀ at the 1% level.

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