Table 3

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

Model

p-MKT

pD

np

ln L

p-value

ω

pω;

sites (95%)


PB2

H0

108

-10489.86

0.037

0.964

na

H1

nfd

0.864

109

-10489.86

1.000

1.000

0.000

none

PB1

H0

116

-10150.60

0.022

0.960

na

H1

nfd

0.528

117

-10150.60

1.000

0.022

0.960

none

PA

H0

110

-9736.96

0.032

0.955

na

H1

nfd

0.940

111

-9736.96

1.000

1.000

0.000

none

HA

H0

158

-10294.27

0.067

0.862

na

H1

nfd

0.066

159

-10288.97

0.001

2.190

0.003

D144T; G172N

NP

H0

110

-6402.15

0.037

0.948

na

H1

nfd

0.965

111

-6402.15

1.000

1.000

0.001

none

NA

H0

154

-8083.65

0.075

0.728

na

H1

nfd

0.611

155

-8078.72

0.002

8.469

0.002

V80K; Q250A; F351Y

M2

H0

224

-1700.43

0.136

0.611

na

H1

nfd

0.824

225

-1697.33

0.013

34.479

0.010

none

M1

H0

142

-3173.37

0.021

0.941

na

H1

nfd

0.569

143

-3173.37

1.000

1.000

0.001

(1 site)

NS2

H0

286

-2341.50

0.082

0.865

na

H1

nfd

0.230

287

-2341.50

0.981

1.000

0.000

none

NS1

H0

182

-4142.63

0.125

0.699

na

H1

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 (pD), 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 <a onClick="popup('http://www.biomedcentral.com/1471-2148/11/6/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2148/11/6/mathml/M2">View MathML</a> distribution (see Methods). Parameter estimates for ω and its proportion of sites pω are 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.

Abdussamad and Aris-Brosou BMC Evolutionary Biology 2011 11:6   doi:10.1186/1471-2148-11-6

Open Data