Table 1. Selection pressure analysis of 9 sites of the HA of avian, mammalian and human IAVs a.
| Site | Substitutions (Syn: Non-Syn) b | Pervasive selection dN/dS, FEL significance for dN≠dS c |
Episodic positive selection number of branches, MEME significance d | Directional selection (target in H, empirical Bayes factor) e | Comparative selection f | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| A | M | H | A | M | H | A | M | H | |||
| -2 | 13:14 | 0:1 | 2:5 | 0.491 * | 0.354 | 1.89 | 0 | 0 | 0 | ||
| 62 | 18:1 | 1:2 | 2:5 | 0.0237 *** | 0.548 | 1.57 | 0 | 0 | 0 | H>A ***, overall *** | |
| 63 | 4:5 | 1:2 | 1:2 | 0.145 *** | 0.767 | 0.782 | 0 | 0 | 0 | N (37) | |
| 81 | 3:7 | 0:0 | 0:1 | 0.378 * | 0 | 0.675 | 5 | 0 | 0 | overall * | |
| 92 | 10:16 | 1:2 | 0:2 | 0.504 * | 0.616 | 0.734 | 0 | 0 | 0 | T (41) | |
| 144 | 13:24 | 0:3 | 1:8 | 0.807 | 1.05 | 3.04 * | 0 | 0 | 0 * | H>A * | |
| 193 | 16:42 | 0:3 | 0:7 | 0.679 | 0.464 | 1.01 | 0 | 3 | 0 | ||
| 226 | 14:0 | 0:0 | 3:15 | 0 *** | 0 * | 6.98 *** | 0 | 0 | 7 *** | H>A ***, H>M ***, overall *** | |
| 228 | 17:0 | 1:1 | 2:0 | 0 *** | 0.23 | 0 ** | 0 | 0 | 0 | ||
a Groups A, M and H contained, respectively, 1492 sequences of avian IAVs, 406 sequences of equine, canine, feline and seal IAVs and 803 sequences of human IAVs isolated in the years from 1968 to the end of 1999 (set H). We restricted analyses only to internal branches (see Materials and Methods). Asterisks depict significance levels for the tests as follows: *, P< 0.05; **, P < 0.01; ***, P < 0.001.
b The number of synonymous and non-synonymous substitutions inferred to have occurred on internal branches in the corresponding group set with the SLAC method.
c Site-level dN/dS estimate along internal branches in the corresponding group inferred using the FEL method. Asterisks show significance levels for the test that dN≠dS. When significant result is obtained, negative selection is inferred if dN/dS < 1, otherwise diversifying positive selection is inferred.
d Site-level characterization of episodic positive selection in the corresponding group inferred using the MEME method. Asterisks show significance levels for the test that dN>dS for some fraction of branches. The number of individual branches where episodic selection may have acted is indicated as well (empirical Bayes factor ≥ 100)
e Site-level characterization of directional selection using the DEPS/FADE method. The residue that is the putative target of directional selection is indicated, with empirical Bayes factor supporting directional selection shown.
f Site-level characterization of differences in selective pressures between branch groups using the Contrast-FEL method. Asterisks show significance levels for the test that dN/dS differ between pairs of branch groups, or among all branch groups (overall). Notation like H>A means that dN/dS for “human” branches is greater than dN/dS for “avian” branches. Only significant results are listed.