Table 2.
Rip coding sequences under strong diversifying positive selection on the protein level
|
T3E gene
|
Number of strains |
Alignment length (nt) |
Population recombination rate,
N
e
r
(
P
LPT
)
a
|
LRT statistic values for codon model pairs
b
|
Proportions of sites in different selection regimes
c
|
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| M0 vs M3 | M1a vs M2a | M7 vs M8 | M8a vs M8 | Strict negative (ω< 0.15) | Relaxed negative (0.15 <ω<0.9) | Neutral (0.9<ω<1) | Positive (ω>1) | ||||
|
RipAA |
10 |
906 |
10 (0.33) |
134.9 |
6.2 |
14.4 |
13.1 |
38% (ω=0.04) |
56% (ω=0.48) |
0% |
6% (ω=2.9) |
|
RipAJ |
11 |
936 |
2 (0.54) |
150.5 |
7.2 |
11.9 |
13.3 |
46% (ω=0.04) |
46% (ω=0.49) |
9% |
7% (ω=3.1) |
|
RipAT |
9 |
1764 |
0 (0.04) |
191.1 |
11.5 |
17.3 |
13.3 |
38% (ω=0.04) |
48% (ω=0.54) |
10% |
5% (ω=3.3) |
|
RipAW |
6 |
1359 |
6 (0.00) |
177.6 |
9.4 |
15.0 |
20.6 |
38% (ω=0.02) |
48% (ω=0.51) |
10% |
5% (ω=4.9) |
|
RipAP |
7 |
2400 |
0 (0.22) |
148.6 |
18.2 |
21.7 |
27.6 |
59% (ω=0.02) |
29% (ω=0.48) |
10% |
2% (ω=10.0) |
|
RipD |
11 |
1971 |
3 (0.18) |
266.5 |
7.2 |
16.7 |
12.7 |
38% (ω=0.04) |
47% (ω=0.47) |
9% |
6% (ω=2.8) |
|
RipG7 |
10 |
2016 |
10 (0.00) |
561.6 |
28.1 |
37.6 |
43.0 |
46% (ω=0.04) |
28% (ω=0.59) |
19% |
7% (ω=3.4) |
|
RipH3 |
9 |
2229 |
4 (0.81) |
145.7 |
19.5 |
29.5 |
25.1 |
29% (ω=0.07) |
57% (ω=0.56) |
10% |
4% (ω=3.8) |
| RipS7 | 7 | 9570 | 0 (0.00) | 329.0 | 30.4 | 34.3 | 42.2 | 48% (ω=0.03) | 38% (ω=0.44) | 10% | 5% (ω=4.0) |
aValues supporting evidence for recombination are shown in bold.
bFor the presented 9 genes all three LRTs for positive selection were significant, as well as the LRT comparing M0 vs M3 supporting strong variability of selection pressure among sites. Codon models are as described in [74].
cEstimates of selection regimes are according to model M8 if LRT comparing M8a and M8 was significant. Otherwise, selection regimes are reported according to model M8a. For strict and relaxed negative selection, the average omega value over respective selection classes is shown. Note that percentages for the four categories do not always add up to 100% due to rounding.