Gu et al. 10.1073/pnas.0409159102.

Supporting Information

Files in this Data Supplement:

Supporting Table 5
Supporting Figure 5
Supporting Figure 6
Supporting Table 6
Supporting Table 7
Supporting Table 8




Table 5. Number of synonymous and nonsynonymous changes in the S288c and YJM789 branches for experimentally verified and unverified genes

 

Verified genes

Unverified genes

 

S*

N*

R = KA/KS†

S*

N*

R = KA/KS†

S288c

6,399.1

3,253.7

0.194

1,943.2

1,146.8

0.226

YJM789

6,235.2

2,729

0.167

1,720.9

902.4

0.200

S288c/YJM789

1.03

1.19

1.16

1.13

1.27

1.13

We used 3,041 verified genes and 979 unverified genes in this analysis. Fisher’s exact test showed that the nonsynonymous evolutionary rate is significantly higher in S288c than in YJM789 for either verified (P < 0.001) or unverified (P < 0.025) genes.

*S and N represent the number of synonymous and nonsynonymous changes, respectively.

†KS and KA represent the number of synonymous and nonsynonymous changes per synonymous and nonsynonymous site, respectively.





Supporting Figure 5

Fig. 5. Absolute increase of evolutionary rate in the laboratory strain for genes in different functional categories. Genes that locate in highly polymorphic regions between S288c and EM93 were excluded from analysis. The groups were ordered by decreasing number of genes in each category. The x-axis represents the absolute increase in evolutionary rate (R = KA/KS) in S288c. ***, P < 0.001 by Student’s t test for increase >0.





Supporting Figure 6

Fig. 6. Schematic relationship between evolutionary rate increase and population size reduction for genes under different negative selection pressure. Ne' and Ne are effective population sizes before and after population size reduction, respectively. As predicted by nearly neutral evolution, –1/2Ne' and –1/2Ne represent the thresholds of selection coefficients for nearly neutral mutation before and after population size reduction, respectively (refs. 1–6). Numbers 1–6 represent distributions of selection coefficients for mutations in genes with decreasing negative selection pressure. It can be reasoned that after population size reduction, the relative increase of the proportion under the curve that becomes nearly neutral (the part to the right of the thresholds) is the highest for the first group but least for the sixth group. The absolute increase, however, might not be the largest for the first group. One important point is that the prediction will not be affected by the underlying distribution of the selection coefficients, as long as the distributions are the same for different groups of genes.

1. Ohta, T. (1972) J. Mol. Evol. 1, 305–314.

2. Ohta, T. & Kimura, M. (1971) J. Mol. Evol. 1, 18–25.

3. Ohta, T. (1973) Nature 246, 96–98.

4. Ohta, T. (1987) J. Mol. Evol. 26, 1–6.

5. Ohta, T. (1993) Annu. Rev. Ecol. Syst. 23, 263–286.

6. Kimura, M. (1983) The Neutral Theory of Molecular Evolution (Cambridge Univ. Press, Cambridge, U.K.).





 

Table 6. Number of synonymous and nonsynonymous changes in the S288c and YJM789 branches after excluding genes with positive selection

  

Genes without adaptive evolution

 

 

S*

N*

R = KA/KS†

S288c

7,601.6

3,649.8

0.182

YJM789

7,313.7

3,086.6

0.160

S288c/YJM789

1.04

1.18

1.14

We used 3,789 genes in this analysis. Fisher’s exact test shows that the nonsynonymous evolutionary rate is significantly higher in S288c than in YJM789 (P < 0.001).

*S and N represent the number of synonymous and non-synonymous changes, respectively.

†KS and KA represent the number of synonymous and nonsynonymous changes per synonymous and nonsynonymous site, respectively.