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Table 3 Mutations Identified by Genome Sequencing.

From: Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage φX174

Genome positiona

Treatmentb

nt change

 

Protein/positionc

Amino acid changed

 

Evidence change is adaptivee

181

C, B

G

T

C17, K44

A, C

S, F

Parallel High frequency Previous (3)

563

C, B

C

T

(D58)

-

-

Parallel High frequency Previous (1)

576

C

C

T

(E3), (D63)

-

-

High frequency Previous (1)

581

C

C

T

E5, (D64)

T,-

I,-

Previous (1)

587

C

G

T

E7, (D66)

W, -

L, -

Parallel High frequency

593

C, B

C

T

E9, (D68)

T, -

I, -

Parallel High frequency Previous (1)

624

B

G

T

D79, E19 E74,

A, L

S, F

None

788

C, B

C

T

(D133)

T,-

M,-

Parallel High frequency Measured

878

B

T

C

J11

C

N

High frequency

1033

C

G

T

F10

M

I

High frequency Previous (1)

1138

H

C

T

(F45)

-

-

None

1216

C

C

T

(F71)

-

-

None

1295

C, B

A

G

F98

N

D

Parallel Previous (6)

1302

C

C

G

F100

T

S

Parallel Previous (1)

1611

C, B

A

G

F203

H

R

Parallel High frequency Previous (4) Measured

1690

C

C

T

(F229)

-

-

None

1702

C, B

T

C

(F233)

-

-

Parallel Previous (1)

2772

B

T

C

(G126)

-

-

High frequency

2971

H

C

T

H14

A

V

High frequency Previous (6)

2973

H

G

A

H15

G

S

High frequency Previous (1)

3039

H

G

T

H37

V

L

High frequency

3129

H

G

T

H67

A

S

Parallel High frequency

3340

C

A

G

H137

G

D

High frequency Previous (4)

  1. a Genome position of nucleotide mutation.
  2. b C = control; B = benign; H = harsh.
  3. c Gene product (indicated by letter) and amino acid position of mutation.
  4. d Effect of the mutation at the amino acid level (from amino acid/to amino acid). Gene product C is involved in DNA replication, D is the external scaffolding protein, E is the lysis protein, F is the major capsid protein, G is the minor capsid protein, H is the pilot protein, J is the DNA binding protein, and K is of unknown function. Because φX174 has overlapping reading frames, some changes affect more than one protein.
  5. e Evidence that a particular change is adaptive includes: Parallel = occurrence in multiple lines of this study; High frequency = occurrence in multiple isolates in a population in this study, indicating the change was at high frequency in the population and that there was no evidence of hitchhiking; Previous (#) = occurrence in previous evolution experiments (the number of evolution lineages that the mutation was observed) [24,26-29, and unpublished data]; Measured = measurement of fitness effects. None = no independent evidence that the mutation is adaptive. Of the mutations considered to be adaptive by the criteria above, hitchhiking could not be ruled out for 2973 and 581. However, both of these mutations have occurred previously under very similar experimental conditions and there are additional indicators that these mutations are adaptive: 581 affects an amino acid two away from another that is adaptive in this experiment (protein E, site 7 vs E7), and is also two sites away from a site known to have a large effect on lysis regulation (E3 [32]). Mutation 2973 at H15 is adjacent to site H14 which showed strong evidence of being adaptive.
  6. Parentheses indicate synonymous substitutions.