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Table 2 Genotypes Identified by Genome Sequencing.

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

Anc

Treatment

Line

aMidpoint genotypes

bTotal

aEndpoint genotypes

bTotal

cCI

dAdap mut

anc

Control

1

788

10/10

788,1611, 563

5/9

n, Y

5

     

788,1611, 587

2/9

  
     

788,1611, 576

2/9

  

anc

Benign

1

788

2/10

1611

2/10

Y, Y

3

   

1611

2/10

1611, 563

3/10

  
   

878

5/10

1611, 593

5/10

  
   

878, 1702

1/10

    

anc

Harsh

1

ND

 

3129

9/9

--, n

1

anc788

Control

2

ND

 

181, 1033

8/10

--, y

3

     

181, 1033, 1216

1/10

  
     

181, 1295

1/10

  

anc788

Control

3

none

1/10

1302

1/10

Y, Y

3

   

1302

3/10

1302, 587

6/10

  
   

1702

1/10

1302, 593

2/10

  
   

3340

4/10

1302, 1690

1/10

  
   

3340, 581

1/10

    

anc788

Benign

2

none

5/9

563

8/10

y, y

3

   

563

2/9

1295

1/10

  
   

587

1/9

181

1/10

  
   

624

1/9

    

anc788

Benign

3

ND

 

563, 2772

8/9

--, n

2

     

563

1/9

  

anc788

Harsh

2

ND

 

3129, 2973

10/10

--, n

2

anc788

Harsh

3

none

2/9

3039

2/10

n, n

2

   

3039, 1138

1/9

3039, 2971

8/10

  
   

3039

6/9

    
  1. a Numbers indicate nucleotide positions that are different from ancestor; rows list the mutational position(s) for a single genotype. ND = not done; Bold = parallel mutations.
  2. b Total number of genotypes over total number of isolates sequenced.
  3. c CI status of mid- and endpoint populations; y means that multiple mutually exclusive genotypes are present (i.e., A versus B, or AB versus AC, but NOT A versus AB; the latter condition is simply a selective sweep in progress, not competition between genotypes). Y = strong CI, where multiple isolates of competing mutations were observed; y = weak CI, where only one competing isolate was observed.
  4. d Number of adaptive mutations in endpoint populations as determined from criteria in Table 3. Data were used for Mann-Whitney U-test of Ho: The number of adaptive mutations sampled in control/benign endpoint populations is similar to the number of adaptive mutations sampled in the harsh populations (i.e., adaptive mutations were not sampled from populations with different distributions of adaptive mutations).