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Table 3 Classification of polymorphisms in Astyanax mexicanus Texas surface vs Pachón cave populations

From: Evidence for late Pleistocene origin of Astyanax mexicanus cavefish

  

Synonymous

Non-coding

Non-synonymous

 

Class

n

%

n

%

n

%

Ancestral fixed SF, derived fixed CF

(1)

540

12.8

157

12.7

301

14.3

Ancestral fixed CF, derived fixed SF

(2)

280

6.7

111

9.0

210

10.0

Polymorphism CF, ancestral fixed SF

(3)

476

11.3

146

11.8

302

14.5

Polymorphism CF, derived fixed SF

(4)

119

2.8

57

4.6

91

4.4

Polymorphism SF, ancestral fixed CF

(5)

2086

49.6

601

48.5

923

43.6

Polymorphism SF, derived fixed CF

(6)

393

9.3

87

7.0

159

7.8

Shared polymorphism

(7)

309

7.4

80

6.5

123

5.9

Divergent

(8)

1

0.0

0

0.0

0

0.0

Total

 

4204

100.0

1239

100.0

2110

100.0

Polymorphism SF

(5 + 6 + 7)

2788

 

768

 

1205

 

Polymorphism CF

(3 + 4 + 7)

904

 

283

 

516

 

Ratio SF/CF

 

3.08

 

2.71

 

2.34

 

Derived and fixed SF

(2 + 4)

399

 

168

 

302

 

Derived and fixed CF

(1 + 6)

933

 

244

 

460

 

Ratio CF/SF

 

2.34

 

1.45

 

1.52

 
  1. Thresholds: 100; MAF > 5%; Score Blast < 10–5; interval > 50 bp (see materials and methods for threshold definitions). CF: Cavefish; SF: Surface fish; numbers in brackets are class identifiers described in Fig. 4