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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