AFLP1 AFLP2 AFLP3
Restriction enzymes EcoRI – MseI EcoRI – MseI EcoRI – TaqI
Selective PCR * 9 6 1
Post-amplification restriction enzymes RsaI - HinfI - MboI
MseI - NlaIII - AluI
Sampling years 2003–2004   2008–2009   2008–2009  
  n Loci n Loci n Loci
Site D 7 322 (141) 22 152 (77)
Site F 10 750 (385) 9 330 (164) 18 154 (75)
Site G 8 317 (154) 20 159 (81)
Site M 6 759 (301) 8 315 (148) 19 156 (75)
Site Y 5 641 (195) 11 329 (159) 23 157 (75)
Total LSP 21 842 (476) 43 349 (214) 102 160 (99)
Lake M2 7 160 (42)
Lake O2 7 174 (86)
All lakes 21 842 (476) 43 349 (214) 116 187 (136)
*Selective combinations used for AFLP 1 (EcoANN×MseCNN) AC×AG, AC×TC, GC×AG, AC×GC, CG×GC, CG×AG, GG×TT, AG×CC, GC×CC; AFLP 2 (EcoANN×MseCNN) AC×TC, CG×GC, AG×CC, GC×TT, AC×TT, AG×AG; AFLP 3 EcoACG×TaqCTA  
Table 2: Characteristics of the different AFLP surveys performed in this study. For each survey, the number of individuals and number of loci surveyed are indicated; polymorphic loci are in parentheses.
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