Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers

Recent development of DNA markers provides powerful tools for population ge netic analyses. Amplified fragment length polymorphism (AFLP) markers resul t from a polymerase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Becaus e AFLP markers have to be analysed as dominant loci in order to estimate po pulation genetic diversity and genetic structure parameters, one must assum e that dominant (amplified) alleles are identical in state, recessive (unam plified) alleles are identical in state, AFLP fragments segregate according to Mendelian expectations and that the genotypes of an AFLP locus are in H ardy-Weinberg equilibrium (HWE), The HWE assumption is untestable for natur al populations using dominant markers. Restriction fragment length polymorp hism (RFLP) markers segregate as codominant alleles, and can therefore be u sed to test the HWE assumption that is critical for analysing AFLP data. Th is study examined whether the dominant AFLP markers could provide accurate estimates of genetic variability for the Aedes aegypti mosquito populations of Trinidad, West Indies, by comparing genetic structure parameters using AFLP and RFLP markers. For AFLP markers, we tested a total of five primer c ombinations and scored 137 putative loci. For RFLP, we examined a total of eight mapped markers that provide a broad coverage of mosquito genome. The estimated average heterozygosity with AFLP markers was similar among the po pulations (0.39), and the observed average heterozygosity with RFLP markers varied from 0.44 to 0.58. The average F-ST (standardized among-population genetic variance) estimates were 0.033 for AFLP and 0.063 for RFLP markers. The genotypes at several RFLP loci were not in HWE, suggesting that the as sumption critical for analysing AFLP data was invalid for some loci of the mosquito populations in Trinidad. Therefore, the results suggest that, comp ared with dominant molecular markers, codominant DNA markers provide better estimates of population genetic variability, and offer more statistical po wer for detecting population genetic structure.