Following the development of PCR methods, molecular techniques have become
widely used for detecting genetic variation in natural populations. Most nu
cleotide changes can be detected by these techniques. Many of these changes
probably reflect silent substitutions that are likely to be selectively ne
utral, making them particularly suitable to population genetic studies. In
this paper, we review the published literature on molecular population gene
tics, with respect to the genome assayed (nuclear, mitochondrial or chlorop
last), the organisms studied, the molecular techniques used, and the biolog
ical problems addressed. Several molecular techniques are then compared usi
ng experimental results obtained from a population genetic study of the Myt
ilus complex in the North Atlantic and Mediterranean. Finally, the most app
ropriate theoretical tools to analyse molecular population genetic data are
discussed.