Various methods from molecular biology reveal sequence polymorphisms in organelle and nuclear DNA that can be used as highly informative markers for the structure and dynamics of genomes at the level of populations and individuals. Molecular markers that can be determined without regard to the phenotype permit an unbiased comparison of the adaptation of organisms to their environment, its genetic basis and its effect on evolution. Several marker types used in ecological research and their uses and limitations are briefly discussed. PCR-based methods, especially arbitrary-primer-based RAPDs, are likely to be most widely used and receive most attention. The limited use of DNA markers for overall quantitative (phenetic) comparisons of 'genetic variability' and 'genetic distance' is stressed and their power as qualitative markers for any and all relevant regions in the genome is emphasized. Specific applications relevant to plant ecology are illustrated. These are: identification of organism and genotype even where morphology is of little help, as in mycorrhiza; identification of clones in asexually reproducing species, even when they are widespread and intermingled; determining if genetic variation in clonal populations comes from mutations within clonal lines or from independent origins of clonal lines; reconstructing the genotype phylogeny and fruit dispersal of clonal (apomictic) and inbred selfing organisms, measuring the degree of outcrossing by offspring exclusion analysis; detecting and analyzing introgression and characterizing recombinant genotypes in hybrid zones relative to differential adaptive responses: tracing the phylogenetic origin and extent of ecologically differentiated races or species; characterizing the genetic basis, mapping and isolating the genes responsible for special adaptive responses. In a final outlook, I speculate about unconventional sources of genetic variation affecting the ecological characteristics of plants that will become accessible to experimental analysis with the new molecular methods.
