Molecular markers in plant ecology

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 arc briefly discussed. PCR-based methods, especially arnitrary-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 'generic distance' is stressed and fheir 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 elonal populations comes from mutations within elonal lines or from independent origins of clonal lines; reconstructing the genotype phylogeny and fruit dispersal of elonal (apomicuc) and inbred selling organisms, measuring the degree of outcrossing by offspring exclusion analysis; detecting and analyzing introgression and characterizing reeombinant 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, 1 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. Contents Summary 403 I. Introduction 404 II. Most ecological applications concern markers in the nuclear geonome 404 III. DNA polymorphisms differ from allozyme pohmorphisms 404 IV. Types of molecular marker 405 V. The application of markers in ecology 409 VI. From marker to character 413 VII. Outlook 414 References 414.