Studying below-ground ecological processes of plants in natural systems can be very difficult. It can be even more difficult to connect individual roots and shoots in population level and ecophysiological studies. To overcome this problem, we demonstrate that rapid and simple polymerase chain reaction (PCR), DNA sequencing, and DNA fingerprinting techniques can be used to reliably link above- and below-ground parts of plants in ecological studies of natural systems. We used PCR and DNA sequencing of the internal transcribed spacer (ITS) region of the ribosomal DNA repeat to determine the species to which roots belong. Then, amplified fragment length polymorphisms (AFLPs) and inter-simple sequence repeats (ISSRs) were used to link individual roots with individual shoots. Using Bumelia lanuginosa syn. Sideroxylon lanuginosum (Sapotaceae) as a test case, we showed, at two different sites, that both ISSR and AFLP approaches to fingerprinting roots and leaves are excellent means of establishing above- and below-ground connections in natural systems. Individuals were readily distinguished and the methods also revealed when stems were ramets from a single genet. We will discuss the strengths and weaknesses of each fingerprinting method for use in ecological studies.

Key words: AFLP, Bumelia lanuginosa syn. Sideroxylon lanuginosum, DNA fingerprinting, ISSR, plant ecology, Sapotaceae