What molecules can tell us about populations: Choosing and using a molecular marker

The rapid development of molecular techniques offers a palette of technical approaches for population biologists interested in a wide range of questions. For example, these tools can be used to determine individual reproductive success or to measure rates of genetic divergence among populations. Which technique is most appropriate for a particular question depends upon (1) the extent of genetic polymorphism required to best answer the question, (2) the analytical or statistical approaches available for the technique's application, and (3) the pragmatics of time and costs of materials. Here we evaluate the application of several major techniques (protein electrophoresis, nuclear and mitochondrial RFLPs [restriction fragment length polymorphisms], minisatellite and microsatellite VNTRs [variable number tandem repeats], RAPDs [random amplified polymorphic DNA], and DNA sequencing) to an array of questions regarding individual identification, exclusion and assignment of parentage, and various levels of population structure. In our evaluation, we briefly explain the technical components of each molecular approach and assess whether the typical outcomes expected from each approach will provide useful information as applied to each level of inquiry. For studies of population genetic structure, protein electrophoresis remains a powerful tool for most taxa, although techniques based on nucleic acids (particularly DNA sequencing and mitochondrial DNA RFLPs) are useful here as well. Recently developed nucleic acid techniques (e.g., VNTRs) can often identify enough genetic variability to address questions of self-identification or parentage. Some of the newest techniques (RAPDs and microsatellites) are potentially useful across a number of levels of inquiry, although procedures for adopting them are still developing.