An assessment of the AFLP method for investigating population structure inthe red alga Chondrus crispus Stackhouse (Gigartinales, Florideophyceae)

The appropriateness of the Amplified Fragment Length Polymorphism (AFLP) te chnique for investigating Chondrus crispus Stackhouse populations in the Ma ritime Provinces of Canada was assessed. The AFLP procedure was first subje cted to reproducibility testing and three shortcomings were noted: 1) failu re to reproduce band intensity between replicate runs for the same individu al and primer pair; 2) failure of some bands to replicate; 3) lack of repro ducibility for complete replicate runs for some individuals and primer pair s. In the last-mentioned case, the lack of reproducibility resulted in char acteristic electropherograms indicative of weak reactions. These weak runs can be attributed to poor restriction digest/ligation reactions and/or subs tandard PCR, these failures ultimately resulting from low and inconsistent DNA quality. We recommend that reproducibility testing should be completed routinely in studies using the AFLP technique. In the current work, only fr agments and individuals that gave reproducible results were used in subsequ ent analyses. The AFLP method resulted in highly variable markers within an d between the populations of C. crispus included in this investigation, whi ch prevented successful resolution of population structure. This situation could result from a lack of suitability for AFLP markers in population gene tic studies, and/or too extensive genetic variation for C. crispus populati ons to be discerned by the AFLP technique. These two possible explanations are discussed.