Table 4 Sources and outcomes of potential biases in the use of fluorescent amplified fragment length polymorphisms
Stage of work stream | Potential source of bias | Outcome |
|---|---|---|
DNA extraction | Tissue | DNA yield is higher for leaves than roots |
Species | DNA yield differs across species | |
Storage | A single freeze–thaw reduces DNA yield | |
DNA amplification | Species | Some species amplify better than others. Their amplification efficiency also depends on the target region |
DNA concentration | There is a weak positive relationship between DNA concentration and amplification efficiency. Some fragments are not detected at low DNA concentrations; detection thresholds depend on target region | |
Fragment size | Depending on target region, detection of smaller fragments tends to be more successful than for large fragments (>600 bp) |