Intra-clonal variation and a similarity threshold for identification of clones: application to Salix exigua using AFLP molecular markers

Although molecular methods are a major advance over phenological or root connectivity studies in the identification of clonal plants, there is still a level of ambiguity associated with two types of error: misidentification of genetically similar seedlings as clones and misidentification of dissimilar fingerprints from clones as genetically distinct individuals. We have addressed the second of these error types by determining the level of variation for AFLP fingerprints in Salix exigua, and then by developing a threshold value of Jaccard's similarity index for assigning individuals to clones or to siblings. Variation in AFLP banding patterns among clones was partitioned into three potential sources; clones, stems within-clones and foliage within-stems. Most of the variation was attributable to clones and then to stems within-clones. To provide an objective means of identifying clones, we developed a method for establishing a threshold similarity index to assign individuals to the same clone. Our method yielded a Jaccard similarity threshold of 0.983 that resulted in a potential pairwise error rate of 8.1% putative clone assigned to siblings and 1.5% sibling assigned to clones. The method was tested on independent clonal and sibling individuals resulting in the same threshold value and similar error rates. We applied our method to assign individuals to clones in a population of S. exigua along the Cosumnes River, California. A total of 11 clones were identified, with one clone including 43% of the individuals sampled. Our results show that this approach can be useful in the accurate identification of clones.