Consequences of genotyping errors for estimation of clonality: a case study on Populus euphratica Oliv. (Salicaceae)

A study including eight microsatellite loci for 1,014 trees from seven mapped stands of the partially clonal Populus euphratica was used to demonstrate how genotyping errors influence estimates of clonality. With a threshold of 0 (identical multilocus genotypes constitute one clone) we identified 602 genotypes. A threshold of 1 (compensating for an error in one allele) lowered this number to 563. Genotyping errors can seemingly merge (type 1 error), split really existing clones (type 2), or convert a unique genotype into another unique genotype (type 3). We used context information (sex and spatial position) to estimate the type 1 error. For thresholds of 0 and 1 the estimate was below 0.021, suggesting a high resolution for the marker system. The rate of genotyping errors was estimated by repeated genotyping for a cohort of 41 trees drawn at random (0.158), and a second cohort of 40 trees deviating in one allele from another tree (0.368). For the latter cohort, most of these deviations turned out to be errors, but 8 out of 602 obtained multilocus genotypes may represent somatic mutations, corresponding to a mutation rate of 0.013. A simulation of genotyping errors for populations with varying clonality and evenness showed the number of genotypes always to be overestimated for a system with high resolution, and this mistake increases with increasing clonality and evenness. Allowing a threshold of 1 compensates for most genotyping errors and leads to much more precise estimates of clonality compared with a threshold of 0. This lowers the resolution of the marker system, but comparison with context information can help to check if the resolution is sufficient to apply a higher threshold. We recommend simulation procedures to investigate the behavior of a marker system for different thresholds and error rates to obtain the best estimate of clonality.