Identification of recaptured individuals
The R package RClone (Bailleul et al., 2016) was used to identify
duplicate genotypes in the dataset and to detect recaptured individuals.
Using the allelic frequencies of the dataset, RClone simulates a
reproduction event and compares the genetic distances between genotypes
in the simulated and the observed populations. This allows for a
threshold to be determined, below which genotypes in the observed
population may be too similar to occur as a result of reproduction.
Thus, the genotypes of all individual pairs that had less than 5
differences at any locus were double-checked with GENEMAPPER, and the
data were crosschecked with field information to identify recaptured
individuals.