Number of Alleles
Here we found that the number of alleles recovered by CHIIMP on the pooled dataset was higher than our manually processed genotypes. The number of alleles per locus stayed the same at two loci (GS-2 and GLSA-12, although a different allele was present in the processed genotypes for both loci; allele ‘96’ in GS-2 and ‘162’ in GLSA-12), and decreased in the other three loci. Due to the nature of the microsatellite loci previously described for G. sabrinus , and implemented here, we may have recovered a higher proportion of stutter alleles due to the dinucleotide repeat motif in all loci (even the complex motif microsatellite GLSA-12 had motifs including dinucleotide repeats; Kiesow et al., 2011; Zittlau et al., 2000).
When comparing our allele counts to those from G. sabrinus we recovered fewer alleles for four loci, GS-2, GS-4, GLSA-22 and GLSA-52, and recovered more alleles in GLSA-12. However, previous research in the sister species G. sabrinus included far more individuals and a wider geographic distribution. Therefore, we do not expect the alleles recovered here to be exhaustive for G. oregonensis , and our allele counts seem reasonable for a sample size of seven individuals.