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.