3.3 GB-RFLP marker analysis for the assignment of the
great lake species A. citrinellus and A. labiatus
Lastly, we designed markers for the two great lake species. As genetic
differentiation between these species is very low (0.015–0.02) compared
to the crater lake or allopatric species pairs (0.07–0.5), we used SNPs
that we have identified based on genome-wide association mapping for the
species–defining trait: lip size (A. labiatus has thick,
hypertrophic lips that A. citrinellus lacks) (Kautt et al., 2020;
Machado-Schiaffino et al., 2017). As the phenotype is largely driven by
a single locus, the variants were on the same chromosome (distance:
113kb). For the two species-specific markers that we designed, we
predicted an accuracy of 92 and 99%, respectively. When tested, the
GB-RFLP markers obtained similar accuracies of 87 and 81%, respectively
(Fig. S4a, b and Fig. 3d–f). Interestingly, even though both loci are
in proximity on the same chromosome, combination of both markers lead to
an accuracy of 100%.