Fig. 5.

Examples of complex RAD loci. Four consecutive restriction sites are shown (1–4) in each of four haplotypes for two F1 parents, with RAD loci on either side of each site shown as arrowheads and labelled a and b. Haplotype C is shared between the parents. Variant alleles at RAD loci are differentiated by colour (black, red and blue). For example, two variant alleles are found at RAD locus 1b, with the black allele shared between haplotypes A and C and the red allele present in haplotype B only; the black allele has two copies in the mother and one copy in the father. Owing to the heterozygous restriction sites 2 and 3, alleles at RAD loci 1b and 4a are derived from restriction fragments of varying lengths, potentially skewing read depths and resulting in incorrect genotypes. For example, at locus 1b, the father's red allele at Haplotype B will be derived from a long fragment ending at RAD locus 3a, whereas the black allele at Haplotype C will be derived from a shorter fragment ending at RAD locus 2a.