Figure 4. Confounding effects of chromosome rearrangements on the estimation of the number and location of recombination events when aligning SNPs to a single, haploid reference genome.

In this example, recombination occurs between haplotypes ABCD and abcd. A. Pairings of two homologous chromosomes (blue and red) during meiosis in haploid genomes with the same organization as the reference genome. The four haplotypes of the gametes are shown after recombination between chromosomes by assortment (assuming no crossing over within chromosomes). Recombination is correctly inferred as occurring between AB and CD based on the presence of four gametic haplotypes. B. Mating between individuals with the same reciprocal translocation relative to the reference genome, but without recombination within or between the two chromosomes. No recombination is inferred: only two gametic haplotypes are present. C. Recombination between chromosomes in individuals with the same reciprocal translocation relative to the reference genome. When the gametic haplotypes are aligned to the reference genome, the gene order changes and three recombination events are inferred, two of which are incorrectly inferred as occurring within chromosomes of the reference genome (dashed arrows).