Mapping intraspecific inversion breakpoints. (A) Comparison of Muller element C between D. melanogaster and the Arrowhead arrangement of D. pseudoobscura revealed a junction in conserved linkage near vestigial (vg). The numbered sections 51E2, 58E1, 49D2, and 58D8 are the D. melanogaster cytological locations that are homologous to 70A, 76B, 70B, and 76C sections on the D. pseudoobscura cytological map, respectively. vg maps near the distal breakpoint of the inversion that converted the Standard arrangement into the Arrowhead arrangement (Schaeffer et al. 2003). The locations of four PCR primers, a, b, c, and d, are shown on the Standard and Arrowhead physical maps. Note that the two internal primers, b and c, are switched in the two chromosomes. (B) PCR results. The Arrowhead-specific primer combinations (a + c and b + d) only amplified Arrowhead DNA, while the Standard-specific primer combinations (a + b and c + d) only amplified breakpoints on Standard arrangements. Sequence analysis of the PCR products from the Standard and Arrowhead backgrounds verifies that PCR amplified the appropriate sequences.