Figure 2.

Proposed steps in the evolution of the scrambled DNA polymerase α gene through a series of recombinations between MDSs and IESs. MDSs are shown as boxes (black numbers and color stripes reference cognate regions in the extant S. lemnae gene; Fig. 1); IESs or noncoding DNA are drawn as thin lines; and pointers are shown as black bars. The first general step takes place in a nonscrambled ancestral version of the gene [shown here with one IES between MDS 1–2 because this IES is conserved in all three species and IESs flanked by TA repeats are the most common in other ciliate species (1)]. Reciprocal exchange at the ×s between an MDS and upstream noncoding DNA creates a scrambled hypothetical MDS order (3-1–2-4; new MDSs in purple) and an inversion (up arrow) between 3 and 1; these MDSs are numbered from the 5′ end (… ) and italicized if on the reverse strand. The juxtaposition of MDSs and IESs now promotes homologous recombination at chance matches, perhaps even at favored sites (Table 1), creating the new pattern 5–3-1–2-4–6. Continued exchange at the ×s, in any order (not just the reasonable one shown here), propagates the odd/even MDS splitting: 17–15-13–11-9–7-5–3-1–2-4–6-8–10-12–14-16–18 is shown as one evolutionary intermediate, finally reaching a dense set of 43 contiguous MDSs very similar to O. nova. At any stage in an ancestor of all three species there could be insertion of an IES in the last MDS and finally translocation of a cluster of MDSs at the 5′ end (probably maintained as a polymorphism initially, allowing substantial overlap in the orange region) by reciprocal exchange with a distant DNA fragment. The precise ordering of the previous steps does not matter, but the most recent step is splitting of MDSs 5–7 (by exchange with an unknown fragment) and 11–13 in an ancestor of S. lemnae and O. trifallax, leading to the pattern in S. lemnae.