Therefore, comparison of the two competing hypotheses with the empirical results is more supportive of an ancestral status for SC. George Gaylord Simpson would probably have been pleased to know that 50 years after he considered the history of gene arrangements in D. pseudoobscura, a molecular evolutionary approach has brought us close to an understanding of the origin of this genetic system.

Although the chromosomal polymorphism for inversions in Drosophila pseudoobscura is one of the best studied systems in population genetics, the identity of the ancestral gene arrangement has remained unresolved for more than 50 years. There are more than 40 gene arrangements, and 4 of them (Standard, Hypothetical, Santa Cruz, and Tree Line) have been considered as candidates for the ancestral type. We propose a framework of competing hypotheses to distinguish among the alternatives. Two conclusions come from contrasting each hypothesis with the results from DNA sequencing and restriction mapping. First, not only Standard but also Hypothetical can be excluded as the ancestral gene arrangement. Second, although either Tree Line or Santa Cruz could be the ancestral type, the available data provide greater support for Santa Cruz.

We thank Danijela Popadic for technical assistance and J. C. Avise, F. Ayala, M. Arnold, M. Ball, Y. Fu, J. Hamrick, E. McCarthy, J. McDonald, R. Meagher, and B. Wallace for comments on the manuscript; B. Bowen provided an especially helpful review. We also thank M. T. Clegg, W. M. Fitch, and E. Mayr for helpful suggestions about our analysis. This work was supported in part by a grant from the National Science Foundation (BSR-8516188 to W.W.A.).

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