ASPECTS OF NONRANDOM TURNOVER INVOLVED IN THE CONCERTED EVOLUTION OF INTERGENIC SPACERS WITHIN THE RIBOSOMAL DNA OF DROSOPHILA-MELANOGASTER

Polymerase chain reaction (PCR)-amplified, sequenced, and digitally ty ped intergenic spacers (IGSs) of the ribosomal (r)DNA in D. melanogast er reveal unexpected features of the mechanisms of turnover involved w ith the concerted evolution of the gene family. Characterization of th e structure of three isolated IGS length variants reveals breakage ''h ot spots'' within the 330-base-pair (bp) subrepeat array found in the spacers. Internal mapping of variant repeats within the 240-bp subrepe at array using a novel digital DNA typing procedure (minisatellite var iant repeat [MVR]-PCR) shows an unexpected pattern of clustering of va riant repeats. Each 240-bp subrepeat array consists of essentially two halves with the repeats in each half identified by specific mutations . This bipartite structure, observed in a cloned IGS unit, in the majo rity of genomic DNA of laboratory and wild flies and in PCR-amplified products, has been widely homogenized yet is not predicted by a model of unequal crossing over with randomly placed recombination breakpoint s. Furthermore, wild populations contain large numbers of length varia nts in contrast to uniformly shared length variants in laboratory stoc ks. High numbers of length variants coupled to the observation of a ho mogenized bipartite structure of the 240-bp subrepeat array suggest th at the unit of turnover and homogenization is smaller than the IGS and might involve gene conversion. The use of PCR for the structural anal ysis of members of the rDNA gene family coupled to digital DNA typing provides powerful new inroads into the mechanisms of DNA turnover affe cting the course of molecular evolution in this family-