Efficient genetic recombination requires near-perfect homology between participating molecules. Sequence divergence reduces the frequency of recombination, a process that is dependent on the activity of the mismatch repair system. The effects of chromosomal divergence in diploids of Saccharomyces cerevisiae in which one copy of chromosome III is derived from a closely related species, Saccharomyces paradoxus, have been examined. Meiotic recombination between the diverged chromosomes is decreased by 25-fold. Spore viability is reduced with an observable increase in the number of tetrads with only two or three viable spores. Asci with only two viable spores are disomic for chromosome III, consistent with meiosis I nondisjunction of the homeologs. Asci with three viable spores are highly enriched for recombinants relative to tetrads with four viable spores. In 96% of the class with three viable spores, only one spore possesses a recombinant chromosome III, suggesting that the recombination process itself contributes to meiotic death. This phenomenon is dependent on the activities of the mismatch repair genes PMS1 and MSH2. A model of mismatch-stimulated chromosome loss is proposed to account for this observation. As expected, crossing over is increased in pms1 and msh2 mutants. Furthermore, genetic exchange in pms1 msh2 double mutants is affected to a greater extent than in either mutant alone, suggesting that the two proteins act independently to inhibit homeologous recombination. All mismatch repair-deficient strains exhibited reductions in the rate of chromosome III nondisjunction.Homologous recombination occurs most frequently between identical DNA sequences. Studies with a variety of organisms have demonstrated that sequence divergence reduces the frequency of recombination (7,16,19,33,53,54,60,73,75). Recombination between two similar but nonidentical sequences (termed homeologous sequences) will form a heteroduplex intermediate containing mispaired DNA. Mismatches formed during recombination are corrected by the mismatch repair system, which provides the molecular basis of gene conversion (4). In Escherichia coli, the long-patch mismatch repair system is the main pathway for correcting errors that arise during DNA replication (reviewed in reference 58). The suppression of recombination between homeologous sequences is strongly dependent on elements of this system (14,16,33,59,60,69). The MutS, MutL, MutH, and UvrD proteins are the central components of the E. coli mismatch repair system. MutS binds to mismatches in duplex DNA. MutL couples MutS to the endonuclease MutH, which nicks the nascent DNA strand, and the helicase UvrD is thought to displace the targeted strand (reviewed in reference 19). Numerous homologs of the E. coli mutS and mutL genes have been identified in eukaryotes. Three mutL (MLH1, MLH2, and PMS1) (40, 56) and six mutS (MSH1 to MSH6) (30,46,52,61,62,66) homologs have been identified in the yeast Saccharomyces cerevisiae. Studies of these genes indicate that only a subset participates in n...