With two copies of every gene, a diploid organism is able to mask recessive deleterious mutations. In this paper we present the analysis of a two-locus model designed to determine when the masking of deleterious alleles favors the evolution of a dominant diploid phase in organisms that alternate between haploid and diploid phases ("alternation of generations"). It is hypothesized that diploidy will be favored whenever masking occurs ("the masking hypothesis"). Using analytical methods, we confirm that this masking hypothesis is essentially correct under free recombination: as long as the heterozygous expression of deleterious alleles is sufficiently masked by the wild-type allele, diploidy is favored over haploidy. When the rate of recombination is lower, however, diploidy is much less likely to be favored over haploidy. In fact, according to our model, the evolution of diploidy is impossible without significant levels of recombination even when masking is fairly strong.
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