The origin and early evolution of sex chromosomes are currently poorly understood. The Neurospora tetrasperma mating-type (mat) chromosomes have recently emerged as a model system for the study of early sex chromosome evolution, since they contain a young (<6 million years ago [Mya]), large (>6.6-Mb) region of suppressed recombination. Here we examined preferred-codon usage in 290 genes (121,831 codon positions) in order to test for early signs of genomic degeneration in N. tetrasperma mat chromosomes. We report several key findings about codon usage in the region of recombination suppression, including the following: (i) this region has been subjected to marked and largely independent degeneration among gene alleles; (ii) the level of degeneration is magnified over longer periods of recombination suppression; and (iii) both mat a and mat A chromosomes have been subjected to deterioration. The frequency of shifts from preferred codons to nonpreferred codons is greater for shorter genes than for longer genes, suggesting that short genes play an especially significant role in early sex chromosome evolution. Furthermore, we show that these degenerative changes in codon usage are best explained by altered selection efficiency in the recombinationally suppressed region. These findings demonstrate that the fungus N. tetrasperma provides an effective system for the study of degenerative genomic changes in young regions of recombination suppression in sex-regulating chromosomes.At present, little is known about the origin and early evolution of sex chromosomes. This is because most ancient sex chromosome systems are so highly deteriorated (e.g., Y in X/Y systems) that they retain few traces of the historical events driving their evolution (8,9,11,12,54). The limited data available to date about early stages of sex chromosome evolution have been derived from young sex chromosomes from certain plants (e.g., Silene [41]) and/or from neo-X/Y systems of Drosophila (4, 5). Thus, model systems for young sex chromosomes are needed (12). The Neurospora tetrasperma matingtype (mat) chromosomes have recently emerged as a model system for the study of early stages of sex chromosome evolution (42).The filamentous ascomycete N. tetrasperma is a self-fertile (pseudohomothallic) organism presumed to have evolved from a self-incompatible (heterothallic) ancestor (15, 50). As with most filamentous ascomycetes, the N. tetrasperma mat chromosomes contain the mat locus, which comprises two dissimilar alleles (mat a and mat A idiomorphs) that regulate mating and sexual reproduction (10, 53). Pseudohomothallism in N. tetrasperma is associated with a specialized meiotic pathway. Specifically, the mat chromosomes contain a young (Ͻ6 million years ago [Mya]), large (Ͼ6.6-Mbp) segment of suppressed recombination, including the segment between the mat locus and the centromere, which ensures first division segregation of mating-type idiomorphs. Spindles align in parallel for the second meiotic cell division, ensuring that nuclei of opposite mating ...