Among yeasts that underwent whole-genome duplication (WGD), Kluyveromyces 
polysporus represents the lineage most distant from Saccharomyces cerevisiae. By 
sequencing the K. polysporus genome and comparing it with the S. cerevisiae 
genome using a likelihood model of gene loss, we show that these species 
diverged very soon after the WGD, when their common ancestor contained >9,000 
genes. The two genomes subsequently converged onto similar current sizes (5,600 
protein-coding genes each) and independently retained sets of duplicated genes 
that are strikingly similar. Almost half of their surviving single-copy genes 
are not orthologs but paralogs formed by WGD, as would be expected if most gene 
pairs were resolved independently. In addition, by comparing the pattern of gene 
loss among K. polysporus, S. cerevisiae, and three other yeasts that diverged 
after the WGD, we show that the patterns of gene loss changed over time. 
Initially, both members of a duplicate pair were equally likely to be lost, but 
loss of the same gene copy in independent lineages was increasingly favored at 
later time points. This trend parallels an increasing restriction of reciprocal 
gene loss to more slowly evolving gene pairs over time and suggests that, as 
duplicate genes diverged, one gene copy became favored over the other. The 
apparent low initial sequence divergence of the gene pairs leads us to propose 
that the yeast WGD was probably an autopolyploidization.