In Saccharomyces, an ancient whole-genome duplication (WGD) and widespread 
duplicate gene deletion resulted in extensive reorganization of adjacent gene 
relationships. We have studied the evolution of adjacent gene pairs' identity, 
orientation, and spacing following whole-genome duplication and deletion (WGD-D) 
using comparative genomic analyses and simulations. Surveying adjacent gene 
organization across the Saccharomyces species complex, we find a genome-wide 
bias toward divergently and convergently transcribed gene pairs in all species 
but a reduction in this bias in the species that underwent WGD-D. Among neutral 
models of WGD-D, only single-gene deletion can produce the appropriate reduction 
in orientation bias and recapitulate the pattern of short, highly dispersed 
deletions we observe in Saccharomyces cerevisiae. To characterize the dynamics 
of WGD-D, we trace the conservation and creation of adjacent gene pairs along 
the S. cerevisiae lineage. We find that newly created adjacencies have a tandem 
orientation bias, while adjacencies conserved from prior to WGD-D have the same 
divergent-convergent bias as found in the species that diverged before WGD. We 
also find that adjacent gene pairs produced by WGD-D gained greater intergenic 
spacing but that this is reduced in the older adjacencies. Given this, and the 
preponderance of short deleted blocks, we argue that the deletion phase of WGD-D 
occurred primarily by small inactivating mutations followed by numerous small 
deletions. Newly created adjacent gene pairs also have an initial increase in 
mean log2 expression ratios and maximal expression levels, suggesting that 
increased intergenic spacing caused a genome-wide reduction in transcriptional 
interference.