BACKGROUND: Genome amplification through duplication or proliferation of 
transposable elements has its counterpart in genome reduction, by elimination of 
DNA or by gene inactivation. Whether loss is primarily due to excision of random 
length DNA fragments or the inactivation of one gene at a time is controversial. 
Reduction after whole genome duplication (WGD) represents an inexorable collapse 
in gene complement.
RESULTS: We compare fifteen genomes descending from six eukaryotic WGD events 
20-450 Mya. We characterize the collapse over time through the distribution of 
runs of reduced paralog pairs in duplicated segments. Descendant genomes of the 
same WGD event behave as replicates. Choice of paralog pairs to be reduced is 
random except for some resistant regions of contiguous pairs. For those paralog 
pairs that are reduced, conserved copies tend to concentrate on one chromosome.
CONCLUSIONS: Both the contiguous regions of reduction-resistant pairs and the 
concentration of runs of single copy genes on a single chromosome are evidence 
of transcriptional co-regulation, dosage sensitivity or other functional 
interaction constraining the reduction process. These constraints and their 
evolution over time show a consistent pattern across evolutionary domains and a 
highly reproducible pattern, as replicates, for the several descendants of a 
single WGD.