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Background  The loss of duplicate genes - fractionation - after whole genome doubling (WGD) is the subject to a debate as to whether it proceeds gene by gene or through deletion of multi-gene chromosomal segments.    Results  WGD produces two copies of every chromosome, namely two identical copies of a sequence of genes. We assume deletion events excise a geometrically distributed number of consecutive genes with mean  µ  ≥ 1, and these events can combine to produce single-copy runs of length  l . If  µ  = 1, the process is gene-by-gene. If  µ  > 1, the process at least occasionally excises more than one gene at a time. In the latter case if deletions overlap, the later one simply extends the existing run of single-copy genes. We explore aspects of the predicted distribution of the lengths of single-copy regions analytically, but resort to simulations to show how observing run lengths  l  allows us to discriminate between the two hypotheses.    Conclusions  Deletion run length distributions can discriminate between gene-by-gene fractionation and deletion of segments of geometrically distributed length, even if  µ  is only slightly larger than 1, as long as the genome is large enough and fractionation has not proceeded too far towards completion.

Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling