The Location-Dispatching Problem consists of determining subsets Li⊆F located at nodes i∈V, minimizing the sum of two costs: a piecewise linear installation cost associated with Li and an access cost for each node of V to reach a copy of each item of F. We formulate this problem as a linear program with binary variables x and integer variables z.
Although L1 elements contribute the most to the genome in terms of total size, Alu elements are the most successful mobile element family in terms of copy number, reaching a copy number of ∼1.2 million in the human genome [6].
It can reach a copy number in excess of 500,000 in the human genome [ 25].
Some of the WSSV-related PREs even reach a copy number in excess of 80,000 (= 400/0.45%) elements per genome.
However, it cannot be excluded that these low copy number MITEs reached a high copy number, as is theoretically possible for the few lineages with high copy number (from 100 to more than 300), which has never before been observed in Drosophila.
We therefore suggest that copies are more likely to get fixed one after another to ultimately reach a large copy number because this scenario involves the fixation of nearly neutral events and is more likely than a one-step amplification.
The observations of copy number of subfamilies in the AluYh and AluYi lineages generally support this, with subfamilies reaching a higher copy number in humans than chimpanzees where they are present in both species.
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Including all sequences obtained by cloning would increase the number of copies per species to almost as many as the number sequenced, but would not alter our broad findings beyond increasing the number of very similar copies within species [see Additional file 3. Saturation curves showed that the number of copies reached a plateau against the number of clones sequenced in each species.
