(If the damned thing takes much longer we're going to have to ask the Editor for an extension!)
It's my fault - I'm stalled at fixing up the Discussion.
The problematic reviewer felt that the model didn't make testable predictions, so I wanted to include a brief discussion of how it could be used to evaluate more complex hypotheses about uptake sequence evolution. Unfortunately, a proper test that includes selection will require the model to follow a population of cells or genomes, rather than a single focal genome. Such a model would necessarily be more complicated than ours, and if it was set up like ours the run times might be prohibitively long. (Of course a clever programmer might find ways to streamline it without losing scientific relevance.)
But I thought of a simple test of whether uptake sequences accumulate near to positions that are under fitness selection in the diverging sibs of the focal genome. Modifying the program to do this took only about 12 lines of code, but getting this code to work properly took me most of a day (spent chasing curly brackets and finding out the correct way to use the Perl 'substr' function).
This new version of the program includes selection at position 5000 of the evolving genome. As before, each DNA fragment in the environment is first scored for sequences matching the uptake motif, and the resulting score determines its probability of recombining with the focal genome. But now, if the fragment overlaps position 5000, it is also checked for its base at that position. Fragments with an A at position 5000 keep their original uptake-sequence score for the recombination step, but fragments with the other bases have their scores reduced by a factor of 0.7, 0.4 or 0.1 (for G, C and T respectively). This is intended to simulate poor survival of cells with these bases. If the focal genome has an A it will have a near-normal recombination around position 5000 (except for the 1/100 fragments that carry mutations to less favoured bases), but if it has one of the other bases it will have reduced recombination except for the higher recombination of fragments carrying mutations there). Recurrent mutation at position 5000 (in the focal genome and in the divergent fragments) may create a recurrent benefit of recombination, and if uptake sequences promote beneficial recombination, might select for uptake sequences close to position 5000. On the other hand, if recombination more often brings in harmful mutations, uptake sequences close to the selected position might be selected against.
So I examined the final locations of uptake sequences in genomes from a bunch of runs that started either with 10 kb random-sequence genomes or with 20 kb genomes pre-seeded with uptake sequences (one very close to position 5000). In the random-sequence genomes there were just as many uptake sequences around position 5000 as anywhere else, and in the pre-seeded genomes the uptake sequence at position 4982 was no more and no less stable than any other uptake sequence.
This isn't a very good test, in lots of ways (in fact it's quite awful), but I think it will show the Editor that the model is indeed testable, and that we have made a reasonable effort to satisfy the reviewer. In the manuscript's Discussion I'll describe it in less detail than I have above, and I won't present any data ("Redfield, unpublished"). And I'll explain that a proper test that incorporates selection for beneficial alleles will require a population-based version of the model.
[I also still have to assemble some new data into a replacement for one of the figures, and to go back over the latest changes one more time before sending them to my coauthors on last time.]
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