More from whois' paper. I am starting to suspect that whois is suddenly regretting ever using this paper. Time will tell.
As discussed earlier, the bacterial populations go through sudden and severe bottlenecks. The population goes from a single bacterium, to a few hundred thousand, and back to a single bacterium in one fell swoop about every 30 generations. Each new population is a randomly selected individual. This, in effect, removes natural selection from the process.
What you see with a hypermutator and these extreme bottlenecks is what happens when you have a lot of mutations and no natural selection. Wouldn't you know it, fitness goes down.
"Using detailed fitness measurements and whole genome resequencing, we studied the evolutionary dynamics of eight replicate mutation accumulation lines of a hypermutator strain of the pathogenic bacterium
Pseudomonas aeruginosa. MA lines were passaged through 28 single-cell bottlenecks followed by rapid population growth over a period of ∼644 generations.
Under this regime, we estimate that the effective population size of MA lines had a lower limit of ∼16, which should be sufficient to prevent natural selection on the vast majority of spontaneous mutations."
http://www.genetics.org/content/197/3/981.full
Just hoping that whois is still willing to discuss the paper.