Wow that is an impressive list of books. She has similar taste in SF as I do (lots of Robert Heinlein). I will have to read some of the books she reviewed and gave high marks to that I have missed over the years.
The authors study how an artificial replication mechanism evolves to cope with emerging faster-replicating parasites in a spatial setting.
Extinction occurs in about half the cases due to quick emergence of the fast-replicating parasites, but if the system survives long enough, the authors observe long-term evolution of intricate replication mechanisms for coping with the parasites, including slower replication and higher mutation rates. Quoting from the OP: "Diverse ecosystems evolve, with relatively long replicators, subdued parasites, and large population densities. The replicators may even subdue parasites to such an extent that the parasites become rare, and then the replicators, not needing the defence against parasites any more, lose their complex countermeasures and become simpler and shorter; but new parasites emerge, reversing this trend again."
20 years ago I found her web page and learnt so much from the books she listed and reviewed. Ye Ole World Wyde Webb:
https://www-users.york.ac.uk/~ss44/index.htm
Still impressive, although it was less of a list back then.