The best way to preserve overall diversity is to isolate the tracts as much as possible. That is what saved the Australian marsupials, until people affected the balance there. So, among the connected topologies, a linear one seems to be the best. The unknowns can have a large effect. Dominant males reduce diversity since the dominant male propagates his genes.
Linkage also reduces diversity.
By contrast, it takes only about 25 generations for all diversity to disappear if every tract is connected directly to every other, males breed according to dominance, and all traits are linked. Of these effects, dominance breeding is the worst for diversity, though it may convey other benefits. The method would go faster if the prisoner could safely reach a cell at the instant a robot is leaving the cell. Schonfeld also described a 24-minute cycle that eliminates the chance of escape for all prisoners below the 20th row. Robot 5 does two passes of row 20.