This may sound like a silly question, TPC, but if mother mates with son, does this adversely affect the Peregrine gene pool. 
Depends on the genetic health of the individuals. If they don't have problematic genes, then no, they are just reinforcing good genes. If they do, it can. They, like pretty much every other species, does try to avoid it however because its does narrow the pool somewhat. The current theory related to cheetahs is that they became inbred (they are almost genetically identical) when a natural disaster of some sort (or sorts) about 10,000 years ago (end of the last ice age I believe) reduced the total world population down to less than 7 individual cheetahs, possibly even just one mom and her cubs. So the species survived through brother-sister, child-parent pairings. They survived but their fertility has been affected. Given the number of peregrines out there, and the frequency with which child-parent or brother-sister pairings occur in conjunction with high first year mortality, the chances of severely damaging the overall gene pool is slim. Damaging our little gene pool if an offspring were to be a dominant breeder would depend on what was in the bird's and his/her mate's genetic make-up.
When Trey and Madame nested together, they had fewer young, but they were perfectly healthy and it was only a couple of years. It may be one of the reasons Trey chose Princess over Madame in 2004, "knew" (in the hardwired instinctive sense) that his genes would do better with an unrelated female.
And for those of you who don't know or don't remember all the minutae of Ivy's background ... he tried to nest (unsuccessfully) with his sister Lucy back in 2007. 2005 - Ivy and Lucy hatched at the Radisson - westside nestbox!
2006 - Ivy went a roving, Lucy returned and held the West Winnipeg territory with a Brandon cousin.
2007 - Ivy reappears and the Brandon cousin did not. Ivy & Lucy had three eggs, none of which hatch.
2008 - Lucy did not return but Ivy did, and Jules appeared. They didn't nest but they did defend the territory.
2009 - Ivy and Jules tried their hand (or talon) at nesting with pretty much the same results as in 2007. Not unusual for young, first-time nesters.
2010 - Jules in West Winnipeg (last we saw her) and Ivy hanging out at the Radisson annoying (so far) his mother, Princess.
