Having read every paper from the biology primary literature (Ducky can attest to the stack of papers I have) i can get my hands on I'll add a little to this:
The research is ongoing. (Important point because fast genetic testing has only been cheap enough to feasible for the past 10 years(maybe a little longer) and with all the creatures in the world, only a handful of people have done work in this area. We will continue to learn a lot in the coming years.
Second, there were some interesting findings.
Brookies seem to have a preference for breeding with other Brookies from their home stream. On streams that trout from multiple locations, there was some assortive mating that appears to dominate the efforts, leading there to be a theory that planting from several streams, especially the further geographically they are from each other, the less the transplants will mate with Brookies from other streams. Like this has been observed in brookie streams that are all on the same mountain, yet geographically isolated from each other. Odd, but they somehow know. Maybe it has to do with the small differences in their mating time, as on one stream they tend to spawn slightly earlier or later and over time the assortive mating will diminish, but again, this is a long term question we are just beginning to really learn a lot about.
Second, this doesn't necessarily equate to low diversity in each of these streams.
Just a couple of things there. When I get a chance to review all the info I have again, maybe I'll add more.