Wow, a lot of stuff. Over in NJ genetic research about 20 years ago indicated many likely native populations in small trickles; hatchery descendents in others (mostly Nassua NH strain). Led to stopping stocking of brook trout. Seems brook trout in one major river, the Musconetcong, have started to recover. I have a couple of spots where I can almost guarantee to catch a brookie or two now.
Also indicated climate change can be a scapegoat to put things we can control in the background. Never thought of it that way, but interesting. Developers could blame climate change for habitat degradation they cause.
Storm water drainage is interesting too and have an NJ case. In one NJ blue line drainage they built a big apartment complex. The stream below the parking lot outflow ceased to have brookies. Water in normal flows was OK, but warm, contaminated flow from summer rains harmed the stream.