It's mostly not what Wisconsin is doing, but what they have, environmentally. And, specifically, only in parts of Wisconsin. From Milwaukee north to Algoma has the highest and most consistent survival in the lake. But Green Bay consistently has some of the worst survival in the lake, which is probably tied to the massive number of walleyes, bass, pike, musky, etc. And far southern Wisconsin also has variable survival.
The reason that central Wisconsin has such excellent survival is that that area has prevailing westerly winds, which cause lots of upwelling, making nutrients available to pelagic zone. This is really important, as the quagga mussels sequester much of the nutrient load on the lake bottom, unless there is upwelling that redistributes it through the water column. They have more rocky substrate, which provides structure, and lots of benthic invertebrates (food). Those same westerly winds that create upwellings also blow a lot of terrestrial insects out in the lake, further subsidizing the food web. All of that combines to offer a lot more food for smolts. More food = better grown and higher survival
Perhaps just as importantly, all those features also attracts baitfish. When there are clouds of baitfish nearshore in May/June, when smolts are most vulnerable to getting eaten by predators, the baitfish act as cover, a predation buffer. When there is no bait nearshore, smolts are much more vulnerable to predation. And then once the smolts are big enough to eat alewives, they have more prey as well.
Following the massive 2010 alewife yearclass, Michigan and Indiana had excellent survival of the 2011 chinook stockings. It's very likely that this was because of the huge numbers of alewife nearshore in early 2011, providing a predation buffer, and then the average size of the 2012 alewife year class provided food for the 1 year old chinooks. But after that, with no good alewife yearclasses in 2013 or 2014, survival plummeted everywhere except where the bulk of the bait was (Wisconsin)
With fewer alewives in the lake, and more patchy distribution, you're starting to see a lot more disparity both in stocking success and fishing success
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In terms of the Huron fish getting caught in Lake Michigan, some context helps. Those particular numbers Mike cited (fish recovered by district) are adjusted for angler effort, but not for the number stocked. The Lake Huron stocking is 700K fish. Most of those are stocked just east of the Bridge, about 10 miles from Lake Michigan... 95% of them are recovered in Lake Michigan. There's not much food for them in Huron, so they swim west until they hit baitfish, usually around Manistique or the Door Peninsula. We count them as stocked in Lake Michigan for management purposes - the Predator Prey Ratio and chinook biomass models all count them as Michigan fish.
Illinois has stocked just over 230K on average since 2012, and Indiana 195K. So when you look at the numbers of fish stocked, it's not all that surprising that Lake Huron fish make up about the same amount of the fishery in southern Lake Michigan as IN/IL fish, since there are way more stocked in northern Lake Huron than there are in IN/IL combined.
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