Lake Michigan used to be somewhat isolated from the predator-prey cycle elsewhere, with no easy access by Mississippi River or European fish.  Then came the St. Lawrence Seaway, with sea lampreys and alewives.  (And the latter had the usual fish habit of spawning, then dying, all over all the beaches.)  Thus did the fisheries managers introduce Pacific salmon to dine on the alewives.  But now there are ominous signs of a collapse of the alewife population.  But now come some particularly messy predator-prey cycles.
The collapse of alewives on Lake Huron had one surprising consequence — it opened the door to a surge in native species like lake trout and walleye. A likely reason is the alewives prey on the young of native fish. Alewives also aren't a good food source for lake trout because they carry an enzyme that makes it difficult for lake trout to produce healthy offspring.

The cause of the alewife crash on Huron has long been a subject of debate among biologists. Some believe it was a function of too many stocked and naturally reproducing salmon for the alewife population to survive. Others say it was triggered by the invasive mussel population that stripped away the food that alewives depend on. Others believe it is a combination of the two. Some biologists have blamed the cold winter of 2003 for the Huron alewife crash.
In Lake Michigan, the complication is that quagga mussels (just another hitchhiker on the few ships plying the spectacularly unproductive St. Lawrence Seaway) are filtering out the plankton that alewife fry (and many other young fish) eat.  I've been following that dynamic for some time, and the same question remains.
The likely outcome will be a collapse of the whitefish population. But when the quaggas exhaust their food supply, the quagga population collapses? The article mentions a seaweed called cladophora that prefers clearer water. What is cladophora's food supply? What fish use cladophora for food?
At the time the whitefish were attempting to eat the quagga, shells and all.

Although the researchers can quantify the various fish and mussel populations in the Lakes, they ought be careful about modulating the cycles.

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