Michigan Department of Natural Resources biologist Jim Johnson greets two visitors who arrived after sunset this fall in his hometown of Alpena with a quick question:

"Do you have hotel reservations?"

Then Johnson remembers: Finding a hotel room in Alpena during the October salmon run isn't a problem anymore.

Finding a salmon is.

"It used to be salmon fishermen flooding into here this time of year, and there were no hotel rooms available," he says of life in Alpena just a few years back. "There's none of that anymore."

That's because the salmon fishing has essentially disappeared in the Michigan waters of Lake Huron, a phenomenon most experts believe was triggered by two factors.

Chinook salmon numbers exploded because the Pacific natives that biologists figured needed to be stocked annually had quietly begun naturally reproducing in big numbers. That phenomenon, coupled with a mussel-driven collapse in plankton levels, doomed the invasive alewife, the chinook's primary food source.

But something unexpected has happened following the salmon-and-alewife collapse: Native species such as perch, walleye and lake trout are making something of a comeback.

"The walleye are dominant, everywhere you look in Lake Huron," says Johnson, noting the number of juveniles has increased several fold in recent years.

Johnson suspects the disappearance of alewives is a big reason for the change; those little invaders feasted on juvenile native species while providing a miserable diet for native predators like lake trout.

"This huge, massive chinook population isn't there anymore, but now we have a little bit of this and a little bit of that," Johnson says.

"It's this ironic thing that has happened and it involved invasive species, but we're actually getting our native species back because of it," says University of Michigan biologist David Jude.

Still, the lake's overall amount of fish pales in comparison with historical numbers, primarily because so much energy is now tied up in the invasive zebra and quagga mussel population smothering the lake bottom, a phenomenon also plaguing Lake Michigan.

This point is made clear with annual water clarity surveys. Scientists drop a plate-sized disc into the water and measure how far down it remains visible.

Historically on Lake Michigan the disc would disappear at depths of around 20 feet.

This spring tests showed the disc at a depth exceeding 100 feet.

"We are approaching some of the clearest freshwater anywhere on the globe," says Gary Fahnenstiel, a researcher with the National Oceanic and Atmospheric Administration.

That isn't a good thing. It doesn't mean the lake is clearer of pollution than it used to be; it just means there is a lot less life floating in the water - the base of the lakes' food chain.

Fellow NOAA researcher Tom Nalepa believes the mussels have already done more damage than the lamprey and alewives did two generations ago, and their impact in Lake Michigan is still growing because the mussel numbers - and the size of the mussels as well - are still growing.

"As their mass increases, their filtering capacity increases, and the impact on the lake increases," he says. "We're still in for some changes, as far as I'm concerned."

That could well mean Asian carp won't be able to find enough to eat if they get out into the open waters of the lakes, though there are still big fears the leaping fish could thrive in the lakes' warmer, more plankton-rich bays, harbors and river tributaries - the places where people and their boats tend to congregate as well.

Lake Michigan's salmon fishery, meanwhile, is hanging on, but there are worries it could be headed to a fate similar to Lake Huron's.

Wisconsin Department of Natural Resources biologist Paul Peeters has been helping to manage the state's salmon program for more than 30 years. He has no idea where things are headed, particularly because the historic pathways for species invasions - the St. Lawrence Seaway and Chicago canal system - remain essentially open to fresh invasions.

Understanding, let alone managing, the lake under such ever-changing conditions, he says, is like trying to hit a triple bank shot in bumper pool - with someone lifting and tilting the table.

"You just can't predict it," he says. "I don't know what else I can say."