Something fishy in the gene pool

Scientists use genetics to study fish populations

Posted: Friday, July 21, 2000

A scientific revolution is under way as researchers decipher the genetic code (genome) of the human race. But the tools used in that quest are already providing new insights into the fish of the Kenai Peninsula.

Cutting-edge genetic science is giving fisheries managers new tools for assuring healthy fish populations into the future and, in the process, revealing some surprises in the salmon and trout family trees, said Bill Spearman, geneticist and project leader for the U.S. Fish and Wildlife Service.

His team is untangling the complexities of mingling multiple stocks, with ramifications for threatened stocks and jurisdictional issues.

This is one application of genetics, he said, to identify population structure.

The Fish Genetics Laboratory at the Fish and Wildlife Region 7 headquarters in Anchorage seems worlds away from fishing holes or spawning creek weirs. Samples of DNA (deoxyribonucleic acid), the chemical blueprint of life, steep in test tubes or whirl in centrifuges. But they all come from wriggling fish plucked from icy waters.

The (human) genome project is probably going to be very useful to us, said geneticist Wally Buchholz.

Advances in studying human biology are having spinoffs for fisheries biologists as well, because fish, people and all the worlds living things are closely related on a molecular level, he said.

In years past, scientists needed large samples of flash-frozen organs to search for the genetic needle in the haystack of flesh and bone. But a process called polymerase chain reaction, developed about 15 years ago, unzips the double strands of DNA and copies them over and over, increasing minute amounts into detectable quantities.

Now the scientists can complete their analyses from a bit of fin smaller than a fingernail, and they no longer need to kill fish to get their samples.

This (chain reaction) is the base of almost everything we do in the lab, Buchholz said. Its a major, major advance in technology. It gives you so much information so fast.

The DNA, preserved in alcohol, looks like a nondescript cream-colored fuzz.

But getting information from the code encrypted in its molecular structure requires additional steps. Scientists are focusing on two parts of the genetic code that are particularly likely to mutate: one from the cell nucleus and one from mitochondria (structures within cells that convert food to energy).

Buchholz explained that only a very small percentage of DNA is known to code for something so far. Geneticists nicknamed other portions found in a cells nucleus junk DNA.

I dont think any of its junk, he said.

Much of this so-called junk DNA is more variable than other genetic material and prone to repeating sections, like a biochemical stutter. The fish have variable repeats, and the more there are the longer the genetic strands are.

DNA is found in other parts of the cell as well, and genetic material in mitochondria has been studied extensively.

Scientists have discovered enzymes (the specialized proteins that build or destroy bodies at a molecular level) that zero in on highly specific DNA sequences, somewhat like a search function in a word processor seeking a designated key word. Called restriction enzymes, they cut the DNA chain at a specific spot wherever they find their trigger word.

Buchholz explained that geneticists use selected restriction enzymes that snip out sections of the mitochondrial genes. The snippets left by the enzymes vary in length from sample to sample, showing genetic variety.

Lying chopped DNA strands alongside micro-minute rulers is not feasible, but science has come up with an easier way to compare the lengths of the molecules.

DNA has an overall negative electrical charge. Samples are injected into a thin layer of gel that conducts electricity when placed in a current. Electromag-netic forces push the DNA fragments across the gel at different speeds depending on how big they are.

As time passes, the fragments spread out, with the smallest ones winning the race to the far end and the larger ones trailing behind.

Thanks to the copies generated by the chain reaction, samples contain enough fragments that they are visible when they bunch up

The result is a series of bands spread along the gel, looking like a bar code pattern.

A state-of-the-art laser scanner, first of its kind in Alaska, reads the pattern, working on the same basic principles as its cousins in the supermarket.

For every fish, the scientists in the lab run 12 gel plates, looking at 12 different parts of either the mitochondrial or junk DNA.

Computers analyze the resulting patterns and generate diagrams showing which fish stocks are more or less similar to each other genetically.

Results show that fish may be close to each other on a map without being closely related.

Doug Palmer, a fisheries biologist for the U.S. Fish and Wildlife Service, has been collaborating with the geneticists from the Kenai Fishery Resource Office on Kalifornsky Beach Road.

What we are seeing, for example with the cohos, he said, is that the main stem fish, which tend to spawn later, are more closely related than tributary spawners.

Last year, Fish and Wildlife released a report on an ongoing study on Kenai River rainbow trout. Initial results showed that trout above Skilak Lake were more closely related to trout from some Bristol Bay streams than from the lower Kenai. This year, the study has been expanded to look at Moose River trout.

Another study is looking at coho salmon throughout the Kenai River watershed, and it is finding significant variation, Palmer said.

Genetic analysis shows four major groups of fish:

Those around Quartz Creek, Tern Lake and the Snow River near Seward;

Salmon in the Moose River, which seem to be more closely related to fish on the West side of Cook Inlet than to other Kenai River stocks;

Russian River cohos and

The fish of the lower river below Kenai Lake.

Spearman explained that the new information can help managers gauge the health of specific stocks and resolve jurisdictional issues because scientists will be able to evaluate fish taken at sea and pinpoint exactly which natal streams, perhaps thousands of miles away, produced them.

The genetic tools can help identify adult runs and timing, assess juvenile salmons use of rearing habitat, and evaluate outgoing smolts to refine forecasts of future returns, he said.

Genetics is a key element in all of this, he said.

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