Raising the dead
The dams blocked salmon on their way upriver to spawn. Fish that managed to circumvent the dams entered spawning beds silted with sawdust from mills and polluted by runoff from farmers’ fields. And when settlers cut down trees to plant crops along the banks of tributaries, the sun beat directly down on the water, causing the water temperature to rise, which was unsuitable for coldwater fish. As local resident W.G. Austin wrote in the mid-1800s in a letter to the Toronto Globe, “The wasteful practices and the murderous engines planted by the greed of man in every spot where this persecuted fish wanders have nearly annihilated the race.” Mere decades after Austin penned that letter, the annihilation was complete.
Not long after the search for Atlantic salmon DNA stalled, Stephen Cox Thomas, a zooarcheologist who specializes in puzzling out which animal bones belong to which species, asked if he might use Haddrath’s lab. He needed to weigh some bones that had been extracted from a dig near the Upper Niagara River in preparation for radiocarbon dating.
“I got chatting with Oliver and found they hadn’t had any luck making the link. I suggested archeological data,” recalls the slim, grey-haired scientist. He told Haddrath of the Atlantic salmon vertebrae he had positively identified in the mid-nineties while working on various digs around Lake Ontario. His suggestion would prove to be a turning point. Haddrath now possessed the much-needed genetic material to continue his detective work.
But substantial challenges remained. The passage of time, the hours the bones had boiled in Iroquoian pots over an open fire and the bacteria that invaded the bones after they were discarded made the work particularly difficult. “The problem with ancient DNA is that the molecules break down. There is very little DNA left. Most of the DNA in the bones is actually not salmon but bacteria and fungi,” notes Haddrath.
As he tried to isolate the salmon’s genetic material, Haddrath wore a head-to-toe contamination suit designed to prevent his DNA from mixing with that of the salmon. He began by pulverizing the bones by hand, using a 15-centimetre piston that fit snuggly into a cylinder. He stripped the calcium and protein from the resulting powder and spun what remained in a centrifuge to separate residual protein and fat from genetic material.
Haddrath ran the miniscule bits of leftover salmon DNA through a toaster-sized machine called a DNA thermal cycler – a sort of super photocopier. Three hours later, the thermal cycler popped out millions of copies of salmon DNA, which Haddrath injected into a gel. Exposing the gel to an electric field caused the DNA to separate out into chunks of various sizes. At this stage, DNA can be seen as a pattern of bands that look very much like the bar codes that cashiers electronically scan at the grocery store. Haddrath photographed the bands and transferred the data to a computer, which searched for patterns that would indicate unique genetic markers.
To date Haddrath has isolated four markers that he believes only Lake Ontario salmon carried. The markers are called microsatellites and consist of stretches of repeating DNA molecules that often are unique to specific populations. “Microsatellites are such powerful markers for telling fish apart that you can actually narrow it down to what river they lived in,” says Haddrath.
By September, he had compared his markers to four distinct salmon populations in the St. Lawrence River and tributaries leading into the seaway, and to one population in New Hampshire. He found no matches. The next step, which he hopes will be completed within a few months, is to compare his markers to other populations in Quebec and south of the border where scientists maintain extensive databases of distinct salmon populations. There are roughly 250 unique Atlantic salmon populations in North America. Just over half of those populations, representing 85 percent of the fish, have been analyzed for microsatellites and are available for Haddrath’s match-making attempts. “I think everybody would be compelled, if we found even a kissing cousin, to get that stock wherever it exists,” says Smitka.
Haddrath has established for himself a most impressive goal: reversing the course of history. And the stage is set. Most of the dams have been removed, and fish-friendly ladders have been installed on those that remain to allow salmon to pass unimpeded from the lake to their fall spawning tributaries. Trout Unlimited Canada, along with other conservation-minded groups, is rehabilitating three spawning streams in preparation for the return of the Atlantic salmon. The same organizations are also planting vegetation along the rivers to shade and cool the water, and to help stabilize the banks and prevent silting. By narrowing channels in some places, currents will become faster and will thus create deeper pools and riffles to oxygenate the river, making the water ideal for spawning. Local conservation authorities and farmers have lent a hand and reduced agricultural runoff along those tributaries most suitable for the salmon.
Now everything depends on finding a match. If the ROM’s project is successful, debate over the best use of limited conservation dollars – especially between people who want to focus on protecting existing endangered creatures and those fighting to bring back locally extinct animals – will no doubt heat up. But Haddrath sees this as the kind of science that will right the wrongs of the past.
“It’s 21st-century technology trying to correct 19th century mistakes. I love the idea that we can restock the lake not with a substitute, but with something that was originally there.” Pointing out that Lake Ontario’s original salmon are not the only locally extinct population in the world, Haddrath adds, “There may be a big demand for this in the future. It could alleviate some of the guilt for wiping out an entire population.”
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Sharon Oosthoek is a Toronto-based journalist and 2006 winner of a Canadian Science Writers’ Association’s Science in Society Journalism Award. Her writing also appears in Canadian Geographic and The Globe and Mail.
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