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Using ancient genetic material to read the past and look into the future

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It smells of chlorine. The room is brightly lit and has no windows. The equipment is frugal – centrifuges and shakers, with pipettes, tweezers and laboratory spatulas on the sterile lab benches. The people who work in the clean-air lab have to be extremely careful to make sure no dust particles contaminate the samples because here, in the basement of the Plant Protection Lab at WSL, researchers are investigating the genetic material of plant and animal remains that are several thousands of years old. This genetic material is present in only the tiniest amounts and is, moreover, fragmented and damaged. Introduced particles from outside, such as flower pollen, could ruin all the analyses.

This is why the researchers take a shower and slip into white overalls before entering their workplace. They also wear face-masks, gloves and protective goggles. They frequently wash the gloves and lab benches with bleach, which destroys DNA and is the source of the unpleasant smell in the lab rooms. The air pressure in the lab is higher than in the open air to ensure no dust particles or flower pollen can get in from outside.

Silver fir in southern Ticino

Ancient DNA allows a glimpse through the keyhole into past eco­systems. “Genetic analyses of long extinct populations have proved helpful in understanding how species react to environmental changes,” says Christoph Sperisen, a population geneticist at WSL. The researcher is bending over a mechanical shaker in which he is grinding ancient wood samples into powder in order to isolate the genetic material.

Recently Christoph and colleagues from the Universities of Lausanne and Bern succeeded in reconstructing the history of a former silver fir stand in Ticino. The researchers analyzed silver fir needles retrieved from the sediment of Lake Origlio (TI). The needles were between 5,800 and 7,100 years old. During this period, settlers there started to clear the forests to obtain farmland. The results show that, with farming, the silver fir stand shrank and, consequently, so did its genetic diversity. About 6,200 years ago, both the stand and the genetic diversity recovered again. Comparisons of the DNA from silver fir needles of different ages indicate that the stand re-established from trees surviving in the area; trees from other regions were probably not involved.

 
 

Avoiding incorrect inter­pretations arising from contamination

In the room next door, Christoph’s colleague, Bertalan Lendvay, is pipetting a prepared solution of genetic material into small plastic tubes. Using a special technique, he will multiply, within a very short time, the small amount of ancient genetic material a million times. Since this process also multiplies the DNA from impurities, the surfaces of the samples must be thoroughly cleaned beforehand.

This process is challenging the researchers, Christoph and Bertelan, in a project that is still ongoing: they are investigating pine stumps that are between 11,400 and 14,000 years old. WSL staff found them preserved in clay in Zürich’s Binz district in 2013. The pine stumps were contaminated with pollen from present-day trees and plants sticking to the wood. The researchers therefore “burned” the wood surface using a special laser technique. They then scraped away the burnt wood together with the impurities. “When analyzing uncleaned wood, we found over a hundred plant species in the DNA analyses. After the cleaning procedure, however, only one out of a thousand molecules does not come from a Binz pine,” says Bertelan.

Now the scientists would like to find out how the pines changed genetically after the Last Ice Age, when the climate became warmer. Thus they are investigating whether the pine trees at that time contained special genetic variants that helped them cope better with the warmer temperatures. “Our findings about whether and how the pines adapted to the changing climate in a relatively short time should give us valuable information about how today’s forests may react to climate change,” says Christoph.

His colleague Bertelan carries the finished preparations of genetic material solution to a neighboring building where he leaves the genetic material to multiply in a machine overnight. The results may soon give us an idea about how the Ice-Age pines adapted to the warmer climate. (Stephanie Schnydrig, Diagonal 2/17)