In Russia, an ancient DNA researcher rewrites the past – Haaretz

If there were a competition for the most godforsaken, remote place on Earth, Wrangel Island in the Arctic Ocean northeast of Siberia would be a worthy contender.

The ground is covered by permafrost and cyclones ravage the landscape on a regular basis. Even on the warmest days temperatures only climb as high as 5 degrees Celsius (41 degrees Fahrenheit), while in the wintertime it plummets to minus 30.

Prof. Love Daln, of the Centre for Palaeogenetics at the Swedish Museum of Natural History and Stockholm University, never thought his academic path would lead him here, of all places. But he kept returning to Wrangel, along with his fellow lab workers. They slept in tents, chased off curious polar bears, and tried to locate a unique find: the remains of the last woolly mammoths to walk the planet.

Throughout history, the location and harsh living conditions on Wrangel have kept humans away, thus creating the conditions that allowed the island to host the last surviving group of mammoths, until 2000 B.C.E. long after the Egyptians began building their pyramids.

It took a long time to collect the samples in conditions of intense cold, with a lot of polar bears around you not easy, the researcher recalls in a Zoom interview with Haaretz.

Daln is among the worlds foremost researchers of ancient DNA, using cutting-edge technology that enables a direct genetic study of evolution on Earth sequencing the genomes of animals and plants that became extinct hundreds of thousands, even millions, of years ago. In December, Nature magazine named him one of its scientists to watch in 2022.

DNA analysis is very important to the understanding of life, says Daln, and ancient DNA allows us to travel back in time. This way, we can learn about evolution at the molecular level in real time. Thats why its so cool. Until recent years, genetic studies always deduced about the past through current DNA, so we could only guess. With ancient DNA, we can really see what happened back then.

Indeed, analysis of ancient DNA heralded a real revolution in the study of the development of life and a series of dizzying discoveries. Thus, for example, we learned that Neanderthals mated with modern humans (Homo sapiens).

All humans currently living outside of Africa carry about 2 percent of Neanderthal DNA in their genetic makeup, and this is something we had no idea about before the study of ancient DNA, Daln says. Before this technology was developed, the argument was that there was no interspecies mating. Those 2 percent, by the way, affect COVID immunity, so its something that impacts us to this day.

Daln adds that ancient DNA studies have discovered that hybridization between species was a very common phenomenon, and not just among hominids. It was revealed, for instance, that modern brown bears carry 3 to 4 percent of the cave bears DNA an extremely large species of bear that lived in Europe and Western Asia, including Israel, but became extinct some 25,000 years ago.

So there was mating there, too, says Daln, and from this we understand that hybridization between species is a natural occurrence, which has happened in the past and may happen in the future.

Today, for example, people are worried that brown bears are reaching further northward due to global warming, and are mating with polar bears, he says. But this is something that has happened again and again over the past 700,000 years, so perhaps we dont need to be so worried about it.

A giant leap backward

The origins of this field of study can be dated back to 2005, when Next Generation Sequencing was developed. This method enables the separation of ancient DNA and contemporary DNA, which would contaminate the ancient findings.

This was a serious scientific breakthrough, Daln says. Until this method was developed, you couldnt ascertain if DNA found in an ancient bone, for example, belonged to the animal itself or to the researcher who found the bone.

If an archaeologist touches an ancient bone, he contaminates it, Daln explains. Its enough to breathe near a bone to contaminate it, because the breath contains many DNA molecules. In a previous study, we showed that this contamination penetrates deep into the bone. We took dog bones, 3,000 to 5,000 years old, sent them for DNA analysis, and found more human DNA than canine even deep in the bone.

The great advantage of Next Generation Sequencing is that it can identify damage to the DNA molecules. This damaged DNA by which we mean old DNA can be separated from the undamaged, or new, DNA. Furthermore, the method allows for the analysis of large quantities of data.

We went from a few hundred bytes of data to billions of bytes that we produce, Daln says. It allows us to reach much stronger conclusions regarding the past.

The research approach pioneered by Daln is called Deep Time Paleogenomics. There have been thousands of studies published about ancient DNA in the past decade, he says, and 99.9 percent of them focus on the past 10,000 years, and on the human genome. There are a few studies on the period from 10,000 to 50,000 years ago, and there are a handful fewer than 10 that go even further back in time.

Daln and his team were the first to successfully study ancient DNA over a million years old. Early last year, they published a pioneering research study that identified a hitherto unknown species: the steppe mammoth. They discovered that this mammoth lived until at least 1.2 million years ago. Our research showed that it is possible to go back at least 1.2 million years that is a huge leap back in time, Daln says.

He relays how, for more than a decade, he held onto the samples in his possession, waiting patiently for the right technology to emerge.

The moment that the information exists, you also need very advanced analysis methods to analyze it, Daln says. We analyzed 10 billion bits of DNA, and 99 percent of them were of bacteria from the soil or from plants, he recalls. In other words, very few came from the mammoths and even these bits were very short.

In order to identify the bits of DNA that belonged to mammoths, the research team needed to develop unique statistical models, which are at the heart of their research. Impressive accomplishment notwithstanding, Daln believes it is possible to go even further back in time. We view it in terms of the degree of preservation of the DNA in mammoths, he says. The analysis would also work if the findings were another half a million years older.

Meanwhile, Daln and his team recently received funding for a large-scale project in which they will seek the DNA of additional species such as moose and lemmings. The remains of some of them are 2.6 million years old, and Im fairly certain we would succeed in extracting DNA from them, he states.

Mosquitoes and bears

Analysis of the distant past would allow us to explore several significant biological issues, including the selection process of animals undergoing evolution. The selection of most of the mammals occurred at least half a million years ago, Daln says. In order to understand this process, you need samples that are at least half a million years old at which point it would be possible to answer basic questions such as, for instance, whether the rate of adaptation in evolution takes place faster when the species has only recently been created. Thats something we dont know. By the way, for the mammoths we investigated, the answer is no, but that is a sampling of a single species. It may be that the rate of adaptation in other species was actually quicker at the start of the species existence.

In order to decipher such riddles, researchers must spend long hours in the laboratory. But there are also intermissions spent in the field such as the trips to Siberia which can last up to six weeks.

It happens with greater frequency than I would like its cold there, Daln smiles. In the summer, the temperature varies between 0 and 5 degrees Celsius. And when the temperature rises just a bit, there are quantities of mosquitoes you wouldnt believe. Its terrible. There are whole swarms all around you, almost making it hard to see. Its a whole cloud around you. Also, youre living with constant noise, 24 hours a day, with that buzzing sound.

Nevertheless, the tough field conditions are critical for carrying out the research: in order to piece together ancient DNA samples, they must be well preserved throughout the entire period of time since they were created. In this case, they must remain frozen for over a million years. Such samples can be found in the Siberian permafrost, in Antarctica, in caves at high altitudes and perhaps also in the depths of the ocean. For the most part, the findings consist of bones and teeth.

Daln relates that many of the mammoth remains in his research are a by-product of the unlawful activity of ivory traders in Siberia. These traders conduct extensive digging in the permafrost in order to locate the valuable tusks, which they then sell in the Chinese market. The length of some of the tunnels dug by the ivory traders run for hundreds of meters and at times the researchers attempt to locate findings in them.

They are interested solely in tusks, not bones, so sometimes we go in after them to see what is left, Daln says. But old tunnels can collapse, and one time that happened to us. Part of the team nearly lost their lives.

Scary as that sounds, it wasnt the researchers most hair-raising experience. The most frightening part is flying in the Russian helicopters theyre very old, Daln admits. Russian engineers are skilled at building aircraft that last for many years and the pilots are very skilled, but nevertheless there are quite a few helicopter crashes. And thats how we get around there.

At times, the researchers also receive samples from collections held in Russian museums. These have already been at room temperature for decades, Daln says. When we dig, we keep the findings frozen in the laboratory.

When they come across any mammoth remains, such as a tooth or a tusk, they take a small bit about the size of a sugar cube as a sample and preserve it in cold storage. They send the rest to museum collections.

However, the ancient DNA research does not focus solely on bones and teeth: scientists are also collecting DNA samples from sediment. In this method, they drill into the stone walls of a cave or into the permafrost, analyzing the DNA found in the sediment. This way, they can acquire data not only on individual specimens, such as in genomic analysis of a bone or tooth, but instead on an entire community.

You take a bit of soil or rock and see what lived there hundreds of thousands of years ago DNA of all the plant life that lived at that time, and of animals that lived there, Daln explains.

Some 20 percent of these sediment samples are composed of organic material originating in animas dead skin, urine and feces. This includes short bits of DNA, which it is possible to piece together. The researchers determine the age of the sample based on bits of plants they find in the sediment, which can be dated. Daln believes that in the near future, it will be possible to use such sediments to discover what happened to entire populations over a million years ago.

The possibilities are mind-boggling. In the past 2.5 million years, Planet Earth has mainly had ice ages of approximately 100,000 years in length, and between them hot periods of about 10,000 years, he explains. Were now in a hot period, and one interesting question is how the ecological systems looked the last time there was a hot period about 120,000 years ago. Thats something that is very interesting to examine. The mammoths became extinct during the current hot period [the Holocene], and other Arctic species are facing a difficult situation. It would be interesting to know what happened last time.

As opposed to the sediment samples, when it comes to gauging the ages of bones and teeth from the past 50,000 years, the researchers use the most common dating system: carbon-14. However, this tool is unsuitable for earlier times. As an alternative, the researchers examine the age of rodents found in the same soil level. Lemmings, for example. The morphology of these animals changes relatively quicker than that of mammoths. Bits of DNA from the rodents skull are examined and their age determined the assumption being that the mammoth found alongside it is of the same vintage.

A third method is paleomagnetic dating, which uses the effect of Earths magnetic field reversal to determine the age of sediments or archaeological findings. The last time the Earths magnetic direction reversed completely was 800,000 years ago, says Daln, and so its possible to know whats earlier than that date. It is impossible to know the exact age, but you can know if something is older than 800,000 years.

DNA, politics and racism

Even though innovative research techniques expand scientific understanding, there are some who have made problematic use of them. For instance, two years ago, then-Prime Minister Benjamin Netanyahu referred to an ancient DNA study which stated that the Philistines may have been of European descent.

In order to avoid political and racist use of the research tool, scholars from 31 countries recently drafted an ethical code for the use of ancient DNA studies.

It is very important to take into account that findings and most certainly those of studies of ancient human DNA can have political implications, Daln says. When you take samples in countries in which there is, for instance, indigenous populations, it can influence the decisions of politicians.

Therefore, he adds, it is important that the research take place in collaboration with, and with the consent of, native populations.

Another ethical issue Daln raises relates the harm to the findings, some of which are extremely rare, that the research causes. Samples of ancient humans are extremely rare and when you investigate the DNA, you harm the sample, he explains. The question can be asked: Do you want results now, or is it better to preserve the findings for generations to come, which may have access to better technology?

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In Russia, an ancient DNA researcher rewrites the past - Haaretz