Ancient DNA reveals well-kept secrets about the migrations, evolution and interbreeding of human populations, but also about the history of pathogens and animals. Third article in the series “The missing genome” on the bubbling science that is paleogenomics.
On the door leading to the laboratory, two posters rather than one announce that access is strictly prohibited. On the other side, in the immaculate space, the scientists Camille Julien and Kariane Larocque, clad in single-use white overalls, bustle around stainless steel equipment. The scene looks like a science fiction movie, and in a way it’s really a bit there.
TRACES, the modern and ancient DNA laboratory of the University of Quebec at Trois-Rivières (UQTR), is reserved for aseptic research on biological remains. The clean room, or clean (according to the specialized jargon), controls the suspended particles in the air and minimizes the introduction, the production and the retention of the particles inside the hermetically sealed place. Positive pressure air is vented approximately every minute. Incoming air is via an independent external outlet. Hence the waterproof suits of the researchers. Even their pens and papers are designed for cleanrooms.
“This laboratory makes it possible to extract DNA from non-traditional sources, on ancient objects or bones for example, and to achieve this, you need very aseptic conditions”, explains Emmanuel Milot, professor of genetics in the Department of Chemistry. – biochemistry of UQTR, which founded and directs this unique place in Quebec. “It’s a long process, and I would say that we are now semi-operational. »
Grants are sought from the Canadian Foundation for Innovation to further improve the lab and make it an even more unique “infrastructure” in Quebec, with equipment in two universities and bridges to large databases populational.
Professor Milot’s research focuses on the interpretation of DNA traces for forensic purposes and on the intergenerational transmission of certain diseases. For example, he participated in research showing how a genetic mutation introduced into New France by a Daughter of the Kingultimately causing blindness, then spread to the Quebec population over the centuries, until today.
Montreal cemeteries
Camille Julien and Kariane Larocque, graduates in forensic chemistry from UQTR, now at the end of their master’s degree in cellular and molecular biology, are working on the remains of ancient and anonymous individuals found in Quebec. They want to help identify them at least by establishing their sex or their original gene pool.
Mme Larocque analyzes the archaeological collections of the City of Montreal from two active cemeteries between the XVIIe and XIXe centuries. Before entering the lab, she exhibited a petrous bone discovered there, now kept under vacuum, with a tiny hole that had been used to extract a sample from it.
“We extract DNA from ancient bones, and for this work, we need the facilities of the clean room, explains Mr.me Larocque. It’s a [échantillon] very degraded and aseptic facilities are needed to minimize contamination. »
If I am able to isolate good enough genetic material in the samples from Cap-des-Rosiers, I should be able to differentiate between what is French-Canadian and what is Irish.
His work continues the pioneering research of Tommy Harding, crossing information from genealogical data with genetic information. In the endnew research using more advanced techniques that would sequence many more nucleotide pairs could make it possible to precisely identify certain deceased people, and thus open avenues of research in epidemiology, historical demography, history, evolutionary biology , in anthropology or in primary archaeology, explains Professor Milot.
“The question of publicly naming people is more delicate,” he notes. There are ethical issues. For the study on the King’s Daughter, carriers of the genetic mutation have been identified who, themselves, may be unaware of it. It’s very tricky and there’s a probabilistic question at play.”
Irish bones
Camille Julien, she works on the results of an excavation in a mass grave carried out in 2016 in Cap-des-Rosiers, in Gaspésie. The bones may belong to seven Irish immigrants shipwrecked from the ship Carricks of Whitehaven in 1847. “There was never any tangible proof that the pit contained these remains,” she says. I try to estimate their biogeographical origin. »
The project comes in part from Georges and Charles Kavanagh, descendants of survivors of the same maritime tragedy, who want to know if other passengers are buried in Gaspésie. “It’s very touching,” said Mr.me Julian. When I started my research, I didn’t think I had such a fascinating subject, which still has significant repercussions today. »
She examines nucleotide polymorphisms, or the variation of base pairs in the genome between individuals. This characteristic may vary from one region of the world to another. The British Isles are very well characterized by The People of the British Isles (PoBI) project launched at the University of Oxford in 2004.
“If I’m able to isolate good enough genetic material in the samples from Cap-des-Rosiers, says Camille Julien, I should be able to differentiate between what’s French-Canadian and what’s Irish. »
The two student friends have also been involved for two years in the development of protocols for clean room research and the extraction of DNA from bones still contaminated by microorganisms, other species or humans, sometimes archaeologists themselves. The residual cells of the castaways are further degraded by the water. A rule in the industry says that the type of conservation has more impact on the quality of DNA than the age of it. An Egyptian mummy in its sarcophagus can be more “talking” than a body of the XXe century poorly preserved or contaminated by human DNA present everywhere in the air.
The fundamental goal would be to centralize and link the methods of the excavation to the analyzes of samples.
The pair of Quebec students will also be at the Musée de l’homme in Paris in August for a so-called cross-validation project. The Paris lab will be used to compare the techniques and results of the Population Genetics Laboratory at UQTR. “We are beginning to establish with this museum research on comparative questions between France and Quebec”, sums up Professor Milot.
Quebec originality
To tell the truth, Quebec represents an almost unique case in the world. “On an international scale, there are very few places with such rich data infrastructures as here,” underlines UQTR professor Marie-Ève Harton, holder of the Canada Research Chair in History. population dynamics in Quebec (XIXe and XXe centuries). “There is of course an interest in the specific historiography of Quebec. We understand our own dynamics with our data. But on different subjects, the information banks here allow research impossible elsewhere, and even to test fundamental hypotheses. »
The small starting population in New France was tracked individually by the Catholic Church, then by the state, for four centuries. The numbers of accumulated information are dizzying. The Balsac file of the University of Quebec at Chicoutimi, founded fifty years ago by historian Gérard Bouchard, contains more than four million civil status records relating to more than six million individuals covering four centuries.
Professor Hélène Vézina, from UQAC, is now piloting the i-Balsac project, to add approximately six million birth and death records from 1850 to 1920. In three years of development, aided by the automatic recognition technique handwritten documents, this new infrastructure will be more imposing than that built in four decades around Balsac.
There are other notable Quebec infrastructures. The University of Montreal manages the Register of the population of ancient Quebec, which “reconstitutes” the Catholic population since the beginning of the colony. The Integrated Infrastructure of Historical Microdata on the Population of Québec, the result of the collaboration of several universities, makes civil status records (1621-1914) and Canadian nominal censuses (1852-1911) accessible. The Center interuniversitaire d’études québécoises has launched a high-resolution mapping project to locate genomic, contextual and geographical data in order to define the mechanisms studied at the individual, family, community or national level.
A sociologist by training, history professor Marie-Ève Harton specializes in the study of fertility and migration based on these infrastructures. In particular, she debunked the myth of the French Canadian always overproducing children by showing the varied cases of large, medium and small families.
“Current population dynamics are an extension of processes initiated in past centuries,” she explains. The demographic transition began decades before the arrival of the contraceptive pill. Fertility declined in the 1920s for the French-Canadian population. »
Genetics enriches socio-historical understanding, for example to “condition certain trends in mortality”, such as the fact that the mortality rate was particularly high among children in the past.
“The more dimensions you add, the more convincing the analyzes become,” says the specialist. By following an individual’s journey, one can understand whether a woman had her children before or after her exile to New England or whether a man’s marriage preceded the migration. The infrastructures make it possible not to focus on single cases, to establish complex mechanisms and multiple causes at the population level. »