Ancient DNA reveals well-kept secrets about the migrations, evolution and interbreeding of human populations, but also about the history of pathogens and animals. Fourth article in the series The missing genome, on the bubbling science that is paleogenomics.
DNA that can be extracted from ancient skeletons is now commonly used to discover the identity of missing persons. The analysis of this genetic information transmitted from generation to generation has made it possible to solve famous historical investigations, including the assassination by the Bolsheviks in 1918 of members of the Russian imperial family, the Romanovs, buried in a mass grave, or of discover the tomb of English King Richard III, who died in 1485.
The search for the tomb of Richard III began in 2011 from historical documents indicating that this last king of the Plantagenet dynasty had been assassinated during the Battle of Bosworth on August 22, 1485, two years after his accession to the throne. from England. These texts also indicated that his remains had been interred in the church of the Gray Friars monastery in the city of Leicester.
The monastery having been destroyed over the following century, it was under a tarmac parking lot that the alleged skeleton of the king was exhumed in 2012. Examination of it first revealed that it belonged to a man aged between 30 and 34, that he had a significant curvature of the spine (scoliosis) and that he bore the marks of violent impacts on the back of the skull, on the ribs and the pelvis, so many signs that agree with the description in the archives of his death at the age of 32 and the abuse inflicted on his body after the battle. A carbon-14 dating then estimated that the skeleton dated back to a period ranging from 1456 to 1530, which therefore covered the date of death, in 1485. All that was missing was genetic evidence to confirm that these bones were indeed those of Richard III .
Find descendants
DNA was therefore extracted from the skeleton, specifically his teeth. Then, it was necessary to find the trace of descendants of King Richard III who were alive, in order to compare their DNA (obtained by a sample of saliva) with that of the skeleton, to see if they were well linked, explains Tommy Harding, specialist in forensic biology at the Laboratory of Forensic Sciences and Forensic Medicine of Quebec. “As Richard III is a well-known figure, it was quite easy to piece together his genealogy and find living descendants,” he says.
An analysis of the DNA present in the nucleus of the cells of the dentin of the teeth first made it possible to confirm that the skeleton was indeed that of a man, due to the presence of the Y chromosome. From this cellular DNA, the researchers were also able to deduce the color of the hair and eyes of the person to whom the skeleton belonged. The results of their analysis indicate that there is a 96% chance that the person had blue eyes and a 77% chance that their hair was blond at birth. However, a portrait of Richard III dating from the 1510s represents him with blue eyes and brown hair, but, knowing that blond hair often darkens during adolescence, researchers believe that the correspondence is likely.
Genetics, archeology and history specialist Turi King of the University of Leicester, who led the survey, focused her efforts on two particular types of genetic material: mitochondrial DNA as well as the DNA that makes up the chromosome. Y.
The advantage of these two categories of DNA sequences lies in the fact that they are not subject to recombination, that is to say genetic mixing. They are transmitted as such from one generation to another, with the exception of a few mutations which can occur with each generation and introduce small modifications, expose the geneticist Damian Labuda, of the CHU Sainte-Justine Research Center, and Frank Crispino, director of the Forensic Science Research Group at the University of Quebec at Trois-Rivières (UQTR).
Mitochondrial DNA is found in the thousands of mitochondria, the little powerhouses in each of our cells. “We can find up to 10,000 copies of this DNA in the same cell. It is therefore easier to recover this DNA, since it is in higher copy number,” says Labuda.
Another peculiarity: it is only the mothers who transmit the mitochondrial DNA to their offspring. “Mitochondrial DNA is present in the egg. There is some in the tail of the sperm, but when the sperm fertilizes the egg, it loses its tail, so the mitochondrial DNA in the fertilized egg is only from the mother. Richard III had therefore received this DNA from his mother, but he could not transmit it in turn, ”says Mr.me King.
“But, since the mitochondrial DNA that Richard III received from his mother was the same as that inherited by his sister [Anne d’York, ou Anne Plantagenêt (1439-1476)]as well as by the descendants of the latter, [les experts] searched and found two descendants of his sister who were alive, whose mitochondrial DNA was sequenced, which was then compared with that extracted from the bones of Richard III”, explains Mr. Labuda.
A mismatched Y
The analysis carried out by the researchers then showed “a perfect concordance between the mitochondrial DNA of the two living descendants of the maternal line of Richard III and that of the skeleton, with the exception of a small difference in the DNA of the ‘one of the descendants, which was probably due to a spontaneous mutation,’ says Mme King. “Such a concordance therefore makes compatible kinship ties between these three individuals by matrilineal descent”, write these researchers in the article describing their discovery, which was published in the journal NatureCommunications.
“We then asked ourselves a question: could it be that we observed a perfect match [entre le squelette et l’un des descendants] by pure chance, because this DNA sequence is very common in the population? adds M.me King. The researchers therefore compared this mitochondrial DNA to that of 26,127 Europeans and 1,832 Britons. They then found no match, indicating that “the sequence is rare”.
The Y chromosome, on the other hand, is present in only one copy in each cell, so it is more difficult to obtain this genetic material in good condition. And, although it is transmitted largely as it is, “it can nonetheless mutate over time,” Mr. Crispino points out.
As the Y chromosome is only carried by males, it is only passed on from the father to his boys. The scientists therefore searched and found in the genealogical tree of the patrilineal line five living descendants of the great-great-grandfather, or the great-grandfather, of Richard III, because this denier had no descendants. The analysis of the Y chromosome of these five individuals, however, revealed no match with that of the skeleton, which led the researchers to conclude that these descendants are not genetically related to the skeleton, that they therefore do not have family ties with him. To explain this discrepancy, they hypothesize that illegitimate sons may have been recognized and integrated into the royal dynasty over multiple generations.
“Leap of Faith”
Mme King wasn’t particularly surprised that she couldn’t find a match in the Y-chromosome DNA. biological father does not always turn out to be who they thought. Kings had children with their mistresses and these children were sometimes legitimized later,” says the researcher.
“You have to remember this adage: the mother, for sure; the father, it may be. Man is an animal whose loyalty is somewhat questionable! […] If the queen mother slept with a beggar and she didn’t tell her husband, the beggar’s child became king”, adds Mr. Crispino, who underlines that the researchers have thus found “an explanation which is admissible and which gives satisfaction for maintaining the hypothesis a priori, but which is unverifiable and which comes out of knowledge”.
Nevertheless, the authors of the study conclude that by virtue of all the accumulated historical, chemical, morphological and genetic clues, “the evidence that the skeleton is indeed that of Richard III is overwhelming”. “We didn’t just use the DNA results to come to a conclusion. We proceeded as in the case of a missing person,” said Ms.me King.
Emmanuel Milot, professor of genetics and forensic science at UQTR, recalls that “DNA can help eliminate leads and sometimes even support a hypothesis about the identity of an ancient individual. However, the scientific conclusion can only be expressed in terms of probability or plausibility. Establishing a person’s identity “definitively”, in the sense of certainty, is not a conclusion that DNA allows directly. Going from probability to certainty is what we call a ‘leap of faith’, in other words a decision, not a scientific fact,” he says.
“Some scientists sometimes tend to claim loud and clear that they have proven that this burial is that of so and so. They don’t prove anything, but support a hypothesis, which may otherwise be highly probable based on genetic observations,” he says.