On October 3, 2022, the Nobel Assembly at Karolinska Institutet announced the 2022 Nobel Prize in Physiology or Medicine had been awarded to Svante Pääbo, director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The Assembly cited his “discoveries concerning the genomes of extinct hominins and human evolution”. They mentioned the highlight of his research: the seemingly impossible task, at the time, of sequencing the Neanderthal genome. The discoveries that followed from this sequencing project continue to redefine our understanding of modern human origins.
The award showcases the technological advancements made in the analysis of ancient DNA. However, Pääbo’s research had an inauspicious beginning. In 1985, he published the results of his early work, cloning and sequencing DNA fragments from a 2,400-year-old Egyptian mummy (1). Unfortunately, later analysis revealed that the samples could have been contaminated by the researchers’ own DNA (2).
Human teeth play a key role in our understanding of how organisms evolve. Whenever a possible new member of the hominid family is uncovered, the shape and number of teeth are used to place that individual in the family tree. Teeth also harbor information about pathogens that have plagued humans for millennia. Because bacteria use our bloodstream as a transport system, protected places that can preserve DNA—like the pulp of teeth—are a rich medium for uncovering information about humans and the microbes that infected them.
Teeth have been the choice for identifying the infectious agent behind the Plague of Justinian in the sixth century and the Black Plague in the 14th century. In fact, Yersinia pestis, the bacterium responsible for these plagues, has infected humans as far back as the Neolithic. But what can we learn about the pandemic strain or strains of Y. pestis described in historical records? A team of researchers from Europe and the US, many of whom have been delving into the history of Y. pestis for the last decade, wanted to further investigate the Plague of Justinian. They studied bacterial DNA extracted from human remains found in Western European communal graves that were dated to around 541–750, the period of the historically documented Plague of Justinian. Their investigation examined the bacteria’s diversity and how far it spread during this “First Pandemic” of plague. Continue reading “Delving into the Diversity of The Plague of Justinian”
There is a grave near the Swedish town of Birka that was the final resting place of a Viking warrior. The grave, called Bj 581, was filled with weapons, including a sword, battle knife, axe, armor-piercing arrows, a spear and two shields as well as a full set of gaming pieces with a board, and the skeletons of two horses—a mare and a stallion. First described in the late 1800s, this grave has been held up as the example of what a Viking warrior burial site would look like because it was so well furnished.
Isolating and sequencing DNA from ancient samples is a highly specialized field of research that easily captures the imagination. For me it started in the early 90’s when I read about researchers using PCR (a relatively new technique at the time) to amplify, and subsequently sequence, the mitochondrial DNA of an extinct subspecies of zebra using a sample collected from a skin rug found at an estate in England.
From samples a few hundred years old to ones that are thousands of years old, scientists have made good use of technological advances to push back the boundaries of time. In this video from Science, Evolutionary Biologist Beth Shapiro talks about working with ancient DNA, and how new advances such as Next Generation Sequencing have made it possible to gather more information from ancient samples.
Science put together a Special Issue focused entirely on the research surrounding ancient DNA. You can find all the articles in this Special Issue here:
When I started writing about research on Yersinia pestis and the Black Death, I was amazed at the ability to recover 14th century bacterial DNA from human remains, show Y. pestis was the caustive agent of the Black Death and then sequence the strain to compare to modern Y. pestis strains. The publications I read always mentioned the three waves of pandemics that devastated human populations in the introduction, and the Black Death was not the oldest one. The putative first pandemic was the Plague of Justinian in the 6th century, named after the Byzantine emperor. Like with the Black Death, there is debate about whether Y. pestis is the causative agent of the Plague of Justinian. The research published in PLOS Pathogens built on earlier work to isolate and genotype the suspected Y. pestis causative agent from human remains in 6th century graves, but this time with more stringent protocols enacted to answer critics who questioned the authenticity of earlier results. Continue reading “Ancient Samples Confirm the Cause of the 6th Century Plague Pandemic”
What is it about the UK and graves and dead people to identify or bacteria to sequence? First, there are Black Death graves, then Richard III under a car park and now a leprosy grave site. While we do know leprosy has been a scourge of human beings for centuries, tracking the different strains and origins of the disease is relatively new. Taylor et al. were interested in this grave site near Winchester, located in southern Britain, north of Southampton and southwest of London, because little is known about the disease organism Mycobacterium leprae during this early medieval period (late 11th to 12th century). What could they learn about the strains that caused leprosy and the possible spread of the disease? Continue reading “Peering into the History of Leprosy”
Smallpox was a disease caused by infection with one of two strains of Variola virus (Variola major and Variola minor) and a worldwide scourge that killed up 35% of the people it infected. Luckily, a vaccine was developed when Edward Jenner noticed milkmaids infected with cowpox did not contract smallpox. While Jenner was not the first to vaccinate against smallpox, his discovery and testing were spread to a wide audience and thus became the basis for the vaccination efforts that have eradicated the virus in our lifetime. Despite all the research on smallpox, not much is known about the evolution of the virus. Sequence data for the virus only span the last 50–60 years. However, recent efforts published in the New England Journal of Medicine uncovered a new source for examining the history of smallpox infection: mummies. Continue reading “Mummies are a Reservior of Viral History”
In central England, an archaeological dig is happening in an unlikely spot—a parking lot in the city of Leicester. The goal: To find the final resting spot of Richard III, the last of England’s Plantagenet kings and perhaps one of its most maligned rulers. Richard III reigned over England for only two years before being killed by Henry Tudor’s army during the Battle of Bosworth Field in August 1485 at the end of the War of the Roses, which pitted Richard’s House of York against the House of Lancaster. Many historical records suggest that Richard’s body was brought to Leicester and buried between the nave and altar at Grey Friars church. You would think that a king’s tomb would be well marked and well remembered, even for an unpopular king like Richard III, but that is not the case here. Henry was said to have erected a memorial for his former rival, but that and any other monuments, along with the church itself, are long gone, destroyed during the Dissolution of the Monasteries, when Henry VIII was named Supreme Head of the Church in England and systematically razed monasteries, convents and friaries throughout England, Wales and Ireland between 1536 and 1541. Since then, the exact location of Richard III’s remains was lost to history. However, thanks to a team of University of Leicester archaeologists and geneticists that might be changing.
Archaeologists have made an interesting discovery while excavating the late Bronze Age/early Iron Age settlement named Cladh Hallan on the island of South Uist in the Outer Hebrides, Scotland. They have uncovered four human skeletons buried at regular intervals beneath three roundhouses dating from the 11th century BC: an adult male, an adult female, a 10–14-year-old girl and a 3-year-old child. The careful arrangement of these burials directly below the roundhouses led archaeologists to initially hypothesize that these might be foundation burials—an ancient practice in which people, usually younger people, were sacrificed and buried under a building’s foundation in the belief that their blood and spirit would protect and strengthen the building and building site. As strange as that custom seems to us, it gets weirder. Two of these skeletons showed signs of mummification and contained skeletal elements from multiple individuals intentionally pieced together to form intact skeletons. Continue reading “DNA Typing Confirms Bronze Age Mix-and-Match Burials”
The pharaoh Tutankhamun ruled ancient Egypt during the 18th dynasty of the New Kingdom (circa 1550–1295 BC), one of the most powerful royal houses in ancient Egypt. Although he sat on the throne for only 9 years and died at the young age of 19, he is one of the most well known pharaohs, due largely in part to the discovery of his intact tomb by archaeologist Howard Carter in 1922. The tomb was filled with riches befitting a king, including an elaborate sarcophagus with a gold burial mask and statues of ancient Egyptian gods such as Osiris and Anubis, as well as gold jewelry, statues and images of servants, ornate furniture, models of boats and other items that the pharaoh would need in the afterlife. A lesser known item discovered in his tomb was an undecorated wooden box in which two small gilded coffins lay side by side. These coffins held the mummified remains of King Tutankhamun’s two stillborn daughters. Recently, researchers examined these remains in detail to determine their gestational ages and characterize any congenital abnormalities that they might have inherited from the boy king.
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