The Black Death’s legacy, Neanderthal family ties, and other ancient DNA secrets

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The fast-expanding field of ancient DNA, formally known as paleogenetics, came of age in 2022, earning its pioneering scientist Svante Pääbo a Nobel prize for medicine and physiology.

Pääbo, the director of the Max Planck Institute for Evolutionary Anthropology in Germany, developed methods to recover, sequence and analyze ancient DNA from fossils — a feat that took decades. Researchers are using the techniques today to answer fundamental questions about human history and the planet’s deep past.

Many of the discoveries upend assumptions about prehistoric times. When Pääbo’s lab in Leipzig sequenced the first Neanderthal genome in 2010, many were startled to learn that our own species Homo sapiens encountered and had babies with Neanderthals.

Paleogenetics has continued to tease out astonishing secrets from DNA hidden in bones, teeth — even dirt. Here are seven things we learned in this fascinating and emerging field 2022.

The Black Death, the world’s most devastating plague outbreak, killed half of medieval Europe’s population in the space of seven years in the 14th century, shifting the course of human history.

But research published in October suggested it was more than luck that determined who lived and who died. Analysis of centuries-old DNA from both victims and survivors of the Black Death identified key genetic differences that helped people survive the plague, according to a study published in the journal Nature.

That genetic legacy continues to shape the human immune system today, with genes that once conferred protection against the plague now linked to a greater vulnerability to autoimmune diseases such as Crohn’s and rheumatoid arthritis. Science magazine named the discovery one of its top breakthroughs of 2022.

Ancient DNA also shed light on the origins of the plague outbreak that caused the Black Death — work detailed in a study published in June.

Genetic material extracted from skeletons buried in a graveyard in Kyrgyzstan, where tombstones referred to a mysterious pestilence, revealed the DNA of the plague bacterium — which scientists call Yersinia pestis — in three people who died in 1338, several years before the disease entered Europe in 1347.

An artist's reconstruction of a Neanderthal father and his daughter from Chagyrskaya cave in southern Siberia.

Scientists uncovered a genetic snapshot of the oldest known family group, using ancient DNA from Neanderthals who lived in Chagyrskaya Cave in southern Siberia in Russia.

The riverside hunting camp about 54,000 years ago was home to a tight community of around 20 Neanderthals, including a father and his teenage daughter, a young male who might have been a nephew or a cousin, and an adult female who was a second-degree relative — perhaps an aunt or a grandmother.

The researchers also detected an unexpected pattern of female migration among the different threads of genetic ancestry.

The diversity of the Y chromosome DNA, which is inherited through the male line, was a lot lower than that of the mitochondrial DNA, which is passed from mothers. The study calculated that, in this group, two male individuals could expect to share an ancestor around 450 years before they lived. By contrast, the equivalent estimate for female individuals was around 4,350 years.

The researchers said the best explanation for this was that more than 60% of the female Neanderthals in the small Chagyrskaya group had migrated from another community. This social structure is common among present-day hunter-gatherer societies and is known as patrilocality.

Scientists in Denmark detected the world’s oldest known DNA sequences in sediment from the ice age.

The core of earth, taken from northern Greenland, revealed the polar region was once abundant with plant and animal life 2 million years ago. Mastodons, reindeer, geese, lemmings and hares lived in an ecosystem that was a mix of temperate and arctic flora and fauna.

The genetic material in the dirt, shed by all of the living organisms in the environment so long ago, tells a more complete story of prehistoric life than the fossil record.

This unparalleled ancient ecosystem has no modern equivalent, but it could provide a genetic road map for how some species might adapt to the climate crisis.

Construction workers breaking ground in 2004 on a shopping mall in Norwich, England, discovered 17 bodies at the bottom of an 800-year-old well.

To understand more about how the six adults and 11 children whose remains were found there died, scientists were recently able to extract detailed genetic material preserved in the bones thanks to advances in ancient DNA sequencing.

The genomes of six of the individuals showed that four of them were related — including three sisters, the youngest of whom was 5 to 10 years old. Further analysis of the genetic material suggested that all six were “almost certainly” Ashkenazi Jews.

Judaism is primarily a shared religious and cultural identity, but as a result of a long-standing practice of marrying within the community, Ashkenazi Jewish groups often carry a distinctive genetic ancestry that includes markers for some rare genetic disorders.

The researchers believe they all died during antisemitic violence that wracked the city — most likely a February 1190 riot related to the Third Crusade, one of a series of religious wars supported by the Catholic church.

Scientists announced earlier this year that they had sequenced the genome of a victim of the eruption of Mount Vesuvius in 79 AD.

Pompeii, preserved in volcanic ash after the eruption of Mount Vesuvius in 79 AD, is one of the world’s most intensively studied archaeological sites, but getting detailed genetic information from the skeletal remains preserved in the city had long eluded scientists.

Earlier this year, scientists said they had for the first time successfully sequenced the genome of a man who died after the eruption.

Before this latest study, only short stretches of mitochondrial DNA from human and animal remains in Pompeii had been sequenced.

It may have been possible to successfully extract ancient DNA from their samples because pyroclastic materials — a burning hot mix of gas, lava and debris — discharged during the eruption may have protected the DNA from environmental factors, such as oxygen in the atmosphere that led to decomposing.

The information shed light on the man’s ancestry and health.

The researchers extracted DNA from kunga skeletons buried at Umm el-Marra, Syria.

A majestic horselike creature known as a kunga that lived 4,500 years ago was the earliest known hybrid animal — with parents from two different species, according to research published in January.

Descriptions and imagery in Mesopotamian art and texts portrayed a powerful animal that pulled war wagons into battle and royal vehicles in parades. Intact skeletons of the creatures were buried alongside high status people from the era.

Its true identity, however, had long puzzled archaeologists. Domesticated horses did not arrive in the region, sometimes referred to as the Fertile Crescent, until 4,000 years ago.

Sequencing of DNA from the animal’s skeleton revealed that it had a Syrian wild ass for a father and a donkey mom, and was likely deliberately bred by humans.

The fossils were found in Red Deer Cave in southwest China.

DNA sequencing revealed the origin of some odd-looking human fossils — a thigh bone and part of a skull — found in a cave in southwest China in 1989.

Primitive features of the bones had vexed scientists, who questioned what species of human the fossils belonged to. Perhaps, they thought, they belonged to a hybrid population of extinct and modern humans or maybe a previously unknown human species that existed alongside our own.

Chinese scientists recently extracted genetic material from the skull cap and found that the skull belonged to a female individual, who was most likely a direct modern human ancestor — a member of Homo sapiens.

The researchers then compared the genome extracted from the ancient DNA to the genomes of other people from around the world — both modern and ancient.

They found that the bones belonged to an individual who was linked deeply to the East Asian ancestry of Native Americans. The researchers believe that this group of people traveled north to Siberia and then crossed the Bering Strait to become some of the first Americans.

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