ancient DNA

skull-long-thought-to-be-cleopatra’s-sister’s-was-actually-a-young-boy

Skull long thought to be Cleopatra’s sister’s was actually a young boy

ancient DNA, ancient egypt, anthropology, Archaeology, cleopatra, forensic archaeology, Science / /

Scientists have demonstrated that an ancient human skull excavated from a tomb at Ephesos was not that of Arsinoë IV, half-sister to Cleopatra VII. Rather, it’s the skull of a young male between the ages of 11 and 14 from Italy or Sardinia, who may have suffered from one or more developmental disorders, according to a new paper published in the journal Scientific Reports. Arsinoë IV’s remains are thus still missing.

Arsinoë IV led quite an adventurous short life. She was either the third or fourth daughter of Ptolemy XII, who left the throne to Cleopatra and his son, Ptolemy XIII, to rule together. Ptolemy XIII didn’t care for this decision and dethroned Cleopatra in a civil war—until Julius Caesar intervened to enforce their father’s original plan of co-rulership. As for Arsinoë, Caesar returned Cyprus to Egyptian rule and named her and her youngest brother (Ptolemy XIV) co-rulers. This time, it was Arsinoë who rebelled, taking command of the Egyptian army and declaring herself queen.

She was fairly successful at first in battling the Romans, conducting a siege against Alexandria and Cleopatra, until her disillusioned officers decided they’d had enough and secretly negotiated with Caesar to turn her over to him. Caesar agreed, and after a bit of public humiliation, he granted Arsinoë sanctuary in the temple of Artemis in Ephesus. She lived in relative peace for a few years, until Cleopatra and Mark Antony ordered her execution on the steps of the temple—a scandalous violation of the temple as a place of sanctuary. Historians disagree about Arsinoë’s age when she died: Estimates range from 22 to 27.

Archaeologists have been excavating the ancient city of Ephesus for more than a century. The Octagon was uncovered in 1904, and the burial chamber was opened in 1929. That’s where Joseph Keil found a skeleton in a sarcophagus filled with water, but for some reason, Keil only removed the cranium from the tomb before sealing it back up. He took the skull with him to Germany and declared it belonged to a likely female around 20 years old, although he provided no hard data to support that conclusion.

It was Hilke Thur of the Austrian Academy of Sciences who first speculated that the skull may have belonged to Arsinoë IV, despite the lack of an inscription (or even any grave goods) on the tomb where it was found. Old notes and photographs, as well as craniometry, served as the only evidence. The skull accompanied Keil to his new position at the University of Vienna, and there was one 1953 paper reporting on craniometric measurements, but after that, the skull languished in relative obscurity. Archaeologists at the University of Graz rediscovered the skull in Vienna in 2022. The rest of the skeleton remained buried until the chamber was reopened and explored further in the 1980s and 1990s, but it was no longer in the sarcophagus.

Skull long thought to be Cleopatra’s sister’s was actually a young boy Read More »

studies-pin-down-exactly-when-humans-and-neanderthals-swapped-dna

Studies pin down exactly when humans and Neanderthals swapped DNA

ancient DNA, ancient genomics, ancient people did stuff, anthropology, Archaeology, Neanderthals, out of africa, Science / /

We may owe our tiny sliver of Neanderthal DNA to just a couple of hundred Neanderthals.

The artist’s illustration shows what the six people buried at the Ranis site, who lived between 49, 500 and 41,000 years ago, may have looked like. Two of these people are mother and daughter, and the mother is a distant cousin (or perhaps a great-great-grandparent or great-great-grandchild) to a woman whose skull was found 130 kilometers away in what’s now Czechia. Credit: Sumer et al. 2024

Two recent studies suggest that the gene flow (as the young people call it these days) between Neanderthals and our species happened during a short period sometime between 50,000 and 43,500 years ago. The studies, which share several co-authors, suggest that our torrid history with Neanderthals may have been shorter than we thought.

Pinpointing exactly when Neanderthals met H. sapiens  

Max Planck Institute of Evolutionary Anthropology scientist Leonardo Iasi and his colleagues examined the genomes of 59 people who lived in Europe between 45,000 and 2,200 years ago, plus those of 275 modern people whose ancestors hailed from all over the world. The researchers cataloged the segments of Neanderthal DNA in each person’s genome, then compared them to see where those segments appeared and how that changed over time and distance. This revealed how Neanderthal ancestry got passed around as people spread around the world and provided an estimate of when it all started.

“We tried to compare where in the genomes these [Neanderthal segments] occur and if the positions are shared among individuals or if there are many unique segments that you find [in people from different places],” said University of California Berkeley geneticist Priya Moorjani in a recent press conference. “We find the majority of the segments are shared, and that would be consistent with the fact that there was a single gene flow event.”

That event wasn’t quite a one-night stand; in this case, a “gene flow event” is a period of centuries or millennia when Neanderthals and Homo sapiens must have been in close contact (obviously very close, in some cases). Iasi and his colleagues’ results suggest that happened between 50,500 and 43,000 years ago. But it’s quite different from our history with another closely related hominin species, the now-extinct Denisovans, with whom different Homo sapiens groups met and mingled at least twice on our way to taking over the world.

In a second study, Arev Sümer (also of the Max Planck Institute) and her colleagues found something very similar in the genomes of people who lived 49,500 to 41,000 years ago in what’s now the area around Ranis, Germany. The Ranis population, based on how their genomes compare to other ancient and modern people, seem to have been part of one of the first groups to split off from the wave of humans who migrated out of Africa, through the Levant, and into Eurasia sometime around 50,000 years ago. They carried with them traces of what their ancestors had gotten up to during that journey: about 2.9 percent of their genomes were made up of segments of Neanderthal ancestry.

Based on how long the Ranis people’s segments of Neanderthal DNA were (longer chunks of Neanderthal ancestry tend to point to more recent mixing), the interspecies mingling happened about 80 generations, or about 2,300 years, before the Ranis people lived and died. That’s about 49,000 to 45,000 years ago. The dates from both studies line up well with each other and with archaeological evidence that points to when Neanderthal and Homo sapiens cultures overlapped in parts of Europe and Asia.

What’s still not clear is whether that period of contact lasted the full 5,000 to 7,000 years, or if, as Johannes Krause (also of the Max Planck Institute) suggests, it was only a few centuries—1,500 years at the most—that fell somewhere within that range of dates.

Artist’s depiction of a Neanderthal.

Natural selection worked fast on our borrowed Neanderthal DNA

Once those first Homo sapiens in Eurasia had acquired their souvenir Neanderthal genes (forget stealing a partner’s hoodie; just take some useful segments of their genome), natural selection got to work on them very quickly, discarding some and passing along others, so that by about 100 generations after the “event,” the pattern of Neanderthal DNA segments in people’s genomes looked a lot like it does today.

Iasi and his colleagues looked through their catalog of genomes for sections that contained more (or less) Neanderthal ancestry than you’d expect to find by random chance—a pattern that suggests that natural selection has been at work on those segments. Some of the segments that tended to include more Neanderthal gene variants included areas related to skin pigmentation, the immune response, and metabolism. And that makes perfect sense, according to Iasi.

“Neanderthals had lived in Europe, or outside of Africa, for thousands of years already, so they were probably adapted to their environment, climate, and pathogens,” said Iasi during the press conference. Homo sapiens were facing selective pressure to adapt to the same challenges, so genes that gave them an advantage would have been more likely to get passed along, while unhelpful ones would have been quick to get weeded out.

The most interesting questions remain unanswered

The Neanderthal DNA that many people carry today, the researchers argue, is a legacy from just 100 or 200 Neanderthals.

“The effective population size of modern humans outside Africa was about 5,000,” said Krause in the press conference. “And we have a ratio of about 50 to 1 in terms of admixture [meaning that Neanderthal segments account for about 2 percent of modern genomes in people who aren’t of African ancestry], so we have to say it was about 100 to maybe 200 Neanderthals roughly that mixed into the population.” Assuming Krause is right about that and about how long the two species stayed in contact, a Homo sapiens/Neanderthal pairing would have happened every few years.

So we know that Neanderthals and members of our species lived in close proximity and occasionally produced children for at least several centuries, but no artifacts, bones, or ancient DNA have yet revealed much of what that time, or that relationship, was actually like for either group of people.

The snippets of Neanderthal ancestry left in many modern genomes, and those of people who lived tens of thousands of years ago, don’t offer any hints about whether that handful of Neanderthal ancestors were mostly male or mostly female, which is something that could shed light on the cultural rules around such pairings. And nothing archaeologists have unearthed so far can tell us whether those pairings were consensual, whether they were long-term relationships or hasty flings, or whether they involved social relationships recognized by one (or both) groups. We may never have answers to those questions.

And where did it all happen? Archaeologists haven’t yet found a cave wall inscribed with “Og heart Grag,” but based on the timing, Neanderthals and Homo sapiens probably met and lived alongside each other for at least a few centuries, somewhere in “the Near East,” which includes parts of North Africa, the Levant, what’s now Turkey, and what was once Mesopotamia. That’s one of the key routes that people would have followed as they migrated from Africa into Europe and Asia, and the timing lines up with when we know that both Homo sapiens and Neanderthals were in the area.

“This [same] genetic admixture also appears in East Asia and Australia and the Americas and Europe,” said Krause. “If it would have happened in Europe or somewhere else, then the distribution would probably look different than what we see.”

Science, 2023 DOI: 10.1126/science.adq3010;

Nature, 2023 DOI: 10.1038/s41586-024-08420-x;

(About DOIs).

Photo of Kiona N. Smith

Kiona is a freelance science journalist and resident archaeology nerd at Ars Technica.

Studies pin down exactly when humans and Neanderthals swapped DNA Read More »

dna-shows-pompeii’s-dead-aren’t-who-we-thought-they-were

DNA shows Pompeii’s dead aren’t who we thought they were

ancient DNA, Archaeology, forensic archaeology, Pompeii, Science / /

People have long been fascinated by the haunting plaster casts of the bodies of people who died in Pompeii when Mount Vesuvius erupted in 79 CE. Archaeologists have presented certain popular narratives about who these people might have been and how they might have been related. But ancient DNA analysis has revealed that those preferred narratives were not entirely accurate and may reflect certain cultural biases, according to a new paper published in the journal Current Biology. The results also corroborate prior research suggesting that the people of ancient Pompeii were the descendants of immigrants from the Eastern Mediterranean.

As previously reported, the eruption of Mount Vesuvius released thermal energy roughly equivalent to 100,000 times the atomic bombs dropped on Hiroshima and Nagasaki at the end of World War II, spewing molten rock, pumice, and hot ash over the cities of Pompeii and Herculaneum in particular. The vast majority of people in Pompeii and Herculaneum—the cities hardest hit—perished from asphyxiation, choking on the thick clouds of noxious gas and ash. But at least some of the Vesuvian victims probably died instantaneously from the intense heat of fast-moving lava flows, with temperatures high enough to boil brains and explode skulls.

In the first phase, immediately after the eruption, a long column of ash and pumice blanketed the surrounding towns, most notably Pompeii and Herculaneum. By late night or early morning, pyroclastic flows (fast-moving hot ash, lava fragments, and gases) swept through and obliterated what remained, leaving the bodies of the victims frozen in seeming suspended action.

In the 19th century, an archaeologist named Giuseppe Fiorelli figured out how to make casts of those frozen bodies by pouring liquid plaster into the voids where the soft tissue had been. Some 1,000 bodies have been discovered in the ruins, and 104 plaster casts have been preserved. Restoration efforts of 86 of those casts began about 10 years ago, during which researchers took CT scans and X-rays to see if there were complete skeletons inside. Those images revealed that there had been a great deal of manipulation of the casts, depending on the aesthetics of the era in which they were made, including altering some features of the bodies’ shapes or adding metal rods to stabilize the cast, as well as frequently removing bones before casting.

DNA shows Pompeii’s dead aren’t who we thought they were Read More »

study:-dna-corroborates-“well-man”-tale-from-norse-saga

Study: DNA corroborates “Well-man” tale from Norse saga

ancient DNA, Archaeology, forensic archaeology, Norse history, Norse mythology, Norse sagas, paleogenomics, Science / /

The results: The Well-man was indeed male, between 30 and 40, with blue eyes and blond or light-brown hair, and his ancestry was traced to southern Norway, most likely present-day Vest-Agder. This is interesting because King Sverre’s men were from central Norway, and it had long been assumed that the dead body thrown into the well was part of that army. It was the invading Baglers who hailed from southern Norway. The authors are careful to note that one cannot definitively conclude that therefore the Well-man was a Bagler, but it’s certainly possible that the Baglers tossed one of their own dead into the well.

As for whether the action was a form of 12th-century biological warfare intended to poison the well, the authors weren’t able to identify any pathogens in their analysis. But that might be because of the strict decontamination procedures that were used to prepare the tooth samples, which may have also removed traces of any pathogen DNA. So they could not conclude one way or another whether the Well-man had been infected with a deadly pathogen at the time of his death.

Seven well-man teeth recovered from excavation

Seven Well-man teeth recovered from the excavation.

Credit: Norwegian Institute for Cultural Heritage Research

Seven Well-man teeth recovered from the excavation. Credit: Norwegian Institute for Cultural Heritage Research

“It was a compromise between removing surface contamination of the people who have touched the tooth and then removing some of the possible pathogens. There are lots of ethical considerations,” said co-author Martin Ellegaard, also of the Norwegian University of Science and Technology. “We need to consider what kind of tests we’re doing now because it will limit what we can do in the future.”

The fact that the Well-man hailed from southern Norway indicates that the distinctive genetic drift observed in southern Norway populations already existed during King Sverre’s reign. “This has implications for our understanding of Norwegian populations, insofar as it implies that this region must have been relatively isolated not only since that time, but also at least for a few hundred years beforehand and perhaps longer,” the authors concluded. Future research sequencing more ancient Norwegian DNA would shed further light on this finding—perhaps even the remains of the Norwegian Saint Olaf, believed to be buried near Trondheim Cathedral.

iScience, 2024. DOI: 10.1016/j.isci.2024.111076  (About DOIs).

Study: DNA corroborates “Well-man” tale from Norse saga Read More »

frozen-mammoth-skin-retained-its-chromosome-structure

Frozen mammoth skin retained its chromosome structure

ancient DNA, Biology, evolution, Genetics, Genomics, mammoths, Science / /
Artist's depiction of a large mammoth with brown fur and huge, curving tusks in an icy, tundra environment.

One of the challenges of working with ancient DNA samples is that damage accumulates over time, breaking up the structure of the double helix into ever smaller fragments. In the samples we’ve worked with, these fragments scatter and mix with contaminants, making reconstructing a genome a large technical challenge.

But a dramatic paper released on Thursday shows that this isn’t always true. Damage does create progressively smaller fragments of DNA over time. But, if they’re trapped in the right sort of material, they’ll stay right where they are, essentially preserving some key features of ancient chromosomes even as the underlying DNA decays. Researchers have now used that to detail the chromosome structure of mammoths, with some implications for how these mammals regulated some key genes.

DNA meets Hi-C

The backbone of DNA’s double helix consists of alternating sugars and phosphates, chemically linked together (the bases of DNA are chemically linked to these sugars). Damage from things like radiation can break these chemical linkages, with fragmentation increasing over time. When samples reach the age of something like a Neanderthal, very few fragments are longer than 100 base pairs. Since chromosomes are millions of base pairs long, it was thought that this would inevitably destroy their structure, as many of the fragments would simply diffuse away.

But that will only be true if the medium they’re in allows diffusion. And some scientists suspected that permafrost, which preserves the tissue of some now-extinct Arctic animals, might block that diffusion. So, they set out to test this using mammoth tissues, obtained from a sample termed YakInf that’s roughly 50,000 years old.

The challenge is that the molecular techniques we use to probe chromosomes take place in liquid solutions, where fragments would just drift away from each other in any case. So, the team focused on an approach termed Hi-C, which specifically preserves information about which bits of DNA were close to each other. It does this by exposing chromosomes to a chemical that will link any pieces of DNA that are close physical proximity. So, even if those pieces are fragments, they’ll be stuck to each other by the time they end up in a liquid solution.

A few enzymes are then used to convert these linked molecules to a single piece of DNA, which is then sequenced. This data, which will contain sequence information from two different parts of the genome, then tells us that those parts were once close to each other inside a cell.

Interpreting Hi-C

On its own, a single bit of data like this isn’t especially interesting; two bits of genome might end up next to each other at random. But when you have millions of bits of data like this, you can start to construct a map of how the genome is structured.

There are two basic rules governing the pattern of interactions we’d expect to see. The first is that interactions within a chromosome are going to be more common than interactions between two chromosomes. And, within a chromosome, parts that are physically closer to each other on the molecule are more likely to interact than those that are farther apart.

So, if you are looking at a specific segment of, say, chromosome 12, most of the locations Hi-C will find it interacting with will also be on chromosome 12. And the frequency of interactions will go up as you move to sequences that are ever closer to the one you’re interested in.

On its own, you can use Hi-C to help reconstruct a chromosome even if you start with nothing but fragments. But the exceptions to the expected pattern also tell us things about biology. For example, genes that are active tend to be on loops of DNA, with the two ends of the loop held together by proteins; the same is true for inactive genes. Interactions within these loops tend to be more frequent than interactions between them, subtly altering the frequency with which two fragments end up linked together during Hi-C.

Frozen mammoth skin retained its chromosome structure Read More »

dna-from-mammoth-remains-reveals-the-history-of-the-last-surviving-population

DNA from mammoth remains reveals the history of the last surviving population

ancient DNA, Biology, evolution, Genetics, Genomics, mammoths, Science, Wrangel Island / /

Sole survivors —

The mammoths of Wrangel Island purged a lot of harmful mutations before dying off.

–

A dark, snowy vista with a single mammoth walking past the rib cage of another of its kind.

Enlarge / An artist’s conception of one of the last mammoths of Wrangel Island.

Beth Zaiken

A small group of woolly mammoths became trapped on Wrangel Island around 10,000 years ago when rising sea levels separated the island from mainland Siberia. Small, isolated populations of animals lead to inbreeding and genetic defects, and it has long been thought that the Wrangel Island mammoths ultimately succumbed to this problem about 4,000 years ago.

A paper in Cell on Thursday, however, compared 50,000 years of genomes from mainland and isolated Wrangel Island mammoths and found that this was not the case. What the authors of the paper discovered not only challenges our understanding of this isolated group of mammoths and the evolution of small populations, it also has important implications for conservation efforts today.

A severe bottleneck

It’s the culmination of years of genetic sequencing by members of the international team behind this new paper. They studied 21 mammoth genomes—13 of which were newly sequenced by lead author Marianne Dehasque; others had been sequenced years prior by co-authors Patrícia Pečnerová, Foteini Kanellidou, and Héloïse Muller. The genomes were obtained from Siberian woolly mammoths (Mammuthus primigenius), both from the mainland and the island before and after it became isolated. The oldest genome was from a female Siberian mammoth who died about 52,300 years ago. The youngest were from Wrangel Island male mammoths who perished right around the time the last of these mammoths died out (one of them died just 4,333 years ago).

Wrangel Island, north of Siberia has an extensive tundra.

Enlarge / Wrangel Island, north of Siberia has an extensive tundra.

Love Dalén

It’s a remarkable and revealing time span: The sample included mammoths from a population that started out large and genetically healthy, went through isolation, and eventually went extinct.

Mammoths, the team noted in their paper, experienced a “climatically turbulent period,” particularly during an episode of rapid warming called the Bølling-Allerød interstadial (approximately 14,700 to 12,900 years ago)—a time that others have suggested might have led to local woolly mammoth extinctions. However, the genomes of mammoths studied through this time period don’t indicate that the warming had any adverse effects.

Adverse effects only appeared—and drastically so—once the population was isolated on that island.

The team’s simulations indicate that, at its smallest, the total population of Wrangel Island mammoths was fewer than 10 individuals. This represents a severe population bottleneck. This was seen genetically through increased runs of homozygosity within the genome, caused when both parents contribute nearly identical chromosomes, both derived from a recent ancestor. The runs of homozygosity within isolated Wrangel Island mammoths were four times as great as those before sea levels rose.

Despite that dangerously tiny number of mammoths, they recovered. The population size, as well as inbreeding level and genetic diversity, remained stable for the next 6,000 years until their extinction. Unlike the initial population bottleneck, genomic signatures over time seem to indicate inbreeding eventually shifted to pairings of more distant relatives, suggesting either a larger mammoth population or a change in behavior.

Within 20 generations, their simulations indicate, the population size would have increased to about 200–300 mammoths. This is consistent with the slower decrease in heterozygosity that they found in the genome.

Long-lasting negative effects

The Wrangel Island mammoths may have survived despite the odds, and harmful genetic defects may not have been the reason for their extinction, but the research suggests their story is complicated.

At about 7,608 square kilometers today, a bit larger than the island of Crete, Wrangel Island would have offered a fair amount of space and resources, although these were large animals. For 6,000 years following their isolation, for example, they suffered from inbreeding depression, which refers to increased mortality as a result of inbreeding and its resulting defects.

That inbreeding also boosted the purging of harmful mutations. That may sound like a good thing—and it can be—but it typically occurs because individuals carrying two copies of harmful mutations die or fail to reproduce. So it’s good only if the population survives it.

The team’s results show that purging genetic mutations can be a lengthy evolutionary process. Lead author Marianne Dehasque is a paleogeneticist who completed her PhD at the Centre for Palaeogenetics. She explained to Ars that, “Purging harmful mutations for over 6,000 years basically indicates long-lasting negative effects caused by these extremely harmful mutations. Since purging in the Wrangel Island population went on for such a long time, it indicates that the population was experiencing negative effects from these mutations up until its extinction.”

DNA from mammoth remains reveals the history of the last surviving population Read More »