Category: Ancient DNA

Early hunters killed mastodons with mastodons (Also, you can chuck a bone spear through a car. Who knew?)

By Ed Yong | October 20, 2011 2:12 pm

To round off my brief stint at the Guardian, here’s a piece about a mastodon specimen with what looks like a spear-tip stuck in its rib. This specimen, the so-called “Manis mastodon” has been a source of controversy for several decades. Is that fragment man-made or simply one of the animal’s own bone splinters? Does it imply that humans hunted large mammals hundreds of years earlier than expected, or not?

Having re-analysed the rib in an “industrial-grade” CT scanner, Michael Waters thinks it’s definitely a man-made projectile. He even extracted DNA from the rib and the fragment and found that both belonged to mastodons. So these early hunters were killing mastodons and turning them into weapons for killing more mastodons. How poetically gittish.

Anyway, read the piece for more about why this matters. In the meantime, I want to draw your attention to this delicious tete-a-tete at the end between Waters and Gary Haynes, who doesn’t buy the interpretation. Note, in particular, the very last bit from Waters, which made my jaw drop.

But despite Waters’ efforts, the fragment in the Manis mastodon’s rib is still stoking debate. “It’s not definitely proven that it is a projectile point,” says Prof Gary Haynes from the University of Nevada, Reno. “Elephants today push each other all the time and break each other’s rib so it could be a bone splinter that the animal just rolled on.”

Waters does not credit this alternative hypothesis. “Ludicrous what-if stories are being made up to explain something people don’t want to believe,” he says. “We took the specimen to a bone pathologist, showed him the CT scans, and asked if there was any way it could be an internal injury. He said absolutely not.”

Waters adds, “If you break a bone, a splinter isn’t going to magically rotate its way through a muscle and inject itself into your rib bone. Something needed to come at this thing with a lot of force to get it into the rib.”

The spear-thrower must have had a powerful arm, for tThe fragment would have punctured through hair, skin and up to 30 centimetres of mastodon muscle. “A bone projectile point is a really lethal weapon,” says Waters. “It’s sharpened to a needle point and little greater than the diameter of a pencil. It’s like a bullet. It’s designed to get deep into the elephant and hit a vital organ.” He adds, “I’ve seen these thrown through old cars.”

Scientists sequence the full Black Death genome and find the mother of all plagues

By Ed Yong | October 12, 2011 1:00 pm

This is an updated version of an old piece, edited to include new information. Science progresses by adding new data to an ever-growing picture. Why should science writing be different?

The road of East Smithfield runs through east London and carries a deep legacy of death. Two cemeteries, established in the area in the 14th century, contain round 2,500 of bodies, piled five deep. These remains belong to people killed by the Black Death, an epidemic that killed between 30 and 50 percent of Europe in just five years. It was one of the biggest disasters in human history and seven centuries on, its victims are still telling its story.

In the latest chapters, Verena Schuenemann from the University of Tubingen and Kirsten Bos from McMaster University have used samples from East Smithfield to reconstruct the full genome of the bacterium behind the Black Death. This species – Yersinia pestisstill causes plague today, and the modern strains are surprisingly similar to the ancient one.

Compared to the strain that acts as a reference for modern plague, the ancient genome differs by only 97 DNA ‘letters’ out of around 4.6 million. Y.pestis may not be the same bacterium that butchered medieval Europe 660 years ago, but it’s not far off. Indeed, Schuenemann and Bos found that all of the strains that infect humans today descended from one that circulated during the Black Death. Even now, people are still succumbing to a dynasty of disease that began in the Dark Ages.

The Black Death is supposedly the second of a trilogy of plague pandemics. It came after the Plague of Justinian in the sixth to eighth centuries, and preceded modern plague, which infects some 2,000 people a year. But some scientists and historians saw features in the Black Death that separates it from other plague pandemics – it spread too quickly, killed too often, recurred too slowly, appeared in different seasons, caused symptoms in different parts of the body, and so on.

These differences have fuelled  many alternative theories for the Black Death, which push Y.pestis out of the picture. Was it caused by an Ebola-like virus? An outbreak of anthrax? Some as-yet-unidentified infection that has since gone extinct? In 2000, Didier Raoult tried to solve the debate by sequencing DNA from the teeth of three Black Death victims, exhumed from a French grave. He found Y.pestis DNA. “We believe that we can end the controversy,” he wrote. “Medieval Black Death was plague.”

Raoult was half-wrong. The controversy did not end. Some people argued that it’s not clear if the remains came from Black Death victims at all. Meanwhile, Alan Cooper analysed teeth from 66 skeletons taken from so-called “plague pits”, including the one in East Smithfield. He found no trace of Y.pestis. Other teams did their own analyses, and things went back and forth with a panto-like tempo. Oh yes, Y.pestis was there. Oh no it wasn’t. Oh yes it was.

In 2010, Stephanie Haensch served up some of the strongest evidence that Y.pestis caused the Black Death, using DNA extracted from a variety of European burial sites. Schuenemann and Bos bolstered her conclusion by taking DNA from bodies that had been previously exhumed from East Smithfield, and stored in the Museum of London. “We sifted through every single intact skeleton and every intact tooth in the collection,” says Bos. They extracted DNA from 99 bones and teeth and found Y.pestis in 20 of them.

Schuenemann and Bos took great care to ensure that their sequences hadn’t been contaminated by modern bacteria. Aside from the usual precautions, they did all of her work at a facility that had never touched a Y.pestis sample, they had the results independently confirmed in a different lab, and they found traces of DNA damage that are characteristic of ancient sequences. They also failed to find any Y.pestis DNA in samples treated in exactly the same way, taken from a medieval cemetery that preceded the Black Death. Finally, it’s clear that the people exhumed from East Smithfield did indeed die from the Black Death – it’s one of the few places around the world that has been “definitively and uniquely” linked to that pandemic.

Even though they had its DNA, deciphering the ancient bacterium’s genome was difficult. The DNA was so heavily fractured that Schuenemann and Bos only managed to extract enough from four of their teeth. They lined up the fragments against a modern plague genome, and looked for overlaps between the remaining stragglers. In the draft that they’ve published, every stretch of DNA has been checked an average of 28 times.

By comparing this ancient genome with 17 modern ones, and those of other related bacteria, Scheuenemann and Bos created a family tree of plague that reveals the history of the disease. They showed that the last common ancestor of all modern plagues, lived between 1282 and 1343 before it swept through Europe, diversifying as it went. The East Smithfield strain was very close to that ancestral strain, differing by only two DNA letters.

This raises some questions about the plague of Justinian. The team think that it was either the work of an entirely different microbe, or it was caused by a strain of Y.pestis that is no longer around and likely left no descendants behind. It was the supposed second pandemic – the Black Death – that truly introduced Y.pestis to the world. This global tour seeded the strains that exist today.

By the time it hit East Smithfield, the plague was already changing. Schuenemann and Bos found that one of their four teeth harboured a slightly different version of Y.pestis, which was three DNA letters closer to modern strains than the other ancient ones. Even in the middle of the pandemic, the bacterium was mutating.

In the intervening centuries, Y.pestis has changed but not by much. None of the few differences between the ancient and modern genomes appear in genes that affect how good the bacterium is at causing diseases. None of them can obviously explain why the Black Death was so much more virulent than modern plague. “There’s no particular smoking gun,” says Hendrik Poinar, who was one of the study’s leaders.

That’s somewhat anticlimactic. In August, Poinar told me: “We need to know what changes in the ancient [bacterium] might have accounted for its tremendous virulence… There is really no way to know anything about the biology of the pathogen, until the entire genome is sequenced.” Now that the full genome is out, it seems to offer precious few clues.

Instead, the team thinks that a constellation of other factors might have made the Black Death such a potent pandemic. At the time, medieval Europe went through a drastic change in climate, becoming colder and wetter. Black rat numbers shot up, crops suffered and people went hungry. “It’s hard to believe that these people living in 1348 London weren’t being infected by various viruses,” says Poinar. “So you probably had an immune compromised population living in very stressful conditions, and they were hit by Y.pestis, maybe for the first time.” They were both physically and culturally unprepared. Their immune systems were naive, they didn’t know what the disease was, and they didn’t know how to treat or prevent it.

In later centuries, it was a different story. Medical treatments helped to cope with the symptoms and affected people were quickly quarantined. Today, we have antibiotics that help to treat plague, and these would be effective against the Black Death strain. We have evolved too. People who were most susceptible to plague were killed, which probably left the most resistant survivors behind. Next, Poinar wants to look at the DNA of people buried in pre-plague and post-plague cemeteries to see if the Black Death had altered our own genome.

Sequencing the Black Death genome may not tell us about why it was so deadly, but it still reveals how the bacterium evolved. Now, Schuenemann and Bos can look at how Y.pestis transformed from a bacterium that infects rodents to one that kills humans and how it evolved over time. That knowledge could be very important, especially since plague is rebounding as a “re-emerging” disease.

The Black Death strain is the second historical pathogen whose genome has been sequenced and certainly the oldest (the first was the 1918 pandemic flu). There are many others to look at, including the Justinian plague strain, and historical versions of tuberculosis, syphilis and cholera.

In the meantime, the East Smithfield bodies have told their story and Bos and Schuenemann are letting them rest. They were very careful with the teeth that they yanked DNA from, and they are now returning these samples to the Museum of London. Having yielded their secrets, they’ll be stuck back into their old skeletons.

Reference: Bos, Schuenemann, Golding, Burbano, Waglechner, Coombes, McPhee, DeWitte, Meyer, Schmedes, Wood, Earn, Herring, Bauer, Poinar & Kruase. 2011. A draft genome of Yersinia pestis from victims of the Black Death. Nature http://dx.doi.org/10.1038/nature10549

Schuenemann, Bos, deWitte, Schmedes, Jamieson, Mittnik, Forrest, Coombes, Wood, Earn, White, Krause & Poinar. 2011. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. PNAS http://dx.doi.org/10.1073/pnas.1105107108

PS Oddly, the team’s new paper, where they publish the full Black Death genome, somewhat refutes their first one, where they had only sequenced fragments. Previously, they identified two mutations in the ancient DNA that weren’t seen in any other strain. But those two mutations aren’t there in the full genome, and it now seems that they were a mistake. Ancient DNA can be chemically damaged so that Cs change into Ts. That’s probably what happened in the previous study. Schuenemann and Bos are more confident that their new sequences are correct. They treated their samples with a method that repairs the C-to-T changes, and they went over every bit of DNA 30 times.

Image: Skeletons from the Museum of London;

Nile crocodile is actually two species (and the Egyptians knew it)

By Ed Yong | September 14, 2011 8:48 am

The Nile crocodile is a truly iconic animal. Or, more accurately, two iconic animals. As I’ve just written over at Nature News:

The iconic Nile crocodile actually comprises two different species — and they are only distantly related. The large east African Nile crocodile (Crocodylus niloticus) is in fact more closely related to four species of Caribbean crocodile than to its small west African neighbour, which has been named (Crocodylus suchus).

Evon Hekkala of Fordham University in New York and her colleagues revealed evidence for the existence of the second species by sequencing the genes of 123 living Nile crocodiles and 57 museum specimens, including several 2,000-year-old crocodile mummies.

The results resolve a centuries-old debate about the classification of the Nile crocodile, and have important implications for the conservation of both species.

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The lost plague – London graveyards suggest that Black Death strain may be extinct

By Ed Yong | August 30, 2011 9:00 am

The road of East Smithfield runs through east London and carries a deep legacy of death. Two cemeteries, established in the area in the 14th century, contain hundreds of bodies, piled five deep. These remains belong to people killed by the Black Death, an epidemic that claimed up to 100 million lives. It was one of the biggest disasters in human history and seven centuries on, its victims are still telling its story.

In the latest chapter, Verena Schuenemann from the University of Tubingen and Kirsten Bos from McMaster University have reconstructed parts of the genome of the Black Death plague bacterium, and found features that are unlike any seen today. In line with another study from last year, Schuenemann and Bos’s work suggests that the great butcher of medieval Europe may no longer exist.

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Did sex with Neanderthals and Denisovans shape our immune systems? The jury’s still out

By Ed Yong | August 25, 2011 2:00 pm

The Neanderthals may be extinct, but they live on inside us. Last year, two landmark studies from Svante Paabo and David Reich showed that everyone outside of Africa can trace 1-4 percent of their genomes to Neanderthal ancestors. On top of that, people from the Pacific Islands of Melanesia owe 5-7 percent of their genomes to another group of extinct humans – the Denisovans, known only from a finger bone and a tooth. These ancient groups stand among our ancestors, their legacy embedded in our DNA.

Paabo and Reich’s studies clearly showed that early modern humans must have bred with other ancient groups as they left Africa and swept around the world. But while they proved that Neanderthal and Denisovan genes are still around, they said little about what these genes are doing. Are they random stowaways or did they bestow important adaptations?

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Massive eggs were the most fragile of any bird (Pocket Science)

By Ed Yong | August 31, 2010 2:00 pm

Moa_egg

Some of the largest bird eggs in history were surprisingly also some of the most fragile. That’s the conclusion from Leon Huynen from Brisbane University, who has been studying the eggs of an extinct group of flightless birds called moas. These giants roamed New Zealand until the 14th century when they were wiped out by humans. Today, all that remains are bones and eggs but some of the broken shells have preserved traces of the moas’ DNA. Earlier this year, Australian scientists sequenced the genes of moas for the first time. Now, Huynen has used the same techniques to work out how these birds cared for their young.

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DNA from the largest bird ever sequenced from fossil eggshells

By Ed Yong | March 9, 2010 7:00 pm

Even extinction and the passing of millennia are no barriers to clever geneticists. In the past few years, scientists have managed to sequence the complete genome of a prehistoric human and produced “first drafts” of the mammoth and Neanderthal genomes. More controversially, some groups have even recovered DNA from dinosaurs. Now, a variety of extinct birds join the ancient DNA club including the largest that ever lived – Aepyornis, the elephant bird. 

In a first for palaeontology, Charlotte Oskam from Murdoch University, Perth, extracted DNA from 18 fossil eggshells, either directly excavated or taken from museum collections. Some came from long-deceased members of living species including the emu, an owl and a duck. Others belonged to extinct species including Madagascar’s 3-metre tall elephant bird and the giants moas of New Zealand. A few of these specimens are just a few centuries old, but the oldest came from an emu that lived 19,000 years ago.

It turns out that bird eggshells are an excellent source of ancient DNA. They’re made of a protein matrix that is loaded with DNA and surrounded by crystals of calcium carbonate. The structure shelters the DNA and acts as a barrier to oxygen and water, two of the major contributors to DNA damage. Eggshells also stop microbes from growing and it seems that ancient ones still do the same. Oskam found that the fossil shells had around 125 times less bacterial DNA than bones of the same species did.

This is important – bacteria are a major problem for attempts to extract ancient DNA and they force scientists to search for uncontaminated sources, like frozen hair. Eggshells, it seems, provide similarly bacteria-free samples. Still, Oskam’s team took every precaution to prevent contamination. They used clean rooms and many control samples. Many of their sequences, like those of Aepyornis, were checked by two independent laboratories.

The Aepyornis sequences are particularly encouraging because many scientists have previously tried to extract DNA from the bones of this giant and failed. Eggshells seem like a more promising source and it certainly helps that the eggs of many of these giant species were massive and thick. But Oskam did also recover DNA from a fossil duck egg, which suggests that it should be possible to sequence the genes of even small extinct birds, like the dodo.

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