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Ever Wonder What a Neanderthal Considered a Delicacy?

I suppose “Neanderthal delicacy” may sound like an oxymoron. Most people think of Neanderthals and other ancient people as cave men, brutes capable of little more than smashing and grunting. To the extent you’ve ever thought about what they ate, you probably assumed it was, well, whatever they could get their dirty hands on.

Or maybe you remember The Clan of the Cave Bear, the 1980 bestseller that helped shape Neanderthals in the popular imagination. In the book, a Homo sapiens girl named Ayla is adopted by Neanderthals who communicate mainly through hand signals and seem incapable of learning.

Yet the more we learn about our ancient cousins, the more sophisticated we find them to be. Amazing work on Neanderthal genetics by Svante Pääbo has found that they possessed a gene called FOXP2 that is key to speech in modern humans, raising the question of whether Neanderthals had language. They may even have been capable of abstract thinking and art.

Now, a new study suggests that the Paleolithic crowd had its own version of fine dining, unsettling as the choice of fare may be. It appears that baby elephants may have been a particular delicacy—basically, pachyderm veal.

Most studies of ancient diets have focused on simply figuring out what people ate, not what they liked. But Ran Barkai of Tel Aviv University and his graduate student Hagar Reshef wondered if there was any way to make a reasonable guess about the tastes of early hominins. They report their findings in an upcoming issue of Quaternary International.

“The direct investigation of taste preference in Paleolithic times is impossible,” says Reshef, but there’s “plenty of circumstantial evidence.”

First, the scientists point to recent evidence that Neanderthals did have a sense of taste. Work by Carles Lalueza-Fox found taste-related genes in Neanderthals, specifically for bitter tastes, that could have shaped their food preferences. The gene varied, as it does in modern humans. “What seems clear is that keeping a wide range of taste perception was key in hominin groups,” Lalueaza-Fox says.

As for what they ate, the butchered bones of mammoths and ancient elephant species, and particularly young elephants, are fairly common in Paleolithic archaeological sites around the world. In some cases, such as the Middle Pleistocene sites Gesher Benot Ya’akov in Israel and Notarchirico in Italy, the skulls of young elephants appear to have been dismantled, perhaps to eat the brain.

Young elephants would presumably be easier to kill than large ones, which could explain why more young ones were eaten. But even young elephants aren’t exactly easy to capture and kill, leaving Reshef wondering whether they were also hunted as a preferred food—because they’re tasty.

That raises one obvious question: Are baby elephants tasty? Here, Reshef and Barkai looked at the historical record and modern-day hunter-gatherers. A 1967 study of the Liangula hunters in East Kenya reported that they preferred young elephants because they tasted better, and reports from other groups followed suit, with the general consensus being that elephants, and especially the young, taste sweet and fatty.

The team also checked out the nutritional value and quality of elephant meat. Studies of the biochemical composition of fat tissue reveals a high nutritional value for young elephants compared with adults.

We can’t wind back time to ask a Neanderthal what he liked, but it seems plausible that they put some effort into finding food they liked, and that baby elephant was on the list. “I would say that both the vulnerability and taste are relevant,” Reshef says.

Why would we care what Neanderthals or other hominins liked to nosh on? They sharpened their flints while dreaming of slicing into baby elephant; I wait in line for two hours to eat fancy ramen noodle soup. To each his own, right?

Perhaps. But it’s also part of understanding what makes us human.

“I believe that taste preference in ancient times was a motivating power in human evolution by pushing creative and technological abilities,” says Reshef.

Just think about that for a second. The quest for deliciousness: a motivating power in human evolution.

I could buy it. Given how much human time, creativity, and effort go into food today (Exhibit A: any Whole Foods store), it’s easy to believe that we are who we are, at least just a little bit, because we have been working for so long on new ways to perfect the snack. Thank you, sense of taste.

(A special thank you to my keen-eyed colleague Mark Strauss for pointing out the elephant study.)

Scrappy Fossils Yield Possible Dinosaur Blood Cells

Last week, a little movie called Jurassic World debuted. You might have heard something about it. Paleontologists certainly have been jawing about it for a while, particularly how the movie’s dinosaurs stack up against the actual animals emerging from the rock.* But all the arguments about enfluffled dinosaurs and bunny hands have missed a more fundamental issue – could scientists ever recover enough intact dinosaur goo to populate a real Jurassic World?

When the first Jurassic Park premiered in 1993, finding non-avian dinosaur DNA seemed a certainty. Two days before the official release of the movie Raúl Cano and colleagues announced that they had sequenced the DNA of a 135-120 million year old, amber-encased weevil. That was old enough to suggest that tatters of DNA from Cretaceous dinosaurs might be found, and, a little more than a year later, S.R. Woodward and colleagues announced that they had sequenced DNA from an 80 million year old dinosaur bone fragment. It seemed that life had found a way.

But as researchers refined the techniques required for ancient DNA analysis, they began to realize that many of these earlier announcements were too good to be true. Geneticists could carefully retrieve and study the DNA of relatively recent organisms – moas, cave bears, Neanderthals, and more – but genetic material is too fragile to last for tens of millions of years. The truly ancient sequences often turned out to be contamination from modern sources – part of the growing pains of developing this new branch of science.

The sad truth is that we’re not likely to ever recover Mesozoic DNA. Not unless there’s some undiscovered mode of preservation that can keep a creature’s genome from going to pieces. But dinosaur blood is another matter. In 2005 Mary Schweitzer and colleagues announced that they had found remnants of blood vessels in a thigh bone from Tyrannosaurus. Four years later, Schweitzer and coauthors described other soft tissue tidbits from the hadrosaur Brachylophosaurus. These weren’t fresh flesh. They had been altered over the course of time. Nevertheless, they seemed to retain some original soft tissue and revealed some details of the small and the squishy within saurians.

A 75 million year old dinosaur claw that possibly preserved blood cells. Image by Sergio Bertazzo.
A 75 million year old dinosaur claw that possibly preserved blood cells. Image by Sergio Bertazzo.

And now, just in time for the release of Jurassic World, Sergio Bertazzo, Susannah Maidment, and colleagues have offered a look at possible 75 million year old dinosaur blood cells. The researchers didn’t pop the champagne on first sight of the microscopic structures. There were other possible explanations. Perhaps someone had accidentally bled on the fossil while it was in storage, for example. (Stranger things have happened in museum collections.) But through visual and biochemical investigations, the researchers were able to rule out human contamination. Additional studies will hopefully test the idea, but, for now, there’s a good chance that the scrappy bones at the center of the study really do preserve some degraded dino blood.

This wasn’t an isolated find. Out of eight dinosaur bones the researchers examined, they found some kind of soft tissue structure – be it blood cells, collagen fibers, or unknown carbon-rich structures – in six of them. This came as a shock. The bones were fragments. The sort of scrap curators are ok with paleontologists using for “consumptive analysis” because they’re unremarkable and often unidentifiable beyond the skeletal element. If these humble fossils could preserve the remains of soft tissues, Bertazzo and coauthors wonder, what about fossils that are heralded as exceptionally-preserved? Paleontologists should have a much closer look at their most prized fossils.

[Scanning electron micrographs and 3D reconstructions from serial sections of blood cell-like structures. Credit: Bertazzo et al., Nature Communications.]

This area of research is still new, but, with more samples, paleontologists may have a new way to investigate the biology and physiology of extinct creatures. Soft tissue preservation may be more widespread than anyone expected, and controversies such as “Were dinosaurs endotherms?” might start to creep closer to resolution. Along with related subfields like histology – the study of bone microstructure – investigations of dinosaur soft tissues hold the most potential to refine our understanding of how these animals really lived.

In order to get more samples paleontologists need to think carefully about how they excavate and preserve fossils. Dinosaur bones are incredibly fragile fossils. In the field, volunteers and scientists douse them with consolidants and sometimes glue broken pieces back together to make sure the bones make the journey back to the prep lab. How these chemical changes might alter, or even destroy, soft tissue clues isn’t yet known, and the realization that soft tissue preservation might be a common phenomenon means that field workers, lab techs, and curators will have to figure out new ways to preserve not only the external anatomy of a bone, but also the secrets held within.

Even as specialists wrestle with these questions, though, the new research from Bertazzo and Maidment underscores how even a sliver of fossil bone can be incredibly informative. An unidentified shard of dinosaur bone isn’t just a throwaway fossil. It’s part of a real animal that was born, grew, was shaped by natural history, perished, and was locked in stone. Knowing the right questions to ask, and the proper tools to use, can unleash unexpected conclusions from even the scrappiest fossil. And even if we’re never going to see a real Jurassic World, such finds may help paleontologists better understand and more accurately reconstruct the creatures that we love to see tear across the silver screen.

*Full disclosure: I was the science adviser for the film’s official website.


Bertazzo, S., Maidment, S., Kallepitis, C., Fearn, S., Stevens, M., Xie, H. 2015. Fibres and cellular structures preserved in 75-million-year-old dinosaur specimens. Nature Communications. doi: 10.1038/ncomms8352

Cano, R., Poinar, H., Pieniazek, N., Acra, A., Poinar, G. 1993. Amplification and sequencing of DNA from a 120-135-million-year-old weevil. Nature. 363: 536-538. doi: 10.1038/363536a0

, S. Poinar, H., Serre, D., Jaenicke-Despres, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L., Hofreiter, M. 2004. Genetic analyses from ancient DNA. Annual Review of Genetics. 38: 645-679. doi: 10.1146/aanurev.genet.37.110801.143214

Schweitzer, M., Wittmeyer, J., Horner, J., Toporski, J. 2005. Soft-tissue vessels and cellular preservation in Tyrannosaurus rex. Science. 307, 5717: 1952-1955. doi: 10.1126/science.1108397

Woodward, S., Weyand, N., Bunnell, M. 1994. DNA sequence from Cretaceous period bone fragments. Science. 266, 5188: 1229-1232. doi: 10.1126/science.7973705


You Just Missed the Last Ground Sloths

When did the last of the ground sloths disappear? The standard answer is “about 10,000 years ago”. That’s the oft-repeated cutoff date for when much of the world’s Ice Age megafauna – from mastodons to Megatherium – faded away. It’s nice and neat, falling just after the close of the last Ice Age and during a time when humans were spreading to new continents. In fact, it’s too clean a cutoff. The shaggy, ground-dwelling sloths that inhabited almost the entire span of the New World didn’t all topple over at once. They very last of their kind, both protected and made vulnerable by life on islands, were still shuffling 4,200 years ago.

Calling the time of death for any species or lineage is always complicated by definitions and details. Should a species be considered extinct when its very last member perishes, or when the population sinks below a level from which they can recover? And in these fading families, should the explanation for extinction be the cause of death of the last individual, or do we assemble a more complex picture that considers factors that made the population vulnerable in the first place? Both science and storytelling influence our answers to these questions, but one thing is abundantly clear. Extinction is a process, not a single fell swoop.

Consider the times when the giant ground sloths disappeared. They were one of the great success stories of the Ice Age – with 19 genera ranging through South, Central, and North America, as well as Caribbean islands at the end of the Pleistocene – but, as reported by paleontologist David Steadman and colleagues in a 2005 study, 90% of the existing Ice Age sloths disappeared within the last 11,000 years.

Megalonyx and other giants from North America were some of the first to go. While Steadman and colleagues stressed that the dates represent “last appearance dates” rather than actual time of species death, the youngest known sloth remains from North America date to about 11,000 years ago. South America’s ground sloths, such the enormous Eremotherium, soon followed – the youngest dung and tissue samples found on the continent date between 10,600 and 10,200 years ago.

But for another 5,000 years, ground sloths survived. They weren’t on the continents, but scattered through the islands of the Caribbean. I had not even heard about these sloths until paleo geneticist Ross Barnett told me about them in a Twitter exchange long ago, and, as reviewed in the paper by Steadman and colleagues, there were at least five genera and thirteen species of large ground sloths that were unique to these islands.

Cuba's extinct ground sloth Megalocnus rodens. Photo by Ghedoghedo.
Cuba’s extinct ground sloth Megalocnus rodens. Photo by Ghedoghedo.

The largest of all was Megalocnus. This sloth hasn’t received nearly as much attention as the other “mega”-prefixed sloths, but, as you can see from the bones on display at the American Museum of Natural History’s fossil mammal hall, this 200-pound sloth was still an impressive beast. Based on remains found in a limestone cave on Cuba, Steadman and colleagues determined that Megalocnus lived until at least 6,250 years ago.

Other smaller sloths persisted even longer. Parocnus, also found on Cuba, lived until about 4,960 years ago, and the small ground sloth Neocnus trundled over Hispaniola until about 4,500 years ago. There’s no direct evidence that people were hunting or eating the sloths, but, based on tentative evidence for human occupation of Caribbean islands around 5,000 years ago, Steadman suggest that the arrival of Homo sapiens tipped the sloth into extinction.

Of course, last appearance dates are often revised with new finds and updated techniques. Two years after the Steadman study, Ross MacPhee and coauthors published a new, youngest date for Cuba’s Megalocnus. From a tooth found on the island, the researchers estimated that the ground sloth survived to at least 4,200 years ago.

Through the lens of geologic time – wherein millions of years are thrown around because the numbers are too big to truly comprehend – extending the lifetime of a ground sloth another 2,000 years might not sound like much. But MacPhee and colleagues underscore the importance of getting good dates for when Ice Age creatures vanished. If people really showed up on Cuba and other sloth-bearing islands around 5,500 years ago, then humans and ground sloths coexisted for over a thousand years and the “blitzkrieg” model of extinction starts to crumble. Humans may have still been responsible for the extinction of the sloths and other species, but the record doesn’t show the pattern of rapid die-off that has sometimes been used to pin our species as the chief cause of megafaunal extinctions.

In time, we may get a clearer picture of why such a diverse and widespread ground of mammals disappeared. Assuming that humans, climate change, or any of the other traditional suspects without more detailed evidence masks the complexity of how extinction happens. But even if paleontologists eventually puzzle together what happened to these great beasts, I’ll still be saddened by the fact that I just missed the ground sloths. Especially because there are habitats – such as vast stretches of desert in the basin and range I call home – that could still host them. Sometimes, when hours of rolling over the interstate starts to addle my brain, I start to imagine them out among the Joshua trees – reminders that we still live in the shadow of the Ice Age world.


MacPhee, R., Iturralde-Vinent, M., Vázquez, O. 2007. Prehistoric sloth extinctions in Cuba: Implications of a new “last” appearance date. Caribbean Journal of Science. 43, 1: 94-98.

Martin, F., San Román, M., Morello, F., Todisco, D., Prevosti, F., Borrero, L. 2013. Land of the ground sloths: Recent research at Cueva Chica, Ultima Esperanza, Chile. Quaternary International. 305: 56-66. doi: 10.1016/j.quaint.2012.11.003

Steadman, D., Martin, P., MacPhee, R., Jull, A., McDonald, H., Woods, C., Iturralde-Vinent, M., Hodgins, G. 2005. Asynchronous extinction of late Quaternary sloths on continents and islands. PNAS. 102, 33: 11763-11768. doi: 10.1073/pnas.0502777102

Book in Brief: How to Clone a Mammoth

“Will there ever be a real Jurassic Park?” I’ve heard this question more times than I can count. The answer is always “No“. Aside from the problem of getting a viable clone to develop inside a bird egg – one that scientists haven’t cracked yet – DNA’s postmortem decay happens too fast to give us any hope of saying “Bingo! Dino DNA!” someday. But just because it won’t work for Tyrannosaurus doesn’t mean that it’s impossible for other forms of life. In How to Clone a Mammoth, ancient DNA expert Beth Shapiro offers a thrilling tour of the science that might – might – recreate lost worlds from the not-too-distant past.

how-to-clone-a-mammothThe book’s title is a bit of a bait-and-switch. On the very first page, Shapiro explains that for long-extinct organisms such as “the passenger pigeon, the dodo, the mammoth – cloning is not a viable option.” If at all, these organisms are going to come back to us piecemeal as revived genetic material expressed in hybrid creatures that may, or may not, look like the lost species. And this cuts to the core of what de-extinction is really all about.

From a purist’s perspective, extinction really is forever. It’s impossible to recreate lost species exactly as they were, down to every last gene and quirk of behavior. But with a broader definition of de-extinction – creating organisms that can fill vacant ecological roles – an elephant with a touch of mammoth trundling around the Arctic steppe would count as what Shapiro dubs an unextinct species. This is the goal of de-extinction efforts – not to recreate extinct species down to the finest detail, but to generate organisms that rehabilitate ecosystems. Not so much resurrection as carefully-crafted reinvention focused on ecosystem-scale repair.

As a researcher who is shaping this field, Shapiro is the perfect guide to the ongoing discussion about de-extinction. While many news items and conference presentations have focused on the technology required to recreate extinct life, Shapiro carefully considers every step along the journey to de-extinction, from choosing a species to revive to making sure they don’t become extinct all over again. As Shapiro says herself, she’s a realist rather than a cynic, and her finely-honed prose cuts through the hype that has clouded the debate around whether or not we should be striving to recreate lost species when so many living species are hanging on by the barest thread.

In fact, Shapiro uses the tension between those advocating for the return of extinct species and critics who argue that the effort would be better spent saving today’s imperiled organisms to propose a third option that has barely been discussed. Whether or not proxy mammoths, dodos, or sabercats come back, exploring such possibilities may give conservationists new tools to manage and assist threatened species and ecosystems. We’re already carrying out conservation triage on the weak and wounded, so why not use every tool at our disposal to sustain – and perhaps even improve – what we’re already managing by hand? Or, as Shapiro writes near the end of the book, “De-extinction is a process that allows us to actively create a future that is really better than today, not just one that is less bad than what we anticipate.”

Will genetically-modified pseudo-mammoths or passenger-ish pigeons be the first symbols of a new age in conservation? That’s still unclear. But even if we never see shaggy elephants or the shade cast by immense pigeon flocks, de-extinction research already underway has the potential to both tell us about the past and provide us with new tools to decide the future shape of nature. Whether you’re all for de-extinction or against it, Shapiro’s sharp, witty, and impeccably-argued book is essential for informing those who will decide what life will become.

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Darwin’s “Strangest” Beast Finds Place on Tree

Toxodon is perhaps one of the strangest animals ever discovered,” wrote Charles Darwin, a man who was no stranger to strangeness. He first encountered the creature in Uruguay on November 26th, 1834. “Having heard of some giant’s bones at a neighbouring farm-house…, I rode there accompanied by my host, and purchased for the value of eighteen pence the head of the Toxodon,” he later wrote.

The beast’s skeleton, once fully assembled, was a baffling mish-mash of traits. It was huge like a rhino, but it had the chiselling incisors of a rodent—its name means “arched tooth”—and the high-placed eyes and nostrils of a manatee or some other aquatic mammal. “How wonderfully are the different orders, at present time so well separated, blended together in different points of the structure of the toxodon!” Darwin wrote.

Those conflicting traits have continued to confuse scientists. Hundreds of large hoofed mammals have since been found in South America, and they fall into some 280 genera. Scientists still argue about when these mysterious beasts first evolved, whether they belong to one single group or several that evolved separately, and, mainly, which other mammals they were related too. “That’s been difficult to address because they have features that they share with a lot of different groups from across the mammalian tree,” says Ian Barnes from the Natural History Museum in London. “To some degree, people have circled around the same set of evidence for 180 years.”

Now, Barnes’ team, including student Frido Welker from the Max Planck Institute for Evolutionary Anthropology and Ross MacPhee form the American Museum of Natural History, have found a way to break out of the circle. They recovered a hardy protein called collagen from the fossil bones of Toxodon and Macrauchenia, another South American oddity that resembled a humpless camel. By comparing these molecules to those of modern mammals, the team concluded

Toxodon. Illustration by Peter Schouten from the forthcoming book "Biggest, Fiercest, Strangest" W. Norton Publishers (in production)
Toxodon. Illustration by Peter Schouten from the forthcoming book “Biggest, Fiercest, Strangest” W. Norton Publishers (in production)

that the two ancient beasts are most closely related to perissodactyls—odd-toed hoofed mammals like rhinos, tapirs, and horses.

Toxodon looks a bit like a hippo and we now know that the features they share with hippos are probably due to convergence,” says Barnes. “Macrauchenia looks a bit like a camel, but we can now see that it’s not particularly well related to camels.. This has been a longstanding mystery and we have an answer, and that’s satisfying.”

The discovery has bigger implications, though. Many scientists, Barnes included, have recovered DNA from very old fossils. They have sequenced the full genomes of mammoths and Neanderthals, worked out the evolutionary relationships of giant birds, and even discovered entirely new groups of early humans. But ancient DNA has its limits.

To fish it out of fossils, you need molecular bait, and to design that bait, it really helps to know what kind of animal you’re looking for and what they’re related to. If you don’t, and your only clue is “er, some kind of mammal”, then recovering ancient DNA is hard. It becomes harder if the fossils are also very old, since DNA has a half-life of around 521 years. And it becomes absurdly hard if the bones come from warm climates, like most of South America, where DNA degrades even faster than usual.

Collagen, however, is exceptionally durable. This rope-like protein gives strength and elasticity to our skin, ligaments, tendons, and other tissues. “In principle, it should survive ten times longer than DNA in bone,” says Barnes. And while bones contain just a tiny amount of DNA, they carry a huge amount of collagen—this one molecule makes up 25 to 30 percent of the total proteins in our body. (This bounty also means that contamination of ancient samples by collagen from scientists or other creatures isn’t really a problem.)

Macrauchenia. Illustration by Peter Schouten from the forthcoming book "Biggest, Fiercest, Strangest" W. Norton Publishers (in production)
Macrauchenia. Illustration by Peter Schouten from the forthcoming book “Biggest, Fiercest, Strangest” W. Norton Publishers (in production)

To analyse the ancient collagen, Barnes worked with Matthew Collins from the University of York. They assembled near-complete sequences of COL1—the most common form of collagen—from both Toxodon and Macrauchenia. They then compared these sequences to COL1 from 76 mammal species (and one chicken) to build a family tree, with Toxodon and Macrauchenia perched at the base of the perissodactyl branch.

But Maureen O’Leary from the Stony Book School of Medicine, who studies mammal evolution, says that this approach is “not methodologically sound”. Before creating their tree, she says, the team should have combined their data with published information on other molecules and physical features.

Alan Cooper, an ancient DNA specialist from the University of Adelaide, adds that ancient proteins have their problems. Collagen does such an important job that it doesn’t change very easily; when it does, it is severely constrained in how it can change. As such, similarities between two collagen sequences might imply that their owners are genuinely related, or that they were independently forced down the same convergent routes. “The phylogenetic resolution of protein sequences”—that is, their ability to tell you what’s related to what—“is pretty ropey,” says Cooper.

That said, he notes that the team’s family tree makes sense. Toxodon and Macrauchenia are so weird that they could sit anywhere, but the rest of the branches and twigs are (mostly) where they should be. “It’s good to see something come out on Macrauchenia at last,” he adds. “A lot of us having been trying to get ancient DNA out of remains for a while. I suspect that’ll finally happen, at which point it’ll be really interesting to see how the [family trees] compare.”

Toxodon and Macrauchenia belong to two separate orders of South America’s weird hoofed mammals. There are three more, and, “unfortunately, the likelihood is that we won’t get similarly nice results from looking at any of them,” says Barnes. They went extinct too early; their fossils are too old. The only option is to identify the features in Toxodon and Macrauchenia’s bones that hint at their affinities with the horses and rhinos. They might then be able to focus at the same features in their other enigmatic neighbours.

Collins hopes that sequencing ancient proteins will provide researchers with another way of understanding prehistoric life, especially in situations where DNA preserves badly. His team, for example, have looked at proteins in ancient dental plaque to study the history of human milk consumption and our longstanding battles against oral infections. “A lot of people are aware that DNA sequencing is changing, but protein sequencing is undergoing a similar revolution in the sensitivity of the instruments,” adds Barnes. “Who’s to say what we can do?”

Reference: Welker, Collins, Thomas, Wadsley, Brace, Cappellini, Turvey, Reguero, Gelfo, Kramarz, Burger, Thomas-Oates, Ashford, Ashton, Rowsell, Porter, Kessler, Fischer, Baessmann, Kaspar, Olsen, Kiley, Eillott, Kelstrup, Mullin, Hofreiter, Willerslev, Hublin, Orlando, Barnes & MacPhee. 2015. Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates. http://dx.doi.org/10.1038/nature14249

PS: Another team of scientists led by Mary Schweitzer claims to have recovered and sequenced collagen from dinosaurs like Tyrannosaurus and Brachylophosaurus. Those results have always been controversial and still are. Toxodon lived a couple of million years ago; these dinosaurs lived at least 65 million years ago. Even collagen has its limits, although Schweitzer’s team argues that the protein’s rope-like structure protected some parts of it. “We’re working within the accepted limits of collagen survival,” says Barnes. “Schweitzer’s work requires a different mechanism, that I don’t understand, and they’d be the first to admit that the results they get are very, very fragmentary.”


Missing the Mastodon

When I look out my front window to the Wasatch Front, I can’t help but feel that there’s something missing. It’s not something seen, but something that comes from knowing what used to be here. The absence takes the shape of big, shaggy elephants called American mastodon. This was their home until not so very long ago.

From a collection of bones described in 1981 – the first such find reported in all of Utah – paleontologists know that the “bubby toothed” proboscideans lived in the Salt Lake Valley during the last Ice Age. That’s practically yesterday. When I write about non-avian dinosaurs or other ancient creatures, I can’t really get my head around just how long a span of time separates me from them. It’s easy to rattle off dates in millions of years. But American mastodon may have trod through the ground that makes up my front yard close to the boundary of when prehistory became history. It seems close enough to almost touch them, but extinction keeps them just as far away from me as any other vanished species.

Why Mammut americanum and many of its Ice Age neighbors – the giant ground sloths, sabercats, and others – died out is a mystery, and a contentious one at that. A slew of possible culprits have been implicated, including climate change, the impact of a comet, disease, and hungry, hungry humans. Some – such as the comet and hypervirulent disease – have been discarded, but even left with climate change and hunting as frontrunners, uncovering the truth about the disappearance of North America’s great megafauna is a fraught undertaking. Tracking the comings and goings of species around us is difficult enough. Replaying prehistory is even more challenging, especially when extinction cannot be boiled down to a single phenomenon such as warming temperatures or the invention of the atlatl.

If we’re going to understand what happened to the American mastodon and its megafaunal ilk, we need a more refined view of when they lived, where they lived, and how their habitats changed through time. Paleontologists are still piecing together this essential picture of Pleistocene life, and one of the latest attempts to do so was published last week in PNAS. Focusing on American mastodon bones from the Arctic, the scientists found that the great beasts had already vanished from the chilly north by the time humans arrived.

American mastodon followed the expansion and contraction of Ice Age forests, only inhabiting the Arctic during warmer, wetter periods. From Zazula et al., 2014.
American mastodon followed the expansion and contraction of Ice Age forests, only inhabiting the Arctic during warmer, wetter periods. From Zazula et al., 2014.

The study was spurred by an anomaly. Despite living during the Ice Age, American mastodons were not cold-weather elephants. They preferred warmer, wetter climes – usually forests dense with conifers and lowland swamps. But radiocarbon dates from rare American mastodon bones found in Alaska and the Yukon suggested that the animals lived there during the last gasp of glaciation between 18,000 and 10,000 years ago. Were the mastodons really living among the open, cold, dry steppe that covered the Yukon then, or were the dates wrong?

Grant Zazula of the Yukon Paleontology Progam joined 14 other researchers to come up with new 53 new radiocarbon dates for 36 American mastodon fossils, including those dated previously. It turned out that the earlier dates were wrong. Contamination – either naturally-occurring or from museum preservation practices – had given erroneously young dates. The mastodons weren’t trundling across the frosty steppe, after all.

The dates Zazula and his colleagues came up with are all over and around 50,000 years ago. This is the limit of radiocarbon dating. What that means is that most, if not all, the American mastodons in their sample perished before 50,000 years ago. And while the difference between 18,000 years ago and more than 50,000 years ago might not seem like much, it made all the difference to the American mastodons.

The Ice Age was not consistently icy. The great glaciers of the north waxes and waned through time, and the last time ice started to take over North America was around 75,000 years ago. The relatively warm forests fell away to make way for chilly, open steppe. And when this happened, Zazula and coauthors write, the American mastodons were extirpated from the Arctic. There was no longer anywhere for them to live, and so their range contracted to those populations living in more southern forests. The new radiocarbon dates – indicating ages over 50,000 years – are in accord with the shifting forests. And it wasn’t just the mastodons that were affected this way. The bones of Jefferson’s giant ground sloth and the giant beaver Castoroides show the same pattern.

This means that the American mastodons had already vanished from the Arctic by the time humans arrived in prehistoric Alaska around 12,500 years ago. “Over-chill” had already made the Arctic inhospitable to the beasts. Humans likely played some role in the ultimate extinction of the mastodon, but humans had to spread southward before meeting the mastodon.

Whatever happened, though, we now live in a world that could still be home to American mastodon. The world may have changed too much for the woolly mammoth, but it’s not very difficult to picture mastodon among the forests and swamps of North America today. In fact, they were making a comeback just before they were snuffed out. In the eastern part of the continent, Zazula and colleagues write, American mastodons were starting to follow forests north as the last great ice sheet receded. And that’s when their time on Earth closed, leaving me to only imagine how wonderful they would have been in life.


Miller, W. 1987. Mammut americanum, Utah’s first record of the American mastodon. Journal of Paleontology. 61 (1): 168-183

Zazula, G., MacPhee, R., Metcalfe, J., Reyes, A., Brock, F., Druckenmiller, P., Groves, P., Harington, C., Hodgins, G., Kunz, M., Longstaffe, F., Mann, D., McDonald, H., Nalawade-Chavan, S., Southon, J. 2014. American mastodon extirpation in the Arctic and Subarctic predates human colonization and terminal Pleistocene climate change. PNAS. doi: 10.1073/pnas.1416072111

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Seals May Have Carried Tuberculosis To The New World

Very few people suspected the seals.

Kirsten Bos from the University of Tubingen certainly didn’t when she and her colleagues started studying three Peruvian skeletons. They were just trying to understand the history of tuberculosis—a disease that has affected humans for millennia and still kills millions every year. Team member Jane Buikstra excavated three early victims from a site in southern Peru; their warped spines and ribs showed unmistakeable signs of the disease.

Even though the bones were around 1,000 years old, the team still managed to extract DNA from them. These included sequences belonging to Mycobacterium tuberculosis, the bacterium that causes tuberculosis. The researchers calculated that these ancient sequences last shared a common ancestor with modern M.tuberculosis strains 6,000 years ago.

That was the first big surprise. The general opinion among scientists who study tuberculosis is that it’s an ancient disease that started infecting humans back when we all lived in Africa—after all, that’s where the strains are at their most diverse. As we spread around the globe, this pernicious partner hitched a ride and co-evolved with us. Genetic studies support this view. A big one, published just last year, estimated that all human tuberculosis strains evolved from a common ancestor that lived 70,000 years ago, before the great expansion out of Africa. But the new results suggest that this ancestral microbe was just 6,000 years old!

It’s not just the discrepancy that’s baffling. By 6,000 years ago, humans had already spread around the world, including all over the Americas. The land bridge that connected Asia and North America had long since flooded. And it would be several millennia before any Europeans sailed across the Atlantic. So if tuberculosis originated in Africa, how did it get into South America?

The team considered the possibilities. Maybe some animal rafted across the ocean, taking the bacteria with it? Maybe some bird flew it over? Or maybe, one of them suggested, seals carried it across. They’re long-distance swimmers, they’re infected with a relative of M.tuberculosis called M.pinnipedii, and people often kill and eat them. But, come on. Seals? Seriously? “We had a good laugh over that,” says Bos. “It seemed so silly.”

Still, it was worth testing. The team compared the genomes of many species of tuberculosis bacteria from a variety of animals—humans, cows, chimpanzees, goats, seals, and more. And they found that the closest relatives of the Peruvian strains weren’t the ones that infect today’s humans… but the ones from seals. Seals! (No, not SEALs. Or Seal. Seals.)

“We couldn’t believe that was what the data was showing, but it was pretty clear,” says Bos. “I got the data and sent a text message to Johannes Krause [the senior author], which just said: Arf!”

“This is a triumph of technical and analytical approaches, and It also delivers a wonderfully unexpected result. It’s great science!” says Mark Pallen from the University of Warwick.

Here’s what Bos thinks might have happened: M.tuberculosis evolved in Africa and could have made it into coastal populations of seals (actually, probably sea-lions). That’s reasonable—these microbes are really good at hopping between mammals, as the furious debate around British badger culls attests to. It adapted to the seals, producing the lineage we know as M.pinnipedii. It then spread throughout the southern hemisphere in its new hosts.

Eventually, some of these sick animals were killed by humans living in coastal Peru. We know that many of these groups used seal hides in funeral rituals. They ate seal meat as a regular part of their menu. They could have caught tuberculosis through these practices. If this sounds implausible, note that seals in zoos have passed M.pinnipedii to people before. And some archaeologists have actually speculated that coastal people who hunted and maybe even farmed seals might have caught tuberculosis from them.

The team’s discovery may help to explain some uncertainty around the smudgy history of tuberculosis in the Americas. Scientists used to think that European colonists brought the disease over, since strains that currently circulate in the New World are closely related to European ones. But once they started finding very old skeletons with signs of infection, they knew this couldn’t be right. And in 1994, one team recovered M.tuberculosis DNA from a thousand-year-old Peruvian mummy. The microbe was clearly in the Americas long before Europeans were.

Could seals have been responsible for this early foothold? “It would be quite a brave extrapolation to make at this stage,” says Terry Brown from the University of Manchester. It’s entirely possible that the seals are red herrings, and some other animal that the team didn’t include in their analysis brought tuberculosis to Peru. After all, they only looked at the genomes of 14 animal strains. “They are just scratching the surface of mycobacterium diversity,” says Hendrik Poinar from McMaster University. “There could be plenty of strains from other animals that will fall closer than seals.” The seal story is plausible, but that doesn’t mean it’s right.

Even if seals were involved, it’s unclear how often they passed tuberculosis to people, or what happened afterwards. Their strains could have jumped from person to person and swept the Americas. Or they could have infected those three unfortunate Peruvians and no one else. “[This could have been] just a one-off zoonotic episode, restricted in time and space, leaving the majority of Pre-Columbia tuberculosis in the Americas unexplained,” says Pallen.

Bos agrees. “These three might just have eaten sick seals, got the infection and died, without transmitting it to their peers.” To show human-to-human transmission, the team would need to find similar strains of M.tuberculosis in skeletons from inland archaeological sites, where people didn’t have direct contact with seals. They’re working on that.

Meanwhile, Brown adds that transmission-by-seal isn’t actually the most important bit of the study. He’s more captivated by the suggestion that tuberculosis is just 6,000 years old, rather than 70,000 as previously suggested.

“These dates are worked out by measuring the amount of genetic diversity among all known strains of TB bacteria, and then using a molecular clock – based on the rate at which genetic changes occur during evolution – to work out how much time was needed for all that diversity to evolve,” explains Brown. “To do this, the molecular clock has to be calibrated—we need to know how rapidly the genetic changes accumulated in the past.”

The earlier study calibrated their clock using imprecise figures, based on estimates of when humans spread through the world. Bos’s team (which actually includes six authors from the previous work) calibrated their clock using one of their skeletons. Thanks to carbon-dating, they knew that it was between 1,000 and 1,200 years old. They could work out how much the bacteria have changed since then, and how much time they needed to evolve before. Hence: 6,000 years.

If that estimate is right, it would totally refute the idea that tuberculosis evolved when we were still confined to Africa, and diversified with us as we colonised the world. Instead, it arose when that worldwide spread was already mostly complete.

Of course, they could be wrong. Pallen says that the study doesn’t explain why another group found signs of tuberculosis in a 17,000-year-old bison from North America.  Brown adds, “They had to make certain assumptions about the way in which tuberculosis bacteria evolve, and those assumptions might not be entirely secure. We definitely need more ancient Mycobacterium genome sequences, for example from Europe or Asia, and from different time periods, to check this result.”

“The study of ancient DNA [will] continue to contribute significantly to filling gaps in our knowledge of tuberculosis, a devastating disease today that still kills many thousands of people each year,” says Charlotte Roberts from Durham University.

Reference: Bos, Harkins, Herbig, Coscolla, Weber, Comas, Forrest, Bryant, Harris, Schuenemann, Campbell, Majander, Wilbur, Guichon, Wolfe Steadman, Collins Cook, Niemann, Behr, Zumarraga, Bastida, Huson, Niesell, Young, Parkhill, Buikstra, Gagneux, Stone & Krause. 2014. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature http://dx.doi.org/doi:10.1038/nature13591


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Extinct Humans Passed High-Altitude Gene to Tibetans

Tibetan people can survive on the roof of the world—one of the most inhospitable places that anybody calls home—thanks to a version of a gene that they inherited from a group of extinct humans called Denisovans, who were only discovered four years ago thanks to 41,000-year-old DNA recovered from a couple of bones that would fit in your palm.  If any sentence can encapsulate why the study of human evolution has never been more exciting, it’s that one.

In 2010, Rasmus Nielsen from the University of California, Berkeley found that Tibetan people have a mutation in a gene called EPAS1, which helps them handle low levels of oxygen. Thanks to this mutation, they can cope with air that has 40 percent less oxygen than what most of us inhale, and they can live on a 4,000-metre-high plateau where most of us would fare poorly. To date, this is still “strongest instance of natural selection documented in a human population”—the EPAS1 mutation is found in 87 percent of Tibetans and just 9 percent of Han Chinese, even though the two groups have been separated for less than 3,000 years.

But when the team sequenced EPAS1 in 40 more Tibetans and 40 Han Chinese, they noticed that the Tibetan version is incredibly different to those in other people. It was so different that it couldn’t have gradually arisen in the Tibetan lineage. Instead, it looked like it was inherited from a different group of people.

By searching other complete genomes, the team finally found the source: the Denisovans! The Tibetan EPAS1 is almost identical to the Denisovan version. It’s now a Tibetan speciality, but it was a Denisovan innovation.

This discovery is all the more astonishing because we still have absolutely no idea what the Denisovans looked like. The only fossils that we have are a finger bone, a toe, and two teeth. Just by sequencing DNA from these fragments, scientists divined the existence of this previously unknown group of humans, deciphered their entire genome, and showed how their genes live on in modern people. Denisovan DNA makes up 5 to 7 percent of the genomes of people from the Pacific islands of Melanesia. Much tinier proportions live on in East Asians. And now, we know that some very useful Denisovan DNA lives on in Tibetans.

Svante Paabo, who sequenced the Denisovan genome, is delighted. “It’s very satisfying to see that gene flow from Denisovans, an extinct group of archaic humans which we discovered only four years ago, is now found to have had important consequences for people living today,” he says.

“It was a complete surprise,” says Nielsen. “It took years after the Denisovan genome was published for us to even try this, because we thought it was so far-fetched.”

The discovery also adds to a growing picture of human evolution—one involving a lot of cross-breeding. Humans evolved in Africa, and everyone outside that continent descends from a relatively small group of pioneers who left it at some point in our prehistory. These trailblazers were adapted to life on the tropical savannah. As they migrated, they experienced all the varied challenges that the world has to offer, such as extreme temperatures and new diseases.

At the time, the world was already populated by other groups of humans, like Neanderthals and Denisovans. As the African immigrants met up with these groups, they had sex. And through these liaisons, their genomes became infused with DNA from people who had long adapted to these new continents. “It’s a new way of thinking of human evolution—a network of exchange of genes between many lineages,” says Nielsen.

Nielsen suspects that modern humans had sex with Denisovans in Asia, somewhere between 30,000 and 40,000 years ago. They inherited the Denisovan version of EPAS1, which lingered in the populations at very low frequencies. The carriers fared better at higher altitudes, and their descendants colonised the Tibetan plateau. This explains why the team found the Denisovan EPAS1 in the vast majority of Tibetans, but also in a couple of Han Chinese people living outside of Tibet.

Denisova_TibetOther scientists have shown that sex with Neanderthals could also have imported useful genes into our genome, including those involved in skin, hair, and the immune system. “What we’re learning from ancient genomes is that while each of them may have contributed only a little to our ancestry, those genetic streams were full of tiny golden nuggets of useful genes,” says anthropologist John Hawks, who emailed me just before visiting Denisova Cave where the Denisovan fossils were found.

“What is a bit surprising is that Denisova is not at high altitude,” says Hawks. It’s in the Altai mountains of Siberia, but it’s not that high up. If Denisovans had the high-altitude version of EPAS1, this could imply that they also spread through the more mountainous parts of China and South Asia. “This gives a route by which Denisovans might have gotten into Southeast Asia where we know modern humans picked up their genes on the way to Australia,” says Hawks.

Nielsen adds that the Denisovans weren’t necessarily adapted to high altitudes. Their version of EPAS1 could have helped them in other ways, and coincidentally allowed the Tibetans to colonise the roof of the world.

If I travelled to the Tibetan plateau, my body would try to cope by making more red blood cells, which transport oxygen around my body. But I’d overcompensate and make too many of these cells. My blood would become thick and viscous, leaving me prone to high blood pressure and stroke. Tibetans don’t have this problem. Their EPAS1 stops them from overproducing red blood cells and helps them acclimatise to the altitude without doing themselves harm. But cold climates can also raise blood pressure by constricting blood vessels. So perhaps the Denisovan version of EPAS1 helped them to adapt to extreme cold, rather than a lack of oxygen.

“To give you a definitive answer, I’d need to find a Denisovan and do some physiological experiments,” he says. “And I can’t.”

Reference: Huerta-Sanchez, Jin, Asan, Bianba, Peter, Vinckenbosch, Liang, Yi, He, Somel, Ni, Wang, Ou, Huasang, Luosang, Cuo, Li, Gao, Yin, Wang, Zhang, Xu, Yang, Li, Wang, Wang & Nielsen. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. http://dx.doi.org/10.1038/nature13408

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Reinventing the Mammoth

The first groaner of the TEDxDeExtinction conference cropped up less than an hour into the program.  Paleontologist Michael Archer was on stage, wrapping up his talk on possibly recreating the gastric brooding frog and the thylacine – two species totally lost from Australia in recent time. Archer laid out the technological particulars of the plans, as well as where the animals might live, but at the end he took a turn for the transcendentalist in justifying the difficult endeavor to resurrect these creatures. Since our species played a prominent role in wiping out both species, Archer argued, we have an obligation to “restore the balance of nature that we have upset.” If I had brought a flask with me, I might have taken a strengthening sip of whiskey right then.

There is no such thing as “the balance of nature.” If sifting through the fossil record has taught me anything, it’s that change is the rule. Balance is only a temporary illusion created by the difficulties of envisioning life on a geological scale. That, and quite a few conversations with practically-minded ecologists and biologists, means that I’ve become a bit allergic to snuggly phrases that are often trotted out to emphasize the inherent goodness of nature – whatever “nature” means – in a way that suggests we can simply restore the complexity of life to a stable state that the ghosts of Thoreau, Emerson, and Muir would honor us for. And the irritation of that line kept with me throughout the rest of the day. Perhaps the closing appeal to the balance of nature was a trifling throwaway, yet that one line underscored the problematic nature of the major proposal the assembled speakers and guests had been called to consider – that we can, and should, resurrect lost life to take some of the tarnish off our ecological souls. The concept falls under the banner of “de-extinction.”


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The Origin of the Friendly Wolf that Confused Darwin

When Western sailors started landing on the Falkland Islands, off the curling tip of South America, they were greeted by a bizarrely tame dog-like creature. It roamed wild across the islands, but would frequently swim out to meet the approaching boats while wagging its tail. Although some called it a fox, it became more commonly known as the Falkland Islands wolf. Its scientific name: Dusicyon australis, the foolish dog of the south.

The name was apt. The wolf’s fearlessness made it extremely easy to kill. People lured it in with meat, and either clubbed or knifed it. By 1880, it was extinct, but not before a young, twenty-something naturalist called Charles Darwin managed to see one for himself in 1834.

Darwin saw the Falkland Islands wolf not as easy meat, but as a strange biological puzzle. What was such a large predator doing on this tiny set of islands, some 460 kilometres away from the South American mainland? Deepening the puzzle, South America is a land dominated by rodents, but none of them had made it to the Falklands. In fact, the wolf was the only mammal there. Where had it come from? And why had nothing else furry followed it?

Some said that early South Americans must have partly domesticated the wolf and brought it over on their boats—hence its unfortunate tameness. Others said that the wolf sauntered across prehistoric land bridges, or rafted over on chunks of ice. “It struck me as an outstanding mystery in natural history,” says Alan Cooper from the University of Adelaide. He was keen to solve it.

Cooper’s speciality is wresting samples of ancient DNA from fossils, and sequencing these millennia-old molecules to better understand their owners. So far, he and others have filled their genetic ark with Smilodon the sabre-toothed cat, American lion, cave lion and American cheetah. They have done the massive short-faced bear, giant jaguar, cave hyena and European bison. They looked at the dodo, New Zealand’s enormous moas, elephant birds, and giant ducks. “We were running out of good ones to do,” he laments. The wolf made the cut.

Illustration of Falkland Islands wolf from Zoology of the Voyage of H.M.S. Beagle. By George R. Waterhouse
Illustration of Falkland Islands wolf from Zoology of the Voyage of H.M.S. Beagle. By George R. Waterhouse

In 1996, Cooper travelled to London’s Natural History Museum to check out one of only six specimens of Falkland Islands wolf that were known at the time. Darwin collected the animal himself, and his handwriting graces the label (although it’s unclear whether he actually clubbed it over the head himself, as some stories claim).

Darwin was meticulous and the skull had been thoroughly cleaned—great for museums, bad for geneticists. Cooper needed organic material that still contained DNA. He suggested to Paula Jenkins, the museum’s curator of mammals, that he could pull out a tooth, cut off part of its root, and put it back in. “Her countenance was not one that suggested this was going to happen,” says Cooper, delicately.

But Darwin had missed a spot. As Cooper turned the skull around, he noticed a tiny sinus on its face—an opening, and one that clearly had something in it. He reached in with some tweezers and pulled out a little piece of nerve and blood vessel. It was just 3 millimetres long and 1 millimetre wide. But it was enough. It was raw tissue, loaded with DNA. “I thought: This is definitely going to work,” says Cooper.

His team have since collected DNA from five of the wolves, including a 7th moth-eaten, stuffed specimen that was gathering dust in an attic at New Zealand’s Otago Museum. “Everyone figured this was a fox that had been taxidermied badly,” says Cooper. His student took a bit of its toe, sequenced it, and confirmed that it was indeed a match for the other Falkland Island wolves.

When they finally analysed their sequences, the team concluded that the Falkland Islands wolf’s closest living relative is the maned wolf, a handsome stilt-legged dog found in South America.* The two species split apart around 6.7 million years ago. That’s useful to know, but it doesn’t tell us anything about the animal’s mysterious origins.

Cooper tried again. This time, he compared the Falkland Islands wolf’s DNA with that of a close relative that lived on the mainland—the similarly extinct Duscyon avus. The DNA revealed that the two species of “foolish dogs” diverged from their common ancestor just 16,300 years ago. That gives a pretty good indication of when the wolf reached the Falkland Islands and started evolving independently from its mainland cousins.

The date ruled out the possibility that humans brought the wolf over to the islands, but it suggested an alternative.

During the last Ice Age, four shallow ice terraces (numbered I to IV) spanned the ocean between Argentina and the Falklands.
During the last Ice Age, four shallow ice terraces (numbered I to IV) spanned the ocean between Argentina and the Falklands.

At the time, Earth had just come out of an ice age. Frozen sheets covered much of the world and sea levels were dramatically lower than they are now. The ocean floor between mainland Argentina and the Falkland Islands is incredibly flat, sloping by just 0.5 degrees for 600 kilometres. “If the sea level goes down, it goes down a hell of a long way,” says Cooper.

So, 16,000 years ago, huge underwater terraces extended off the coast of Argentina, like the shallow end of a swimming pool. Meanwhile, the Falklands were about four times bigger than they are now. The gap between them and the mainland was just 20 to 30 kilometres wide, and 10 to 30 metres deep. “I’d put money on the fact that it would have frozen over at some point,” says Cooper.

Such a crossing would have been easy for the wolf’s ancestors. Perhaps it behaved like modern Arctic foxes, taking advantage of the glut of seabirds, baby animals and washed-up carcasses on the frozen shoreline. “By tracing along and using these food supplies, it would have had a high chance of hitting the Falklands,” says Cooper.

But rodents would have found the same distance far more daunting. “If you were a small rodent and looked out on 20 to 30 kilometres of ice, that wouldn’t have been a great option,” says Cooper. The ice terraces acted as an ecological filter—a opportunity for a large predator to seize, but a forbidding no-go area for smaller animals.

Reference: Austin, Soubrier, Prevost, Prates, Trejo, Mena & Cooper. 2013. The origins of the enigmatic Falkland Islands wolf. Nature Communications http://dx.doi.org/10.1038/ncomms2570

* (The maned wolf isn’t really a wolf, and neither is the Falkland Islands one. Fox would be closer, but they’re not foxes either. They belong to an independent branch of the dog evolutionary tree, and one whose members are largely extinct.)

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

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.”

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

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;

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

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

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

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?