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IT IS the only part of your body that fossilises while you’re still alive,” says , Germany.

To see what she is describing, stand in front of a mirror and examine the rear surfaces of your lower front teeth. Depending on your dental hygiene, you will probably see a thin, yellowish-brown line where the enamel meets the gum. This is plaque, a living layer of microbes that grows on the surface of teeth – or, more accurately, on the surface of older layers of plaque. If it isn’t brushed or scraped off, plaque hardens as minerals dissolved in saliva precipitate out into it, killing the microbes and petrifying them into a stony substance called dental calculus or tartar.

To you and me, this rock-hard excrescence might seem rather repulsive, but it has become a chewy topic of research among archaeologists. Where it was once considered mere gobshite to be scraped off and discarded, it is now recognised as a time capsule extraordinaire. “Dental calculus is a treasure trove of information,” says . Over the past 20 years, it has revealed some surprising and often quirky details of the lives of our ancestors. But recent research is far more ambitious. “We spent a number of years trying to understand dental calculus and how to use it to really get at some deeper evolutionary questions,” says Warinner. That is now paying off, and dental calculus is throwing light on big questions about where humans came from and where we are going.

Warinner isn’t exaggerating when she says plaque “fossilises” – the process is exactly like permineralisation, when minerals in groundwater penetrate a dead organism and precipitate out, turning it into a fossil. Unlike underground fossilisation, however, dental calculus forms very rapidly: plaque can be . The speed at which it fossilises means it captures vast amounts of biological detail over a lifetime. The principal component is entombed denizens of the oral microbiome, the huge and diverse assemblage of bacteria, archaea and fungi that live in and around your mouth. They account for about 90 per cent of calculus by volume, says Guschanski. But it also traps other things, including bits of food, pathogens, an individual’s own DNA and environmental debris such as dust and smoke particles. In fact, anything that finds its way into your mouth can end up being trapped in calculus. People’s . It has even been proposed as a way of .

“Anything that finds its way into your mouth can end up fossilised in calculus”

The first hints that this gubbins might reveal intimate details from the past came in 1975, when Philip Armitage, at what was then called the British Museum (Natural History) in London, described a calculus of ancient cattle to work out what they ate. In the 1980s, the method was , Neanderthals and extinct apes. Nevertheless, dental calculus remained largely unloved by archaeologists for decades – which, perhaps, isn’t surprising. his doctorate at the University of Oxford in the early 2000s, his supervisor gave him two specimens from which to attempt to recover ancient DNA. One was hair, the other a jawbone sporting what he exaggeratedly describes as “a golf ball-sized lump of calculus”. He chose the hair. “To be honest, the dental calculus sample was so repulsive I literally couldn’t look at it without feeling sick, so I hid it away and never went back to it,” he says.

Frozen in time

Luckily, some researchers weren’t so squeamish and began to use new tools being developed for genetics and molecular biology to dig deeper into dental calculus. The level of detail they found was exquisite. “There’s tremendous preservation of microbes and biomolecules within dental calculus because of the way that it calcifies during life,” says Warinner. “You can see individual bacterial cells really frozen in time.” What’s more, it is so rich in DNA that this is visible with a microscope, she says. The preservation of proteins is remarkable too. “In the archaeological record generally, we have tremendous decomposition and degeneration after death,” says Warinner. “However, fortunately for us, there is a long-term bioarchive that is dental calculus.”

In the past few years, a growing number of researchers – including Gilbert, now at the University of Copenhagen in Denmark – have come to recognise the value of this archive. Their studies reveal some fascinating details about the lives of our ancestors. One, for example, found that people in the Levant were 3700 years ago, revealing early, hitherto unknown contact between the eastern Mediterranean and south Asia. Another showed that the medieval illuminated manuscript industry was an equal-opportunities employer, as demonstrated by the discovery of the blue pigment nun from Dalheim, Germany. And Gilbert was part of a team that last year bacterium Mycobacterium leprae in the calculus of a 16th-century Norwegian woman with no clear signs of the disease on her skeleton. By then, leprosy was in decline across most of Europe, but hit Norway hard for two more centuries, for unknown reasons. The discovery of the bacterium entombed in calculus could help solve the mystery.

“Ice-age Neanderthals and humans had near-identical oral microbiomes”

Earlier this year came results from the . Warinner and a huge team from 41 institutions in 13 countries sequenced DNA extracted from the dental calculus of 124 individuals: 52 members of our species, Homo sapiens, dating from 30,000 years ago to the present day; 17 Neanderthals; 21 chimps; 29 gorillas and five howler monkeys. The subjects included the Red Lady of El MirÓn, an 18,700-year-old H. sapiens skeleton discovered in 2010 in a cave in Spain, and that has the oldest oral microbiome ever reconstructed. “We were able to show that bacterial DNA from the oral microbiome preserves at least twice as long as previously thought,” says the study’s lead author, James Fellows Yates at the Max Planck Institute for the Science of Human History.

The main goal of the research was to track the evolution of the oral microbiome in primates. The researchers expected a lot of variation, but, to their surprise, found strong similarities across all the specimens. This makes the mouth very different from the gut, where microbiomes vary hugely from individual to individual according to diet and location, both in space and time. Even though the five species under investigation had distinct oral microbiomes, they all shared a core group of 10 types of bacteria. The fact that these are even found in South American howler monkeys – which diverged from African monkeys 40 million years ago – suggests that all primates share an ancient oral microbiome, conserved over millions of years of evolution.

The researchers also found that Neanderthals and H. sapiens from ice age Europe had near-identical oral microbiomes: the Red Lady and the Pešturina Neanderthal, although separated by more than 80,000 years and 2000 kilometres, were essentially the same inside their mouths. This is consistent with previous research suggesting extensive contact and interbreeding between the two species in that period. By 14,000 years ago, however, the H. sapiens oral microbiome had altered markedly – and it has changed little to this day. This seems to mirror genetic evidence indicating that mysterious incomers from the south largely replaced the existing northern European population around 14,500 years ago.

The study may also help resolve a long-standing question in human evolution: how did our ancestors get such big, energy-guzzling brains? In 1995, Leslie Aiello at University College London put forward the , which proposed that to become so big-headed, our ancestors must have simultaneously shrunk their guts, which also require a lot of energy to maintain. “There must have been a trade-off, a dietary shift associated with more energy-dense foods,” says Warinner. “What that food was, however, has long been disputed.” Some suggest it was raw or cooked meat, but has argued that the magic ingredient was cooked starches from plant tubers and bulbs.

The starch story is backed up by DNA evidence showing that humans have several copies of the gene for the starch-digesting enzyme salivary amylase, whereas chimps have only one. Research published in 2016 concluded that this duplication lineage split off from ours about 600,000 years ago. However, , indicating that energy-dense carbohydrates were important in their diet too.

The new study makes sense of this. It reveals that humans and Neanderthals both have a distinct type of bacterium in their mouths that is absent from chimps and gorillas. These oddball members of the Streptococcus clan are specialised for feeding on starch: they filch amylase molecules out of saliva and use them to digest starch for their own table. This suggests that the Homo oral microbiome evolved after the split from chimps, but before the one from Neanderthals, says Warinner, and hence that starch was an important source of energy for both. “We can start to use these clues from the oral microbiome to make inferences about our own evolution,” she says.

The zoo in your mouth

The researchers predict that this study is the start of a golden age of evolutionary research on dental calculus. “The oral microbiome is truly extraordinary,” says Warinner. “It is absolutely teeming with life and it contains a truly extraordinary range of diversity that is part of our bodies, but underappreciated.” For one thing, many of the 10 core bacterial groups in the mouths of primates are all but unknown: three of them don’t even have formal scientific names and many individual species are new to science.

In addition, it is a mystery how the starch-munching Streptococci evolved two proteins that can bind to amylase in saliva. One appears to have been acquired by a process called horizontal gene transfer, in which chunks of genetic material are passed directly from one organism to another – but where it came from and when isn’t known. Answering these questions would further refine our understanding of that epochal dietary shift.

Warinner also wants to understand more about how dental calculus forms and what other secrets it may hold. It is clearly laid down in layers that are about 20 to 200 micrometres thick. “But exactly how this works is not well known,” she says. “It’s not annual, but it is regular, almost annual. You could potentially do a time series of the microbiome, which I think would be amazing – though I don’t know how to do that!”

Then there is a whole biosphere of dental calculus from other animals to be explored. Warinner and her co-authors are particularly keen to study baboons such as geladas, which live in an environment similar to the one we probably evolved in and also eat starchy tubers, so hence may help further understand our dietary past.

Other researchers are beginning to study dental calculus in a wider range of animals. “It looks quite different in non-humans,” says Guschanski. “Instead of this nice, solid deposit we’re used to seeing in humans, non-human mammal dental calculus is usually formed as a dark biofilm that is not very flaky.” Nevertheless, it is becoming clear that calculus builds up on the teeth of all mammals, including marine ones, and probably holds a . For example, Guschanski and her colleagues have recently analysed calculus from to the present day. Some of it contains antibiotic-resistant bacteria, which must have been circulating in the environment because the bears weren’t in contact with antibiotics or even living near humans. The research indicates that dental calculus can help us understand global environmental trends and the effectiveness of policies to remedy them.

Dental calculus may even provide a window into the deep past. The oldest yet discovered is , Dryopithecus carinthiacus, housed in a museum in Klagenfurt, Austria, near where it was discovered in 1957. It is unlikely that such old material will contain recoverable DNA, says Warinner, but it may yield intact ancient proteins, the study of which is also coming on in leaps and bounds.

“There’s so much more information out there that we haven’t tapped into yet,” says Warinner. Provided, of course, that curators haven’t scraped all that calculus off and thrown it away.