5,700-Year-Old Lola, Her Genome Sequenced from Gum, Joins Other Named Forebears

About 5,700 years ago in southern Denmark, a woman enjoyed a meal of hazelnuts and duck, then chewed gum made from the boiled, tar-like gunk of birch bark. Pieces of DNA extracted from the ancient gum and overlapped to reconstruct her genome reveal that she had dark brown hair, dark skin, and blue eyes.

Her discoverers named her Lola, perhaps in honor of the eponymous Kinks song: “I asked her her name and in a dark brown voice she said, ‘Lola.’”

Researchers from the University of Denmark and elsewhere published the findings in Nature Communications. If it seems like old news, it is. Despite the journal having sent out an embargoed press release last week and the media running the story as news, a preprint appeared a year ago at bioRxiv.

Dark Lumps Discovered During Tunnel Excavation

Lola lived on the island of Lolland, east of Rødbyhavn in southern Denmark, where today an 11-mile-long tunnel is being dug to link to the German island of Fehrmarn. Archaeologists from the Museum Lolland-Falster are at the site, the largest from the Stone Age in Denmark. It’s called Syltholm, and Lola, technically, the “syltholm individual.”

”Syltholm is unique. Almost everything is sealed in mud, which means that the preservation of organic remains is phenomenal,” said Theis Jensen, who did his PhD work on the find and is first author of the report.

The ancient gum was a blackish-brown lump of pitch made from the bark of a birch tree, Betula pendula. Use of the gooey stuff goes back to the Middle Pleistocene of about 760,000 to 126,000 years ago, as an adhesive to attach bone, metal, or stone to a handle or strap. Tooth imprints in birch pitch suggest that ancient people may have popped it into their mouths now and then to keep it pliable for toolmaking.

Chewing traps the chewer’s DNA in the pitch. Here the aseptic surroundings keep microbes out and the hydrophobic nature beads up moisture, stifling decay. Unlike dental plaque, which takes years to build up and harbors broad evidence of past diet, DNA in gum captures a scene, a moment in time, like the meal of hazelnuts and duck.

Heated birch pitch may have had healing properties. Betulin is an antiseptic component used to soothe toothaches. The black stuff might have been used to calm hunger pains, as chewing gum does today, or as a toothbrush of sorts.

Digging into Lola’s DNA

DNA clues in the toothmarks reveal the species with which Lola interacted long ago, while the human DNA yielded a full genome sequence, even though people left no remains. The mitochondrial genome indicates the K1e haplogroup lineage. The Tyrolean ice man from 5,200 years ago was an offshoot of that group.

It was a find comparable to that of DNA extracted from teeth and bones. A bonanza. ”It is amazing to have gotten a complete ancient human genome from anything other than bone,’’ said Hannes Schroeder, who led the research.

It’s fascinating to assemble an image of a person from bits of DNA. A New York City artist runs a gallery of faces reconstructed from DNA she finds in discarded cups, errant hairs, cigarette butts, and yes, chewing gum. A variation on that theme is forensic DNA phenotyping, which tracks dozens of genome sites to deduce hair, skin, and eye color.

Like consumer DNA tests today, the findings from the ancient gum provide hints of Lola’s physical traits, her health, and her ancestry.

The ratio of DNA snippets from the X and Y chromosomes – some and none – reveal her gender.

She was lactose intolerant. That’s not surprising, because this was normal before agriculture came along and gave those who could easily digest milk an advantage.

The combination of dark skin and light eyes, known in other European hunter-gatherers, suggests that white skin came later.

Clues in Her Oral Microbiome

The team compared DNA from mouth critters shotgunned into analyzable sizes using a computational tool called MetaPhlan and compared the yield to 689 microbial profiles catalogued in the Human Microbiome Project. Lola’s oral microbiome was similar to that of people today. But evidence of Porphyromonas gingivalis and two other species indicate a bit of gum disease.

Lola’s mouth housed a few harmless species of Streptococcus, but also S. pneumoniae, which today causes pneumonia that is responsible for one to two million infant deaths worldwide annually.

Strep species mix and match their virulence factors, and so reconstructing how these bacteria interacted in Lola’s mouth could provide clues to managing outbreaks and illness today. “It can help us understand how pathogens have evolved and spread over time, and what makes them particularly virulent in a given environment. At the same time, it may help predict how a pathogen will behave in the future, and how it might be contained or eradicated,” said Schroeder.

Like 90 percent of us today, Lola carried the Epstein-Barr virus. It’s usually harmless but can cause mononucleosis and lymphoma.

Other species represented in the gum were sparse, except for the birch, the hazelnuts, and the duck, all abundant in the area. The information is incredibly valuable, for we have few human remains from Lola’s time.

Hunter-Gatherers Thrived Longer Than Thought

Where did Lola’s ancestors come from? To find out, the researchers compared nearly 600,000 single nucleotide polymorphisms (SNPs; places in the genome where a population varies) from her genome to profiles from more than 1,000 modern Europeans and to more than 100 published ancient human genome sequences. A picture emerged from this sample of one.

After the ice sheets ebbed away from 12,000 to 11,000 years ago, people came from two directions, south via Denmark from Europe, and northeast, along the coast of present-day Norway. Lola, according to her DNA, descended from western hunter-gatherers from mainland Europe rather than from northern hunter-gatherers from central Scandinavia.

She lived during the overlap of the Mesolithic (c. 7300–5900 years BP) with the Neolithic 5900–5300 years BP), from when evidence of stone tools grew more scarce and that of pottery more abundant. Animal domestication was beginning.

But did agriculture sweep in, or did pockets of hunting-and-gathering persist? Lola’s mitochondrial group K1 includes early farmers, but the non-human DNA in her bitemarks reveals the earlier practice, supporting the idea that hunting-and-gathering reappeared or surged in Europe 5000 to 7000 years ago.

“Archaeological finds suggest that the people who occupied the site were heavily exploiting wild resources well into the Neolithic, when farming and domesticated animals were introduced into southern Scandinavia,” Jensen said.

The Rockstars of Prehistory

Lola joins other named ancestors.

Ardi, a member of Ardipithecus ramidus, lived about 4.4 million years ago in the Afar rift valley of Ethiopia. She could climb trees using all four limbs, but also venture out onto the plains in a stooped, two-legged stance.

A family of three left their footprints 3.7 million years ago, in the Laetoli region of Tanzania. Preserved in volcanic ash, the footprints are the earliest evidence of bipedalism, from Austalopithecus afarensis.

A million years later, the famed Lucy, also A. afarnesis, dwelled in the Afar Valley. I stand transfixed at her partial skeleton whenever I visit the American Museum of Natural History. Fossils from others of her kind who lived 3.4 million years ago were found with tools used to slice meat from bones.

The Dikika infant died in a flash flood, perhaps while trying to catch fish in rivulets of the Awash river delta near where Lucy lived 300,000 years earlier.

Turkana Boy lived about 1.6 million years ago in Kenya, a member of Homo erectus. His tall, thin body influenced descriptions of the species for two decades until the discovery of more specimens revealed the varied heights and builds of this human ancestor.

A million years ago, another H. erectus, Daka, dwelled in the Afar region. He had a shallow forehead, massive brow ridges, a brain about a third smaller than ours, and strong, thick legs. Daka lived on a grassland, with elephants, wildebeests, hippos, antelopes, various pigs, and giant hyenas.

For a time “the hobbit” Homo floresiensis captured public attention when bits of jaws and teeth from three stunted individuals were found on the island of Flores in Indonesia. The remains were initially dated to about 700,000 years ago, then when anthropologists discovered that charcoal had been analyzed by mistake, the date was changed to 100,000 to 50,000 years ago. Researchers consider her an offshoot of H. erectus with a small body, something that tends to happen on islands.

On a summer day in 1856, quarry workers blasted from a limestone cave in Neander Valley, Germany bones from Neanderthals – the first found. The “Old Man” of La Chapelle-aux-Saints in France followed, inspiring the depiction of slow-witted and stooped individuals. “Nandy,” found with ten others in Shanidar Cave in Iraq with flowers and tools, was old – 40 to 50. His dental plaque held grains of cooked starch. The Shanidar people lived from 65,000 to 35,000 years ago, but Neanderthals go back 400,000 years.

“Oase1” lived about 40,000 years ago in Romania. DNA from a jawbone revealed 6 to 9 percent Neanderthal ancestors who lived about 100,000 years ago, an intermediate between then and now as our genomes diverged. I’m proud to report that my AncestryDNA test showed the near-maximal amount of Neanderthal DNA variants in a modern human. The metric indicates percent of ancestors, not percent of the genome (the media often get this wrong).

My favorite forerunner is Denise  (See “The Denisova Genome and Guys Banging Rocks”). Her story began in 2008 with discovery of thousands of bone and teeth fragments in Denisova Cave in the Altai Mountains of southern Siberia. Analysis of part of her genome in 2010 from a pinky finger bone revealed that she had dark skin and brown eyes and hair. She lived 32,000 to 50,000 years ago.

Since then other discoveries revealed that the cave was a den of mixing and matching archaic human genomes – SEX. (See “The Cave Where it Happened: The Daughter of a Neanderthal Mom and a Denisovan Dad”).

Like the Neanderthals, the Denisovans didn’t just vanish. Remnants of their genomes remain in our own today. The modern people most closely related to the Denisovans are from Papau New Guinea, Melanesia, Oceania, and Polynesia, and aboriginal Australians.

The Tyrolean Ice Man Ötzi, from 5,300 years ago, brings us back to Lola in time. Hikers discovered remains of the frozen man in 1991 in the Alps of northern Italy. He was wearing furry leggings, leather suspenders, a loincloth, fanny pack, bearskin cap and cape, and snowshoes. His skin bore tattoos, his ears indentations.

Ötzi carried mushrooms that had antibiotic properties and berries that indicate late summer or early fall. His last meal was ibex and venison. Ötzi’s paternal descendants lived in Sardinia and Corsica, according to his Y chromosome, but his maternal line died out about 5,000 years ago, according to his mitochondrial genome. One scenario: male ancestors left the isolated Alps, moving toward the Mediterranean sea, while the women perished in the harsh alpine environment.

Lola and perhaps other long-ago gum-chewers will inspire more stories of our past. What really fascinates me is how very much we do not know.

(Thank you to Theis Jensen for the image of the pitch and to artist Tom Björklund for the stunning portrait of Lola).