DNA in unlikely places helps piece together family trees of ancient humans

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One hundred thousand years ago, the Neanderthals gathered in a cave perched 3,000 feet above sea level in the Atapuerca Mountains in Spain. While cooking and watching the young people struggle, they littered the ground with DNA in the skin, sputum and other bodily debris.

Dirt has accumulated and protected genetic material for millennia, even as humans and animals shelter in it. At the site, known as Estatuas, archaeologists have discovered abundant stone tools and animal bones since 2008. The only Neanderthal bone found – a toe tip with the consistency of Swiss cheese – appeared too valuable to be crushed for DNA analysis. Scientists were therefore unable to elucidate the genetic traits of the inhabitants and the links with other Neanderthal clans.

Instead, they searched the dirt for loose DNA. In 2018, researchers fell into pits in Estatuas and collected sediment in layers that formed between 70,000 and 113,000 years ago. They had recovered nearly 800 sediment samples in 2017 from the Chagyrskaya and Denisova caves in southern Siberia, promising places that had already yielded DNA-bearing fossils of Neanderthals and their Denisovan relatives.

At the Max Planck Institute in Germany, Benjamin Vernot and his colleagues separated human DNA from sequences belonging to animals, plants and microbes. The resultant Science and Nature The papers have shown that dirt devoid of fossils and artefacts can hide genetic treasure. At Denisova Cave, researchers extracted fragments of human DNA from more than 220 sediment samples, compared to nine fossils with genetic material. The dirt indicated that lineages of Neanderthals, Denisovans, or Homo sapiens lived there in different places.

Ancient stools revealed that early humans likely had much more diverse gut microbiomes than people today. (Credit: Karl Reinhard)

These results were consistent with previous fossil analyzes, proving the usefulness of the methods for Estatuas, which lacked DNA data from fossils. There, sediments revealed that a new group of Neanderthals arrived around 100,000 years ago and differed genetically from inhabitants of previous millennia.

These filthy findings set an important precedent. Artifacts like stone tools are common, but fossils are not, especially those whose DNA has survived. Studies have recovered mitochondrial DNA (mtDNA) from sediment, but this genome extract only reflects a maternal branch of the evolutionary tree. “His [been] impossible, on sites where DNA has not been found, to link genetics to the really detailed work that archaeologists do ”by analyzing artefacts, explains Vernot.

At least, so far: Vernot’s team has captured nuclear DNA, a complete family tree record, from some samples and amassed significantly more mtDNA than previous studies.

In 2021, other labs fished in cave soil in the countries of Georgia and Mexico and recovered DNA spanning the Ice Age genome. Homo sapiens, wolf, bison and bear. Meanwhile, scientists from Harvard University and the Joslin Diabetes Center searched the paleofeces. Discovered decades ago in rock shelters in Utah and Mexico, the 1,000 to 2,000 year old droppings contained digested food, including corn and grasshoppers. At the University of Montana, molecular anthropologist Meradeth Snow dissolved small portions to extract DNA from the bacteria that once made up people’s microbiomes.

Snow’s colleagues reconstructed 181 ancient microbial genomes and compared them to hundreds of modern stool samples from eight countries. Posted in May Nature volume, the results indicated that today’s human microbiomes are much less diverse, likely due to antibiotics, processed foods, and improved sanitation.

“It’s a little mind-boggling to begin to realize how [gut flora] we don’t have any more, ”says Snow. The revelation could improve health today, as reduced microbiome diversity can contribute to diseases like obesity, diabetes, and autoimmune diseases.