Mixed with dirt, traces of prehistoric human DNA

SIFTING THROUGH clay and sand scraped from the floors of caves, German researchers have managed to isolate ancient human DNA — without turning up a single bone. Their technique promises to open new avenues of research into human prehistory.

“It’s a bit like discovering that you can extract gold dust from the air,” said Adam Siepel, a population geneticist at Cold Spring Harbor Laboratory. “An absolutely amazing and exciting paper,” said David Reich, a Harvard genetics professor.

Until recently, the only way to study the genes of ancient humans like the Neanderthals and their cousins, the Denisovans, was to recover DNA from fossil bones. But they are hard to find, which has greatly limited research — the only Denisovan bones and teeth that scientists have, for example, come from a single cave in Siberia.

Looking for these genetic signposts in sediment has become possible only in the last few years, with recent developments in technology, including rapid sequencing of DNA. Although DNA sticks to minerals and decayed plants in soil, scientists did not know whether it would ever be possible to fish out gene fragments that were tens of thousands of years old and buried deep among other genetic debris.

Bits of genes from ancient humans make up just a minute fraction of the DNA floating around in the natural world. The German scientists, led by Matthias Meyer at the Max Planck Institute for Developmental Biology in Tübingen, have spent years developing methods to find DNA even where it seemed impossibly scarce and degraded.

The study involved searching for ancient DNA in four caves in Eurasia where humans were known to have lived between 14,000 and 550,000 years ago. Dr Meyer and his colleagues figured out which DNA in the cave sediment was prehistoric by looking for telltale signs of degradation at the ends of the molecules.

They then plucked out DNA from Neanderthals and Denisovans by using molecular hooks to snare genes in mitochondria — the cells’ energy factories — that are unique to these humans.

The scientists also built a robotic system to analyse the samples quickly; the old way, pipetting by hand, required several days to analyse only a fraction as many samples. The efficiency was important because from different dirt samples, they recovered between 5,000 and 2.8 million DNA fragments. The number of DNA fragments per sample that were from ancient humans was minuscule and ranged from 0 to 8,822, depending on the site in the cave.

— THE NEW YORK TIMES