Skip to main content
Premium Trial:

Request an Annual Quote

Ancient Mammal Genetic Sequences Detected in Prehistoric Soil Samples

NEW YORK (GenomeWeb) – A new study is highlighting the feasibility of teasing out genetic sequences from long-dead mammal — including hominins such as Neanderthals and Denisovans — from DNA left behind in ancient soil sediments.

Members of an international team led by investigators in Germany used a combination of hybrid capture and shotgun sequencing to detect mitochondrial DNA sequences from ancient hominins and other mammals in dozens of Pleistocene sediment samples collected at sites in France, Belgium, Spain, Croatia, and Russia.

"We show that mtDNA can be efficiently retrieved from many Late and some Middle Pleistocene cave sediments using hybridization capture," first author Viviane Slon, an evolutionary genetics researcher at the Max Planck Institute for Evolutionary Anthropology, and her co-authors wrote in their new Science study. "Encouragingly, this is possible also for samples that were stored at room temperature for several years. Sediment samples collected for dating, site formation analyses, or the reconstruction of ancient environments at sites where excavations are now completed can thus be used for genetic studies."

Ancient hominin fossils are relatively rare finds, the team noted. But the information gleaned from them can have enormous implications for understanding human evolution, population histories, and relationships with other hominins, prompting interest in strategies to expand available ancient DNA sample sources — including sediments —for genetic analysis.

While past studies suggested that DNA does linger in soil, the authors noted that bacterial DNA can overwhelm samples, making it tricky to successfully pick out mammalian DNA and match it to its source.

For their new proof-of-principle analysis, the researchers relied on a strategy that involved extracting DNA from sediment samples and capturing mammalian DNA with probes matched to hundred of mitochondrial DNA sequences. From there, they did shotgun sequencing on single-stranded DNA libraries and analyzed the resulting sequences by binning taxonomically related reads.

When the team applied its approach to 85 Pleistocene-aged sediment samples — ranging in age from around 14,000 years old to more than 550,000 years old from seven European sites — it generated reads for anywhere from 14 to more than 50,000 mammalian DNA fragments per library. Authentic ancient reads were subsequently validated based on nucleotide substitution patterns and read distribution across the relevant mitochondrial genome.

Overall, the researchers identified mammalian mtDNA sequences in 14 of the 33 Middle Pleistocene samples and 47 of 52 Late Pleistocene samples. And across the samples, they saw representatives from a dozen mammal families, including animals that appeared to be related to deer, dogs, horses, hyenas, ruminants, and elephants. Using genetic variation patterns and other clues, the team traced reads back to ancient mammals such as woolly rhinos, cave hyenas, and Eastern European cave bears.

The sampled sediment sites appeared to have been home to hominins, too: the researchers repeated their hybrid capture and sequencing scheme with human-specific mtDNA probes, uncovering hominin DNA in samples from El Sidrón, Denisova, Trou Al'Wesse, and Chagyrskaya caves.

"Although compared to other animals, hominins constitute a rare taxon at most sites, we were able to detect Neanderthal DNA in the sediments of four of the six sites containing Late Pleistocene layers," the authors wrote. "The automation of laboratory procedures to generate DNA libraries and isolate DNA by hybridization capture now makes it possible to undertake large-scale studies of DNA in sediments."

Filed under