Dirty DNA

SCIENCE

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Discussion Ideas

A genuinely exciting new study documents how scientists extracted ancient DNA from the dirt of ancient caves. What is DNA?
- DNA (deoxyribonucleic acid) is a molecule found in almost every living organism. DNA contains specific genetic information about that organism. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).
  - In this study, researchers analyzed mitochondrial DNA. “Unlike the rest of our genes, mitochondrial DNA is inherited only from our mothers—and it generally doesn’t undergo recombination. Even though hominin mitochondrial DNA is made up of more than 16,000 individual genetic ‘letters,’ constituting 37 different genes, in terms of inheritance, it behaves more like a single, extremely short gene. Mitochondrial DNA is inherited as a single unit without being broken up.” This makes it really, really valuable to geneticists.

From cave sediments, researchers extracted the DNA of Neanderthals and Denisovans. Who are these hominins? Take a look at the graphic above for some help.
- Neanderthals and Denisovans are both extinct species related to us—modern humans (Homo sapiens).
  - Fossils and tool evidence of Neanderthals have been found throughout Europe and Central and Northern Asia. Neanderthals coexisted with ancient Homo sapiens. We know this because today, most Europeans and Asians have between 1% and 2% Neanderthal DNA.
  - Fossil evidence of Denisovans has only been found in a single location, Denisova Cave in Central Siberia, Russia. Like Neanderthals, Denisovans also existed with ancient Homo sapiens. Today, most Melanesians and Aboriginal Australians have about 3% to 5% Denisovan DNA.
  - The good folks at the Genographic Project explain: “According to one theory, Neanderthals, Denisovans, and modern humans are all descended from the ancient human Homo heidelbergensis. Between 300,000 to 400,000 years ago, an ancestral group of H. heidelbergensis left Africa and then split shortly after. One branch ventured northwestward into West Asia and Europe and became the Neanderthals. The other branch moved east, becoming Denisovans … Homo sapiens—our ancestors—did not begin their own exodus from Africa until about 60,000 years ago.”

Extracting DNA from dirt is a breakthrough. How do archaeologists, paleontologists, and geneticists usually obtain DNA from Neanderthals, Denisovans, and other ancient hominins?
- DNA is usually extracted from bone, which can be very rare. (The entire Denisovan population, for instance, is represented by two teeth and part of a finger.) The procedure requires the destruction of part of the bone itself. “In a lot of cases, you can get bones, but not enough,” says Hendrik Poinar, an evolutionary geneticist. “If you just have one small piece of bone from one site, curators do not want you to grind it up.”

By some accounts, the sediment study recovered a whopping 2.8 million DNA fragments. Only a fraction of those fragments (no more than 8,800) were of ancient hominins. Where did the rest of that DNA come from?
- Plants, other animals, fungi, microbes … Any living thing that was ever in those caves could have left DNA.

How did ancient hominins leave their DNA in the caves?
- Mineral and organic components in sediments can bind DNA even as the source of the DNA (bones, blood, etc.) vanishes.
- Scientists knew where they were looking. (Caves can lack light, but the archaeology here was not a shot in the dark!) The 85 sediment samples were taken from seven caves where Neanderthals, Denisovans, and genetically modern humans lived for thousands of years.
- Most likely, the ancient DNA fragments are traces of everyday life in the Pleistocene. DNA could come from blood, urine, saliva, feces, hair, or bone. Scientists say the DNA concentration hints at it “originating from excreta or the decay of soft tissue.”
- Less likely but more gruesome is the possibility that the DNA fragments are traces of death. Researchers found a lot of hyena DNA in the caves. “Maybe the hyenas were eating human corpses outside the caves, and went into the caves and left feces there, and maybe entrapped in the hyena feces was human DNA.”

How might this method of finding DNA in dirt expand archaeological activities?
- Researchers hope it encourages scientists to look for evidence of ancient hominins at open-air sites, not just isolated and protected sites like caves. “If it worked, it would provide a much richer picture of the geographic distribution and migration patterns of ancient humans, one that was not limited by the small number of bones that have been found,” says geneticist David Reich. “That would be a magical thing to do.”
- The process could change how archaeologists excavate sites. “Save the dirt!” says one paleoecologist.

What dirt are archaeologists digging up next?
- They’re going deep. The team that extracted the DNA from cave dirt is now sampling seafloor sediments off the coast of Great Britain, in search of ancient settlements that might have been submerged following the last glacial period.