Ancient DNA From Cave Dirt

Usually, ancient DNA samples come from the interior of teeth for tooth enamel protects them from the elements for thousands or even tens of thousands of years. But, improved methods are making it possible to recover ancient DNA from less well guarded sources. Basically, scientists can now do CSI class forensic DNA work from scenes that are up to 240,000 years old.

The fragments, predominantly of mtDNA, aren't necessarily good enough to do much more than identify a species of the contributing source of the DNA. But, these scraps can put better definition on the geographic and temporal range of hominin and other mammal species.

This is particularly notable in the case of the Denisova cave, where these scraps add considerably to the time period in which we can document the existence of the archaic hominin species named after the cave, even though we will don't know what Denisovans looked like because we have no reasonably complete skeletal remains.

Slon’s work continues that tradition—she found Denisovan DNA in sediment that’s far older than any of the unearthed fossils. “It’s evidence that Denisovans occupied the cave for tens of thousands of years earlier than we thought,” she says.

The quotation above is from a story in The Atlantic that profiles the results in the Science article from a layman's perspective. The Denisovan bones that were found in 2008 were 30,000 to 50,000 years old. The new Denisovan ancient DNA was found in a Middle Paleolithic layer (MP) as opposed to a Lower Paleolithic layer (LP). 

Conventionally, the Upper Paleolithic is about 50,000 to 10,000 years ago (corresponding to pre-farming Out of Africa and behaviorally modern humans more generally), the Middle Paleolithic is about 300,000 to 50,000 years ago (basically, the Neanderthal years in Europe and the rise of modern humans in Africa), and, the Lower Paleolithic is about 3,300,000 to 300,000 years ago (basically, the pre-Neanderthal, pre-modern human time period in which there were still archaic hominids of some kind). 

The dawn of farming in the Neolithic era marks the end of the Upper Paleolithic era, which yields to the Chalcolithic era (the Copper Age) (ca. 3600 BCE to ca. 2500 BCE), the Bronze Age (ca. 2500 BCE to 1200 BCE), the Iron Age (ca. 1200 BCE to 500 CE), the Middle Ages (ca. 500 CE to 1500 CE), and the Modern Period (ca. 1500 CE to the present). These technologically defined time periods, however (especially the Neolithic Revolution which takes about 4000 years to spread from its point of inception in the Fertile Crescent to the farthest reaches of Europe) reach different places at different times.

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found.

Viviane Slon, et al., "Neandertal and Denisovan DNA from Pleistocene sediments" Science (April 27, 2017).