Tag Archives: Ancient DNA

Denisovan(?) remains in the garden

On the edge of the small town of Lingjing near Xuchang City in Henan Province, China, local people have long practiced intensive vegetable gardening because the local soil is naturally irrigated by the water table beneath the flood plain deposits of the Yinghe River. In the mid 1960s, around a small spring, they began to find dozens of small stone tools together with animal bones. Only in 2005, after the spring had stopped flowing, did systematic excavation begin (Li, Z.-Y. et al. 2017. Late Pleistocene archaic human crania from Xuchang, China. Science, v. 355, p. 969-972; doi: 10.1126/science.aal2482) About 3.5 m below the surface tools and bone fragments, including one with a carved representation of a bird, occurred just above the base of the modern soil profile. Radiocarbon dating of charcoal from the layer clustered around 13 500 years ago, just before the start of the Younger Dryas cooling episode; probably products of modern humans, although no human remains were found in the layer. Continued excavation penetrated sediments free of fossils and tools down to a depth of 8 m, when stone tools and bone fragments began to turn up again through the lowest 2 m of sediment. Optically stimulated luminescence (OSL) dating of mineral grains, which shows the last time that sediments were exposed to sunlight, produced much older dates between 78 to 123 ka. The thousands of stone flakes and cores, and cut marks on the animal bones found through the fossil-rich layer suggests that this was a site long used for tool making and food preparation, that had begun in the last interglacial period. Among the bones were fragments of the crania of as many as five individual humans.

Who were they? Their age range is tens of thousands of years before anatomically modern humans began to migrate into east Asia, so they are likely to have been an earlier human group. Homo erectus is known to have inhabited China since as early as 1.6 Ma ago and may be a possibility. The other possible group are the Denisovans, known only from their DNA in a small finger bone from a cave in eastern Siberia. Fragments of Denisovan DNA are famously present in that of many living indigenous people from eastern Asia, Melanesia and the Americas, but hardly at all in west Asians and Europeans. They also interbred with Neanderthals and may share a common ancestor with us and them, who lived about 700 ka ago.

Map showing the proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia. (Credit: Sankararaman et al./Current Biology 2016;  http://dx.doi.org/10.1016/j.cub.2016.03.037)

Map showing the proportion of the genome inferred to be Denisovan in ancestry in non-Africans. The color scale ranges from black – 0, through greens – present to red – highest . (Credit: Sankararaman et al./Current Biology 2016; http://dx.doi.org/10.1016/j.cub.2016.03.037)

Unfortunately the human bones are completely fragmented and lack any teeth, jaw bones or elements of the face. However, the Chinese-US team used sophisticated computer refitting of CT-scanned fragments to reconstruct two of the crania, revealing one individual with prominent brow ridges and a flat-topped skull extended towards the back, similar to that of Neanderthals but with a much larger brain than H. erectus. The semi-circular canals associated with the ears, but used in balancing, are well preserved and also resemble those of Neanderthals. Yet east Asia has yielded not a single Neanderthal fossil. Could these be the elusive Denisovans? Even if more diagnostic bones turn up, especially teeth, such is the state of late hominin taxonomy that only DNA will provide definitive results: the Denisovans are defined entirely by DNA. The authors, perhaps wisely, do not speculate, but others may not be able to resist the temptation.

For more information on recent human evolution see here.

Gibbons, A. 2017. Close relative of Neandertals unearthed in China. Science, v. 355, p. 899; doi: 10.1126/science.355.6328.899