Detecting mitochondrial DNA from Neaderthal and Denisoain DNA in “cave sediments”

Today, modern humans are called Homo sapiens sapiens, which have survived from earlier tribes of hominins such as Homo sapiens neaderthaliensis that had lived in various regions of the planet at least 25,000 years ago. Scientists can now discover what hominids existed long ago, where they were located, and their dispersal to other geographic areas; these discoveries have relied mostly by means of whole-genome sequencing (WGS) of DNA fragments that can be isolated from fossils such as teeth and bones. This research led, for example, to the discovery of Homo sapiens denisova, a previously unknown group of archaic hominins in Asia who were distantly related to Neanderthals.

Neanderthals, the better known of the two species, left Africa about 300,000 years ago and settled in Europe and parts of western Asia. The Denisovans are a much more recent addition to the human family tree. In 2008, paleo-anthropologists digging in a cave in southern Siberia unearthed a 40,000-year-old adult tooth and an exquisitely preserved fossilized fifth-finger bone that had belonged to a young girl who had died between ages five and seven years old. However, hominin fossils are rare. Authors [see attached article] therefore chose to investigate whether hominin DNA may survive in sediments [translation: fossilized fecies] at archaeological sites in the absence of macroscopically visible skeletal remains.

Mineral and organic components in fecal material can bind DNA, and amplification of short stretches of mitochondrial (mt) or plant chloroplast DNA from sediments by polymerase chain reaction (PCR) has been used to establish the past presence of animals and plants at several archeological sites. More recently, DNA extracted from sediments has been converted to DNA libraries, from which DNA fragments were sequenced directly (“shotgun” sequencing); this approach is preferable to PCR, because it allows the entire sequence of DNA fragments to be determined. This is important, because it makes it possible to detect cytosine (C) to thymine (T) substitutions near the ends of DNA fragments, which are caused by the deamination of cytosine bases, and which indicate that the DNA is of ancient origin. However, the abundance of bacterial DNA in sediments and the difficulty in assigning short nuclear DNA sequences to mammalian taxa limit the utility of shotgun sequencing for analyzing DNA from sediments.

Using targeted enrichment of mitochondrial DNA (mtDNA), authors demonstrate [in attached article] that cave sediments of excrement represent a rich source of ancient mammalian DNA –– that often includes traces of hominin DNA, even at sites and in layers where no hominin tooth or fossil remains have been discovered. By automation-assisted screening of numerous sediment samples, authors detected Neanderthal DNA in eight archeological layers from four caves in Eurasia. In Denisova Cave, authors retrieved Denisovan DNA in a Middle Pleistocene layer (781,000 to 126,000 years ago) near the bottom of the stratigraphy. This approach opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains have ever been found..!!

Science 12 May 2o17; 356: 605–608

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