Pleistocene sediment DNA from Denisova Cave
Sediment DNA tracks 300,000 years of hominin and animal presence at
Denisova Cave

Date:
June 23, 2021
Source:
Max Planck Institute for Evolutionary Anthropology
Summary:
Researchers have analyzed DNA from 728 sediment samples from
Denisova Cave. Their study provides unprecedented detail about
the occupation of the site by both archaic and modern humans over
300,000 years. The researchers detected the DNA of Neandertals and
Denisovans, the two forms of archaic hominins who inhabited the
cave, and the DNA of modern humans who appeared around the time
of the emergence of an archaeological culture called the Initial
Upper Paleolithic around 45,000 years ago.



FULL STORY ========================================================================== Denisova Cave is located in the Altai Mountains in southern Siberia and
is famous for the discovery of Denisovans, an extinct form of archaic
humans that is thought to have occupied large parts of central and eastern Asia. Neandertal remains have also been found at the site, as well as
a bone from a child who had a Neandertal mother and Denisovan father,
showing that both groups met in the region. However, only eight bone
fragments and teeth of Neandertals and Denisovans have been recovered so
far from the deposits in Denisova Cave, which cover a time span of over
300,000 years. These are too few fossils to reconstruct the occupational history of the site in detail, or to link the different types of stone
tools and other artefacts found in Denisova Cave to specific hominin
groups. For example, the discovery of jewelry and pendants typical
of the so-called Initial Upper Palaeolithic culture in approximately 45,000-year-old layers has prompted debates as to whether Denisovans, Neandertals or modern humans were the creators of these artefacts.


========================================================================== Michael Shunkov of the Siberian Branch of the Russian Academy of Sciences,
who leads the excavations at Denisova Cave, assembled an interdisciplinary
team of archaeologists, geneticists, geochronologists and other scientists
to study this unique site. The team has now performed the largest analysis
ever of sediment DNA from a single excavation site. "The analysis of
sediment DNA provides a wonderful opportunity to combine the dates
that we previously determined for the deposits in Denisova Cave with
molecular evidence for the presence of people and fauna," says Richard
'Bert' Roberts from the University of Wollongong in Australia. The team
of geochronologists led by him and Zenobia Jacobs collected more than
700 sediment samples in a dense grid from the exposed sediment profiles
in the cave. "Just collecting the samples from all three chambers in the
cave, and documenting their precise locations, took us more than a week," Jacobs says.

When the samples arrived at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Elena Zavala, the lead author of the study,
spent another two years in the lab to extract and sequence small traces
of ancient hominin and animal mitochondrial DNA from this huge collection
of samples.

"These efforts paid off and we detected the DNA of Denisovans, Neandertals
or ancient modern humans in 175 of the samples," Zavala says.

When matching the DNA profiles with the ages of the layers, the
researchers found that the earliest hominin DNA belonged to Denisovans, indicating that they produced the oldest stone tools at the site between 250,000 and 170,000 years ago. The first Neandertals arrived towards the
end of this time period, after which both Denisovans and Neandertals
frequented the site -- except between 130,000 and 100,000 years ago,
when no Denisovan DNA was detected in the sediments. The Denisovans
who came back after this time carried a different mitochondrial DNA,
suggesting that a different population arrived in the region.

Modern human mitochondrial DNA first appears in the layers containing
Initial Upper Palaeolithic tools and other objects, which are much
more diverse than in the older layers. "This provides not only the first evidence of ancient modern humans at the site, but also suggests that they
may have brought new technology into the region with them," says Zavala.

The scientists studied animal DNA and identified two time periods where
changes occurred in both animal and hominin populations. The first,
around 190,000 years ago, coincided with a shift from relatively warm (interglacial) conditions to a relatively cold (glacial) climate, when
hyaena and bear populations changed and Neandertals first appeared in the
cave. The second major change occurred between 130,000 and 100,000 years
ago, along with a shift in climate from relatively cold to relatively
warm conditions. During this period, Denisovans were absent and animal populations changed again.

"I believe that our Russian colleagues who excavate this amazing site
have set the standards for many future archaeological excavations with
their careful collection of many samples from each archaeological
layer for DNA analysis," says Svante Pa"a"bo who initiated the
study with the Russian team. "Being able to generate such dense
genetic data from an archaeological site is like a dream come true,
and these are just the beginnings," says Matthias Meyer, the senior
author on the study. "There is so much information hidden in sediments
-- it will keep us and many other geneticists busy for a lifetime." ========================================================================== Story Source: Materials provided by Max_Planck_Institute_for_Evolutionary_Anthropology. Note: Content may
be edited for style and length.


========================================================================== Journal Reference:
1. Elena I. Zavala, Zenobia Jacobs, Benjamin Vernot, Michael
V. Shunkov,
Maxim B. Kozlikin, Anatoly P. Derevianko, Elena Essel, Cesare
de Fillipo, Sarah Nagel, Julia Richter, Fre'de'ric Romagne',
Anna Schmidt, Bo Li, Kieran O'Gorman, Viviane Slon, Janet Kelso,
Svante Pa"a"bo, Richard G.

Roberts, Matthias Meyer. Pleistocene sediment DNA reveals
hominin and faunal turnovers at Denisova Cave. Nature, 2021; DOI:
10.1038/s41586-021- 03675-0 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/06/210623113857.htm

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