New DNA analysis techniques reveal twists in Neanderthal history

April 15, 2021
More detail has been filled in for the history of Eurasian Neanderthals. (AP Photo/Martin Meissner)

More detail has been filled in for the history of Eurasian Neanderthals. (AP Photo/Martin Meissner)

Researchers have further filled out the history of Eurasia's ancient Neanderthals, using crucial genetic evidence previously hidden in cave sediments to shed light on the hominins' population history and evolution over thousands of years.

In an article published April 15 in Science, a team of 34 researchers reported the results of newly developed DNA enrichment techniques that allowed them to reconstruct missing pieces of Neanderthal population genetics using trace amounts of nuclear DNA recovered from cave sediments.

Nuclear DNA, which is most readily available from fossilized bones and teeth, hadn't before been successfully extracted and analyzed from the mix of material deposited on cave floors, limiting prior research aimed at uncovering genetic insights from the archaic humans known to have lived there.

Complete or partial nuclear genome sequences have been recovered from just 23 archaic human individuals to this point, according to the paper, including 18 Neanderthals, the species widely considered modern humanity's closest genetic relatives.

"There are many sites … where we know Neanderthals lived, because we find their tools, the animals they ate, etc.," corresponding author Benjamin Vernot told The Academic Times. "From those things we can learn a lot about what they did — but without the DNA, it's hard to say who they are, and how they related to other groups."

By recovering nuclear DNA from what's lying at the bottom of a cave, he continued, the researchers could contribute important new pieces to the Neanderthal family tree — a method that could pave the way for further breakthroughs going forward.

"Fossils are rare … but dirt is everywhere," Vernot said. "I think this will allow us and other researchers to dramatically expand the number of sites where we can learn about ancient people."

The researchers focused their analyses on three Paleolithic cave sites, all with evidence of hominin mitochondrial DNA in their respective sediments. While such DNA can be recovered from sediments dating to that period, they noted, it isn't always reflective of the complete population history.

"Nuclear DNA contains far more information, but its retrieval from sediments presents substantial challenges," the researchers wrote.

The Denisova Cave and Chagyrskaya Cave, both located in the Altai Mountains of central Asia, were chosen to enable comparisons to previously discovered nuclear genomes generated from bones from these sites. Spain's Galeria de las Estatuas, a cave where hundreds of stone tools but only one Neanderthal fossil has been found, represented a location where sediment analysis could be the only way to learn about the genetic makeup of its ancient inhabitants.

To recover nuclear DNA from sediments from each site, the researchers designed a test to check for DNA fragments that overlapped any of 1.6 million single nucleotide polymorphisms, or biological markers indicating genetic variation. They took steps to cut down on mismapping DNA that didn't come from hominin species such as Neanderthals or Denisovans.

"In this case, what we did is develop a method to place each sediment sample on the overall Neanderthal tree" as defined by three preexisting genomes mapped with fossil remains, Vernot said. 

Depending on where a sample landed on the tree, he added, the researchers could infer who the individuals represented in that sample were related to and whether a given cave had hosted more than one population group.

The researchers discovered evidence both from individual Neanderthal genomes and from sediment samples that suggests two separate "radiations" of Neanderthal populations occurred, one about 135,000 years ago and the other around 100,000 to 115,000 years ago. Vernot said the evidence sheds light on how various Neanderthal lineages rose and fell over time.

"It means that at two points in Neanderthal history, it looks like you have most Neanderthals disappearing, and only one lineage surviving," he said. "We don't know why that happened — it could just be chance, or it could be that some event wiped out most of the Neanderthals."

Experts don't know what caused Neanderthals' ultimate extinction, although new research continues to refine science's understanding of the hominins' migration patterns and evolution. Research published in March estimated that the archaic humans disappeared from Northwestern Europe about 44,200 to 40,600 years ago, while a study released earlier in April revealed that modern Homo sapiens may have been mixing with Neanderthals more often than was widely assumed.

Because there was a period when modern people lived alongside Neanderthals, researchers have sometimes struggled to determine exactly who lived at various sites and was responsible for making the tools found there.

Vernot said his and his co-authors' new techniques for studying sediment DNA could help scientists solve that problem, allowing them to go to "literally hundreds" of sites and figure out who lived where.

"There were lots of tools that were made [about] 50,000 years ago, where we don't know if they were made by modern humans, or by Neanderthals," he said. "This will help us to figure that out."

The article "Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments," published April 15 in Science, was authored by Benjamin Vernot, Elena I. Zavala, Fabrizio Mafessoni, Frédéric Romagné, Alice Pearson, Martin Petr, Steffi Grote, Elena Essel, David López Herráez, Sarah Nagel, Birgit Nickel, Julia Richter, Anna Schmidt, Benjamin Peter, Janet Kelso and Matthias Meyer, Max Planck Institute for Evolutionary Anthropology; Asier Gómez Olivencia, Universidad del País Vasco-Euskal Herriko Unibertsitatea, Sociedad de Ciencias Aranzadi, Donostia, and Centro Mixto UCM-ISCIII de Evolución y Comportamiento; Zenobia Jacobs, Bo Li and Richard G. Roberts, University of Wollongong; Viviane Slon, Max Planck Institute for Evolutionary Anthropology, Tel Aviv University; Nohemi Sala and Adrián Pablos, Centro Mixto UCM-ISCIII de Evolución y Comportamiento and CENIEH; Arantza Aranburu, Universidad del País Vasco-Euskal Herriko Unibertsitatea and Sociedad de Ciencias Aranzadi, Donostia; José María Bermúdez de Castro, CENIEH; Eudald Carbonell, Universitat Rovira i Virgili; Maciej T. Krajcarz, Polish Academy of Sciences; Andrey, I. Krivoshapkin, Russian Academy of Sciences and Novosibirsk State University; Kseniya A. Kolobova, Maxim B. Kozlikin, Michael V. Shunkov and Anatoly P. Derevianko, Russian Academy of Sciences; Bence Viola, University of Toronto; Juan-Luis Arsuaga, Centro Mixto UCM-ISCIII de Evolución y Comportamiento and Universidad Complutense de Madrid.

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