Ancient human DNA recovered from a Palaeolithic pendant

[Tautalus]

[h=2]Abstract[/h]Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000–25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.

See https://www.nature.com/articles/s41586-023-06035-2

 

[Palermo Trapani]

Thanks, looks like an interesting paper. Will take a look at it.

 

[Duarte]

Thanks Taulatus.

The comparative analysis of the human nuclear DNA extracted from this deer tooth pendant with human DNA of ancient and modern populations is interesting:

“For nuclear DNA analysis, hybridization capture was performed using libraries from the second and third 90 °C phosphate fractions, targeting sites in the human genome that are known to be polymorphic in modern or archaic humans and that are located in regions of high sequence divergence between humans and other mammals⁸. Sequence information was obtained for 336,429 of these sites (71.5% of the sites targeted), with estimates of present-day human and faunal contamination both below 1%. Comparisons with present-day human populations²⁶ using ƒ3-statistics and D-statistics^27,28 show high affinities to Native Americans (Extended Data Fig. 5). When projected into a principal component analysis with other ancient human individuals (Fig. 3c), DCP1 falls within a group of Ancient North Eurasian individuals from further east in Siberia, which includes the approximately 24 ka Mal’ta 1 and the approximately 17 ka Afontova Gora 3 individuals^29,30. Both of these individuals are genetically closer to DCP1 than non-Ancient North Eurasian individuals when tested with D-statistics (Extended Data Fig. 6b), and all three show similar affinities to ancient Siberians and Native Americans with ƒ3-statistics and D-statistics (Extended Data Fig. 6a,c). In addition, shotgun data were produced from one of the libraries to allow a comparison of sequence coverage for the X chromosome and the autosomes, which is compatible with the human DNA in the 90 °C fraction originating predominantly from a female individual (Fig. 3b and Supplementary Information 7).”

 

[Palermo Trapani]

Duarte:

Thanks for posting that part of the paper. I noticed that part as well, that is this ancient DNA (DCP1) is close to Mal'ta 1 from 24k years ago, further supporting the Ancient North Eurasian cluster documented back in 2013.

 

[celtiberian-II]

Significant work. Is there information extracted from the DNA about skin, eye and hair colour of this ANE woman?