A minimally destructive protocol for DNA extraction from ancient teeth

Harney, Éadaoin; Cheronet, Olivia; Fernandes, Daniel; Sirak, Kendra; Mah, Matthew; Bernardos, Rebecca; Adamski, Nicole; Broomandkhoshbacht, Nasreen; Lawson, Ann Marie; Oppenheimer, Jonas; Stewardson, Kristin; Zalzala, Fatma; Anders, Alexandra; Candilio, Francesca; Constantinescu, Mihai; Coppa, Alfredo; Ciobanu, Ion; Dani, János; Gallina, Zsolt; Genchi, Francesco; Nagy, Emese Gyöngyvér; Hajdu, Tamás; Hellebrandt, Magdolna; Horváth, Antónia; Király, Ágnes; Kiss, Krisztián; Kolozsi, Barbara; Kovács, Péter; Köhler, Kitti; Lucci, Michaela; Pap, Ildikó; Popovici, Sergiu; Raczky, Pál; Simalcsik, Angela; Szeniczey, Tamás; Vasilyev, Sergey; Virag, Cristian; Rohland, Nadin; Reich, David; Pinhasi, Ron

doi:10.1101/gr.267534.120

Cited by 37 publications

(32 citation statements)

References 46 publications

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“…DNA was extracted from its cementum using the methods described in ref. 63 with a modified incubation time of ~18 h. The library was prepared according to the protocol in ref. 48 with the modifications from ref.…”

Section: Methodsmentioning

confidence: 99%

Grey wolf genomic history reveals a dual ancestry of dogs

Bergström

Stanton

Taron

et al. 2022

Nature

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The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

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Section: Methodsmentioning

confidence: 99%

Grey wolf genomic history reveals a dual ancestry of dogs

Bergström

Stanton

Taron

et al. 2022

Nature

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“…Most items were sampled using the new minimally-destructive extraction procedure presented here. It is based on the protocol described by (Harney et al, 2021) with a number of modifications detailed below.…”

Section: Ancient Dnamentioning

confidence: 99%

“…Here we present the results of the first aDNA analysis of a diverse set of 42 antler and bone hunting weapons, including also some domestic tools from Palaeolithic and Neolithic sites (c. 39-8 ka) from South-Western Europe (France, Spain), Central Europe (Austria, Czech Republic), the Caucasus (Georgia), and the Levant (Lebanon, Israel). We present and utilise a minimally-invasive aDNA sampling method originally developed for human teeth (Harney et al, 2021) that we optimised for osseous objects. The method is combined with a new customcreated set of capture baits for the mitochondrial DNA of 54 mammalian species.…”

Section: Introductionmentioning

confidence: 99%

A minimally-invasive method for ancient DNA sampling of Prehistoric bone and antler tools and hunting weapons

Tejero

Cheronet

Gelabert

et al. 2023

Preprint

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Internal and external bony tissues from diverse mammalian taxa are one of the primary animal raw materials exploited for technical and symbolic purposes by Eurasian Upper Palaeolithic hunter-gatherers. Identifying the source species used for osseous raw material is critical to gain insights into these populations' behaviour, technology, and subsistence. The study of osseous tools has advanced in the last few years by combining archaeological and biomolecular methods. Ancient genomics opens many new analytical opportunities. Ancient DNA (aDNA) can provide a wealth of information about the animal sources of these objects. Unfortunately, aDNA analyses often involve destructive sampling. Here, we develop and apply a minimally-invasive aDNA sampling method for an assemblage of 42 prehistoric hunting weapons and tools from various Eurasian archaeological sites. We evaluated the impact of our approach on the specimens visually, microscopically and through Micro-CT scans. The surface impacts are marginal, ranging from 0.3-0.4 mm. Using a custom-made DNA capture kit for 54 mammalian species, we obtained sufficient aDNA to identify the taxa of 33% of the objects. For one of the tools, we recovered enough endogenous aDNA to infer the genetic affinities of the individual. Our results also demonstrate that ancient antler, one of the primary raw materials used during a large part of prehistory, is a reliable source of aDNA. Our minimally-invasive aDNA sampling method is therefore effective while preserving osseous objects for potential further analyses: morphometric, technical, genetic, radiometric and more.

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“…Researchers should develop a strategy through consultation with other stakeholders to balance concerns about protecting remains with their scientific analysis. Researchers should not collect human remains without training in best practice techniques to minimize damage while maximizing yield of useable data 11,12,[73][74][75][76] . Researchers should not sample more material than necessary to be able to address their scientific questions, should provide documentation to those responsible for human remains noting when sampling occurred, and should report negative results to prevent repeated analysis using similar methods on remains with poor DNA preservation.…”

Section: Five Globally Applicable Guidelinesmentioning

confidence: 99%

Ethics of DNA research on human remains: five globally applicable guidelines

Alpaslan-Roodenberg

Anthony

Babiker

et al. 2021

Nature

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We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3)

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A minimally destructive protocol for DNA extraction from ancient teeth

Cited by 37 publications

References 46 publications

Grey wolf genomic history reveals a dual ancestry of dogs

Grey wolf genomic history reveals a dual ancestry of dogs

A minimally-invasive method for ancient DNA sampling of Prehistoric bone and antler tools and hunting weapons

Ethics of DNA research on human remains: five globally applicable guidelines

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