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Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains
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Ancient pathogen DNA in human teeth and petrous bones.

Ashot Margaryan1,2, Henrik B Hansen1, Simon Rasmussen3

  • 1Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark.

Ecology and Evolution
|April 3, 2018
PubMed
Summary

Ancient pathogen DNA is more readily recovered from teeth than petrous bones. While petrous bones offer high endogenous DNA for genomics, teeth provide greater microbial diversity for pathogen detection in ancient DNA studies.

Keywords:
Yersinia pestisancient DNAancient pathogensmetagenomicspetrous boneplague

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Area of Science:

  • Paleogenomics
  • Microbial Evolution
  • Bioarchaeology

Background:

  • Ancient DNA (aDNA) studies reveal pathogen evolution and history.
  • Teeth and postcranial bones are common sources for pathogen aDNA.
  • Petrous bones are favored for high endogenous DNA yield in ancient genomics.

Purpose of the Study:

  • To compare pathogen DNA recovery potential between teeth and petrous bones.
  • To evaluate the metagenomic yield from these two skeletal elements.

Main Methods:

  • Shotgun sequencing of DNA extracted from teeth and petrous bones of five ancient skeletons.
  • Comparative metagenomic analysis of teeth and petrous bones from 10 historical skeletons.

Main Results:

  • Four of five plague victims showed detectable *Yersinia pestis* DNA in teeth; petrous bones yielded no pathogen DNA.
  • Teeth exhibited significantly higher microbial diversity, including pathogenic and oral taxa, compared to petrous bones.
  • *Yersinia pestis* DNA was detected in teeth but not in petrous bones.

Conclusions:

  • Petrous bones are excellent for endogenous DNA but limited for pathogen metagenomics.
  • Teeth offer superior potential for recovering diverse microbial DNA, including pathogens.
  • Sampling strategies for aDNA projects must consider this trade-off between endogenous DNA yield and metagenomic potential.