Ancient DNA

@article{Hofreiter2001AncientD,
  title={Ancient DNA},
  author={Michael Hofreiter and David Serre and Hendrik N. Poinar and Melanie Kuch and Svante P{\"a}{\"a}bo},
  journal={Nature Reviews Genetics},
  year={2001},
  volume={2},
  pages={353-359}
}
DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied. 

Isolation and analysis of DNA from archaeological, clinical, and natural history specimens.

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Evaluating Neanderthal Genetics and Phylogeny

Using Bayesian inference and the largest dataset to date, strong support is found for a monophyletic Neanderthal clade outside the diversity of contemporary humans, in agreement with the expectations of the Out-of-Africa replacement model of modern human origin.

Human evolution: a tale from ancient genomes

Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time.

The fate of European Neanderthals: results and perspectives from ancient DNA analyses

An analysis of additional Neanderthal and early modern human remains from Western and Central Europe do not provide any evidence of gene flow between the two groups, and under reasonable assumptions of human demography, these data rule out a major genetic contribution by Neanderthals to the modern human gene pool.

Conserved primers for DNA barcoding historical and modern samples from New Zealand and Antarctic birds

Two sets of conserved primers are reported that allow the amplification of the entire DNA barcoding region in either three or five overlapping fragments, which allow the recovery of DNA barcodes from valuable historical specimens that in many cases are unique in that they are unable or unlikely to be collected again.

Determination of a complete lemur mitochondrial genome from feces

The mt-genome sequence of sifaka is obtained, the phylogeny of primates is estimated, and the evolutionary rate acceleration occurred in the Anthropoids lineage after they diverged from tarsier.

Evaluating bacterial pathogen DNA preservation in museum osteological collections

Samples from 59 eighteenth and twentieth century individuals known to have been infected with either Mycobacterium tuberculosis or Treponema pallidum were analysed and no reproducible evidence of surviving pathogen DNA was obtained, despite the use of extraction and PCR-amplification methods determined to be highly sensitive.

Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse.

This study is, to its knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.
...

References

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Neanderthal DNA: Not just old but old and cold?

The thermal history of a range of Holocene and Pleistocene bones whose DNA quality has been tested is calculated and it is found that in only very few sites with Neanderthal remains is the preservation of DNA likely to match the quality of that from the skeleton found at Mezmaiskaya Cave.

Nuclear DNA sequences from late Pleistocene megafauna.

The nuclear sequences retrieved from the mammoths suggest that mammoths were more similar to Asian elephants than to African elephants and under some circumstances, nucleotide sequence differences between alleles found within one individual can be distinguished from DNA sequence variation caused by postmortem DNA damage.

Problems of reproducibility – does geologically ancient DNA survive in amber–preserved insects?

Attempts to reproduce DNA sequences from amber– and copal–preserved bees and flies have failed to detect any authentic ancient insect DNA, suggesting that DNA does not survive over millions of years even in amber, the most promising of fossil environments.

DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen.

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A molecular analysis of dietary diversity for three archaic Native Americans

  • H. PoinarM. Kuch S. Pääbo
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2001
Human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

The retrieval of ancient human DNA sequences.

These results show that more experimental work than is often applied is necessary to ensure that DNA sequences amplified from ancient human remains are authentic and quantitation of the numbers of amplifiable molecules is a useful tool to determine the role of contaminating contemporary molecules and PCR errors in amplifications from ancient DNA.
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