Authenticating Ancient Human Mitochondrial DNA

@article{Montiel2001AuthenticatingAH,
  title={Authenticating Ancient Human Mitochondrial DNA},
  author={Rafael Montiel and Assumpci{\'o} Malgosa and Paolo Francalacci},
  journal={Human Biology},
  year={2001},
  volume={73},
  pages={689 - 713}
}
The use of ancient DNA techniques in human studies has been hampered by problems of contamination with modern human DNA. The main problem has been that the object of study belongs to the same species as the observer, and the complete elimination of the contamination risk is seemingly unlikely. Contamination has even been detected in the most specialized laboratories in this field. In these kinds of studies it is therefore very important to detect contamination and to distinguish contaminants… 

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References

SHOWING 1-10 OF 60 REFERENCES

Authenticating DNA Extracted From Ancient Skeletal Remains

TLDR
Work with a range of Holocene skeletal material from domestic animals and humans suggests that more than 50% of skeletal remains from the past two thousand years are likely to contain amplifiable endogenous DNA, but that in the case of human material great care is needed to distinguish this from contamination introduced before the samples reach the laboratory.

The retrieval of ancient human DNA sequences.

TLDR
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.

Mitochondrial DNA sequences from a 7000-year old brain.

TLDR
The sequences show that this ancient individual belonged to a mitochondrial lineage that is rare in the Old World and not previously known to exist among Native Americans, bringing to three the number of maternal lineages known to have been involved in the prehistoric colonization of the New World.

Ancient and modern mitochondrial DNA sequences and the colonization of the pacific

TLDR
Results of mtDNA analyses on modern‐day Pacific populations indicate reduced genetic variability, and suggest that the Polynesians descend from people who migrated relatively recently from island Southeast Asia and that a population bottleneck occurred during the settlement of the central Pacific.

Phylogenetic affiliation of ancient and contemporary humans inferred from mitochondrial DNA.

TLDR
Phylogenetic analysis indicated that part of the Asians, including the Japanese, subsequently diverged from the majority of Africans, and that Asians can therefore be separated into two distinct groups.

Ancient HLA genes from 7,500-year-old archaeological remains

TLDR
Using DNA obtained from one individual, distinctive patterns of nucleotide substitution in the cloned heavy chain gene segments permit tentative assignment of the HLA-A,B type of the ancient individual.

[Amplification of mitochondrial DNA fragments from ancient human teeth and bones].

TLDR
This work extracted and visualized DNA from ancient human teeth and bones of 150 to 5,500 years B.P. from three deposits from the south of France and showed that this sequence is identical to the homologous region of human mitochondrial DNA.

Classification of European mtDNAs from an analysis of three European populations.

TLDR
The conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations, is supported.

A MITOCHONDRIAL DNA DATABASE Applications to Problems of Nomenclature and Population Genetics

TLDR
A database of the variability of the control region sequence (segment I), formatted in a Microsoft Excel file, can be used for easily grouping published sequences and showing further subdivision in monophyletic clusters (sub­ haplogroups) and pointing out the mutation hierarchy.
...