Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

@article{Briggs2009TargetedRA,
  title={Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes},
  author={Adrian W. Briggs and Jeffrey Martin Good and Richard E. Green and Johannes Krause and Tomislav Maricic and Udo Stenzel and Carles Lalueza-Fox and Pavao Rudan and Dejana Brajkovi{\'c} and Željko Ku{\'c}an and Ivan Gu{\vs}i{\'c} and Ralf W. Schmitz and Vladimir Doronichev and Liubov V. Golovanova and Marco de la Rasilla and Javier Fortea and Antonio Rosas and Svante P{\"a}{\"a}bo},
  journal={Science},
  year={2009},
  volume={325},
  pages={318 - 321}
}
Economic Ancient DNA Sequencing Analysis of ancient DNA is often limited by the availability of ancient material for sequencing. Briggs et al. (p. 318; see the news story by Pennisi) describe a method of ancient DNA sequence retrieval that greatly reduces shotgun sequencing costs while avoiding the many difficulties associated with direct PCR-based approaches. They generated five complete and one near-complete Neandertal mitochondrial DNA genomes, which would have been economically impossible… 

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...

References

SHOWING 1-10 OF 70 REFERENCES

Identification of ancient remains through genomic sequencing.

A genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old is developed and applied, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination.

Sequencing and Analysis of Neanderthal Genomic DNA

The characterization of Neanderthals from a new perspective is described, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis, and the finding that the Neanderthal and human genomes are at least 99.5% identical is found.

No Evidence of Neandertal mtDNA Contribution to Early Modern Humans

The biomolecular preservation of four Neandertals and of five early modern humans was good enough to suggest the preservation of DNA, and in combination with current mtDNA data, this excludes any large genetic contribution by Ne andertals to early modern human humans, but does not rule out the possibility of a smaller contribution.

Mitochondrial genome variation and the origin of modern humans

The global mtDNA diversity in humans is described based on analyses of the complete mtDNA sequence of 53 humans of diverse origins, providing a concurrent view on human evolution with respect to the age of modern humans.

Genetic analyses from ancient DNA.

The precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences are discussed, which highlight some significant results and areas of promising future research.

Patterns of damage in genomic DNA sequences from a Neandertal

DNA sequences determined from a Neandertal, a mammoth, and a cave bear show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation.

Molecular analysis of Neanderthal DNA from the northern Caucasus

Phylogenetic analysis places the two Neanderthals from the Caucasus and western Germany together in a clade that is distinct from modern humans, suggesting that their mtDNA types have not contributed to the modern human mtDNA pool.

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

Five new complete mitochondrial DNA genomes of Siberian woolly mammoth are reported, sequenced with up to 73-fold coverage from DNA extracted from hair shaft material, demonstrating the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence.

Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions, which could allow ancient specimens to be genotyped with unprecedented accuracy.
...