The Neandertal genome and ancient DNA authenticity

  title={The Neandertal genome and ancient DNA authenticity},
  author={Richard E. Green and Adrian W. Briggs and Johannes Krause and Kay Pr{\"u}fer and Hern{\'a}n A. Burbano and Michael F. Siebauer and Michael Lachmann and Svante P{\"a}{\"a}bo},
  journal={The EMBO Journal},
  pages={2494 - 2502}
Recent advances in high‐thoughput DNA sequencing have made genome‐scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to… 
Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture
It is shown that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of ~99.8% microbial DNA.
Methodchallenges in the analysis of ancient DNA
These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments and show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
Neanderthal Mitochondrial DNA
The mtDNA genomes of six Neanderthals from four countries have been fully sequenced and the hypervariable regions of several other specimens have been analysed, indicating that either behavioural or biological barriers to interbreeding may have existed.
A Draft Sequence of the Neandertal Genome
The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Neanderthal genomics and the evolution of modern humans.
Attempts to obtain genomic sequence from Neanderthal, the closest known relative of modern humans, are discussed and a reconstructed Neanderthal genome sequence could be integrated into human-primate genome comparisons to help reveal the evolutionary genetic events that produced modern humans.
Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
It is found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males and remained stable for overall mt/nc ratios below 200 but became more variable above that ratio.
Ancient human genome sequence of an extinct Palaeo-Eskimo
This genome sequence of an ancient human obtained from ∼4,000-year-old permafrost-preserved hair provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
A statistical framework is designed to isolate endogenous ancient DNA sequences from contaminating sequences using postmortem degradation patterns and was able to reduce high-contamination fractions to negligible levels.
Analysis of ancient human genomes
  • B. Shapiro, M. Hofreiter
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2010
Recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large‐scale genome‐wide analysis of ancient human diversity a reality, providing a fresh look at human population history.


Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes
Targeted sequencing improves Neandertal mitochondrial DNA retrieval and reveals low diversity among individuals, and together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Ne andertals was smaller than that of modern humans and extant great apes.
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.
Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae
The phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant, and the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.
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.
Sequencing the nuclear genome of the extinct woolly mammoth
This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction.
Analysis of one million base pairs of Neanderthal DNA
A 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA is identified and it is revealed that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago.