Neanderthal genomics and the evolution of modern humans.

@article{Noonan2010NeanderthalGA,
  title={Neanderthal genomics and the evolution of modern humans.},
  author={James P. Noonan},
  journal={Genome research},
  year={2010},
  volume={20 5},
  pages={
          547-53
        }
}
  • J. Noonan
  • Published 1 May 2010
  • Biology
  • Genome research
Humans possess unique physical and cognitive characteristics relative to other primates. Comparative analyses of the human and chimpanzee genomes are beginning to reveal sequence changes on the human lineage that may have contributed to the evolution of human traits. However, these studies cannot identify the genetic differences that distinguish modern humans from archaic human species. Here, I will discuss efforts to obtain genomic sequence from Neanderthal, the closest known relative of… 

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References

SHOWING 1-10 OF 80 REFERENCES
Sequencing and Analysis of
TLDR
This initial analysis of the Neanderthal genome advances understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.
No Evidence of Neandertal mtDNA Contribution to Early Modern Humans
TLDR
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.
The Neandertal genome and ancient DNA authenticity
TLDR
It is argued that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination, and a similar ‘boot‐strap’ approach is suggested in which interim approaches are applied until sufficient data for more definitive directAssays are acquired.
Initial sequence of the chimpanzee genome and comparison with the human genome
TLDR
It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
Neanderthal genome to be unveiled
TLDR
The German team sequencing Neanderthal DNA says that its single-read of the Neanderthal genome is sufficient for publication because the technique used does not rely on the same DNA reassembly process used in conventional ‘shotgun’ sequencing.
The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals
Analysis of one million base pairs of Neanderthal DNA
TLDR
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.
Sequencing the nuclear genome of the extinct woolly mammoth
TLDR
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.
The application of molecular genetic approaches to the study of human evolution
TLDR
Co-evolution of genes with language and some slowly evolving cultural traits, together with the genetic evolution of commensals and parasites that have accompanied modern humans in their expansion from Africa to the other continents, supports and supplements the standard model of genetic evolution.
...
...