Ancient DNA (Proc Biol Sci. 2005 Jan 7;272(1558):3-16.)

Ancient DNA.

Willerslev E, Cooper A.

Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

ABSTRACT : In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

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general bias toward CG->TA transitions and to a lesser extent AT->GC

overcome posr-mortem modifications : Uracil-N-glycosylase (UNG), N-phenacylthiazolium bromide(PTB), Pfu and Taq Hifi

survive for no more than 10kyr, maximum 100kyr at colder latitudes

critical steps such as the cloning and independent replication of results have been widely accepted

Air movement created wen opening PCR tubes or transferring liquids will create and disperse microscopic aerosol droplets

aDNA laboratories must be completely isolated both physically and logistically

autoclaving does not prevent the amplification of short DNA fragments (less than or equal to 150bp)

independent replication in a separate laboratory is so crucial

Quantification of template copy number by real time PCR is useful

Insertion of mtDNA and cpDNA sequences in nuclear chromosomes - nuclear insertions (numts)

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