Ancient DNA: Do It Right or Not at All

By A. Cooper, H. Poinar. Science, 2000

1,245 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/569128ac8014d20b889efec5ab5c7b5f015df1d1

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Citations in the corpus

Persistence of Environmental DNA in Freshwater Ecosystems (2011, background): “Environmental DNA is rare and preacautions similar to those used for ancient DNA analysis must be taken [31].”
Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus) (2015, methodology): “, 2014 and the present work, dealing with the same species, in the same country and using modifications of the same method) and to maintain zero false positive rates, as the throughput of samples increases, particularly by ensuring that laboratory design, operation and protocols are similar to those”
Ancient plant DNA in archaeobotany (2008, background): “This is because even with all the criteria of authenticity fulfilled (Cooper and Poinar 2000), the authenticity of aDNA can never be fully guaranteed (Gilbert et al. 2005).”
DNA species identification of archaeological salmon bone from the Pacific Northwest Coast of North America (2004, methodology): “Any possibility of contamination from modern sources must be excluded before amplified DNA can be accepted as authentic ancient DNA, and then used to address any specific research questions [16,18,23,39].”
Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data (2015, background): “Blank and positive controls are key tools to identify these taxa (Cooper & Poinar 2000; De Barba et al. 2014).”
Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus (2012, methodology): “Because of the rarity of DNA in the water samples, the analysis was performed with similar precautions as those used for ancient DNA studies to reduce contamination and poor-quality DNA results (Taberlet et al. 1996; Cooper & Poinar 2000).”
The top 10 list: criteria of authenticity for DNA from ancient and forensic samples (2003, background): “To ensure authentic DNA results from both ancient as well as forensic samples, I have listed below 10 ‘‘criteria of authenticity’’ [1].”
Learning about human population history from ancient and modern genomes (2011, background): “Even in the first years of ancient DNA research, criteria were established to ensure the authenticity of results: for example, independent replication”
Acquiring DNA sequence data from dried archival red algae (Florideophyceae) for the purpose of applying available names to contemporary genetic species: a critical assessment (2012, background): “Colleagues studying archival herbaria collections may argue that the level of stringency advocated here, and considered necessary for authentication by the ancient DNA community (Cooper and Poinar 2000; Willerslev and Cooper 2005), is excessive.”
DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity (2017, methodology): “This results in fewer amplifiable templates, sequencing artefacts and preferential amplification of undamaged DNA, with a potential increase in false results or misidentifications if proper sequence authentication measures are not followed (Cooper and Poinar 2000).”
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses (2014, background): “Issues of contamination have plagued studies, with highprofile examples in the fields of novel virus discovery, such as in the false association of XMRV and chronic fatigue syndrome [40], and the study of ancient DNA of early humans and pathogens [41,42].”
Ancient DNA analysis of 101 cattle remains: limits and prospects (2004, background): “Several researchers in the field have set out various criteria to measure the authenticity of ancient (aDNA) results (for example [8,31]).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “…DNA by DNA of modern origin mean that a wealth of information is available on the handling of DNA in appropriately designed laboratories to avoid, or at least minimise, contamination in both pre- and post-PCR processing environments (Cooper & Poiner 2000; Knapp et al. 2012a; Pedersen et al. 2015).”