(Un)usual sources of ancient DNA

Working with ancient DNA can be quite painful at times, but hard work pays off (or so they say) and scientists are starting to reap great benefits from their effort by exploring more and more things to extract DNA from.

In the longest infographic ever, I made an attempt to list all of the weird things that people have managed to get ancient DNA from, but it’s quite difficult to evaluate what is weird and what is normal, so just to be sure, I’m also listing the more common sources of samples.

Disclaimer: By no means do I want to say that this is a complete list. I’ve probably missed some cool things, and I’ll be happy if you add them in the comments. Also, I’m only mentioning one study per sample type and it purely serves as an example, so if I didn’t pick your study, please, don’t hate me.

References

Der Sarkissian, C., Pichereau, V., Dupont, C., Ilsøe, P. C., Perrigault, M., Butler, P., Chauvaud, L., Eiríksson, J., Scourse, J., Paillard, C. and Orlando, L. (2017), Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol Ecol Resour. Accepted Author Manuscript. doi:10.1111/1755-0998.12679

Grealy et al. Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell, Molecular Phylogenetics and Evolution, Volume 109, April 2017, Pages 151-163, ISSN 1055-7903, http://doi.org/10.1016/j.ympev.2017.01.005.

M. D. Teasdale, N. L. van Doorn, S. Fiddyment, C. C. Webb, T. O’Connor, M.Hofreiter, M. J. Collins, D. G. Bradley. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing. Phil. Trans. R. Soc. B 2015 370 20130379; DOI: 10.1098/rstb.2013.0379.

Zepeda Mendoza ML, Lundberg J, Ivarsson M, Campos P, Nylander JAA, et al. (2016) Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante’s Cave, Northern Sweden. PLOS ONE 11(3): e0151577. https://doi.org/10.1371/journal.pone.0151577

O’Sullivan NJ, Teasdale MD, Mattiangeli V, Maixner F, Pinhasi R, Bradley DG, Zink A.A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing. Sci Rep. 2016 Aug 18;6:31279. doi: 10.1038/srep31279.

da Fonseca R. R. et al. . The origin and evolution of maize in the Southwestern United States. Nat Plants 1, 14003, doi: 10.1038/nplants.2014.3 (2015).

Kuch, M., Rohland, N., Betancourt, J. L., Latorre, C., Steppan, S. and Poinar, H. N. (2002), Molecular analysis of a 11 700-year-old rodent midden from the Atacama Desert, Chile. Molecular Ecology, 11: 913–924. doi:10.1046/j.1365-294X.2002.01492.x

Wales et al. The limits and potential of paleogenomic techniques for reconstructing grapevine domestication, Journal of Archaeological Science, Volume 72, August 2016, Pages 57-70, ISSN 0305-4403, http://doi.org/10.1016/j.jas.2016.05.014.

Martin, M. D. et al. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun. 4:2172 doi: 10.1038/ncomms3172 (2013).

Warinner C, et al. (2014) Pathogens and host immunity in the ancient human oral cavity. Nature Genetics 46(4):336-344. doi:10.1038/ng.2906. http://www.nature.com/ng/journal/v46/n4/full/ng.2906.html

Murray DC, Haile J, Dortch J, White NE, Haouchar D, Bellgard MI, et al. (2013) Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages. Sci Rep 3.

Parducci, L., Suyama, Y., Lascoux, M. and Bennett, K. D. (2005), Ancient DNA from pollen: a genetic record of population history in Scots pine. Molecular Ecology, 14: 2873–2882. doi:10.1111/j.1365-294X.2005.02644.x

Ermini, L. et al. Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr. Biol. 18, 1687–1693 (2008).

Graham RW, Belmecheri S, Choy K, Culleton BJ, Davies LJ, et al. (2016) Timing and causes of mid-holocene mammoth extinction on st. paul island, alaska. Proceedings of the National Academy of Sciences: 201604903. pmid:27482085

Rasmussen M., et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).

Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA, Bland H, Evershed RP, Possnert G, Pääbo S.1998 Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281,402–406. doi:10.1126/science.281.5375.402

Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. 1984. DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282–284. doi:10.1038/312282a0

Olalde I et al. 2014 Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225–228. doi:10.1038/nature12960

Orlando et al. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78. doi:10.1038/nature12323

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About Patrícia Pečnerová

I am a PhD candidate at Stockholm University. I study paleogenomics of the last population of the woolly mammoth before its extinction and I am mainly interested in combining ancient DNA, population and conservation genomics to trace pre-extinction changes in genetic diversity.
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  • Jonathan Harris

    The origin of life on planet Earth

    A “cloud” falls from infinite space. Then, in the crust of the planet, as in the depths of the primitive oceans, could be observed the existence of a viscous element that covered the whole Earth. With this gelatinous mass, protoplasm was born. This matter, amorphous and viscous, with its condensation gave origin to the birth of the nucleus. The earliest inhabitants of Earth are albuminoid cells, amoebae, and all unicellular organisms that have multiplied in the warm waters of the oceans. These beings only reveal a sense: of touch, which gave rise to all others.

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