Analysis of ancient and museum DNA

Subject description

Students will be introduced to the concept of ancient DNA isolated from the biological material of organisms that lived in the past. They will learn about the history of ancient DNA and the first research in this field. The course will include topics about what ancient DNA is and what its properties are (specifics due to its degradation). “Museum DNA” is a colloquial term for DNA isolated from organisms stored in museum collections. The term partially overlaps with the expression ancient DNA, and we will address their similarities and differences. The work in museum collections, in the past and today will be presented together with the importance of museum collections in preserving biodiversity.

The course will cover the differences in the analysis of ancient (museum) DNA and the analysis of standard DNA, from the first steps of isolation to bioinformatics analysis. Students will be introduced to a wide range of scientific fields in which ancient DNA is used (from anthropology and climate change to population genetics).

Finally, some outstanding examples of the analysis of ancient DNA, which enabled new insights in their respective fields, will be presented/ discussed:

(1) Human evolution: Analysis of the ancient DNA of Neanderthals and Denisovans, what did we inherit from one or the other, the mysterious fourth species whose DNA is visible in the genome of the other three.

(2) Extinctions of certain animal species (mammoths, Tasmanian tigers, dodos), what do their genomes tell us?

(3) Climate change and the answers offered to us by ancient DNA.

(4) Jurassic Park: how far are we from the revival of dinosaurs, mammoths, Neanderthals – technical limitations and ethical-moral aspects.

The subject is taught in programs

Objectives and competences

The objectives of the course are to present the properties of ancient DNA and the many scientific fields where it is used. In this context, the focus will be on studies and concrete cases where the application has made a key contribution to clarifying research questions. The so-called museum DNA and work in museum collections will also be introduced as this subject is currently not represented in the curriculum.

Students' competences after completing the course include knowledge of ancient and museum DNA and their ability to incorporate the newly acquired knowledge into their current research or for future use.

Teaching and learning methods

Teaching methods will depend on the number of students enrolled. In case of lectures (more than five students enrolled), the theoretical foundations and the above-mentioned concrete examples will be presented. In case of a small number of students, they will learn these basics and examples through studying the cited literature, followed by consultations. Depending on the field of research or interest, students will prepare a seminar (either in a form of a lecture or text), within one of the topics. The practical work will be adapted to the abilities / time of the students: it will be possible to visit the Natural History Museum in Vienna and our laboratory, which specializes in working with museum and ancient DNA, or the practical work will be of bioinformatics nature. Depending on the field of research of the doctoral student, the analysis of ancient DNA can also be concretely included in the doctoral research and published in the form of a scientific article.

Expected study results

Students will gain theoretical and practical knowledge of:

– properties of ancient and museum DNA,

– work in museum collections,

– the scientific fields where ancient and museum DNA are used (and have contributed key insights to their development),

– differences in analysis compared to "standard" DNA – from laboratory to bioinformatics,

– practical work that will prepare the student for the actual use of ancient DNA in the chosen field.

Basic sources and literature

Splošno o starodavni DNA (General about aicent DNA):

Kjær, K.H., Winther Pedersen, M., De Sanctis, B. et al. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612, 283–291 (2022).

Fulton TL & Shapiro B. 2019. Setting up ancient DNA Laboratory (book chapter).

Derkarabetian S., Benavides L.R., Giribet G. Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault. Mol. Ecol. Resour., 19 (2019), pp. 1531-1544.

Bouwman A, Rühli F. 2016. Archaeogenetics in evolutionary medicine. Journal of Molecular Medicine (Berl), 94(9): 971–7.

Cappellini E, Prohaska A, Racimo F. 2018. Ancient Biomolecules and Evolutionary Inference. Annual Review of Biochemistry, 87: 1029-106.

Hagelberg E, Hofreiter M, Keyser C. 2015. Ancient DNA: the first three decades. Philosophical Transactions of the Royal Society B: Biological Sciences, 370: 20130371.

Zupanič Pajnič I. 2019. Molekularnogenetski vidiki preiskav starodavne DNA,Zdravniški vestnik, 88.

Timm R, Schwentner M, Bober S, Lörz AN. 2021. Testing the impact of non-destructive DNA extraction on setae structure of Amphipoda (Crustacea). Zootaxa.

O muzejskih zbirkah in »muzejski« DNA (About museum collections and »museum« DNA):

Boessenkool S, Star B, Scofiled RP, Seddon PJ, Walters JM. 2010. Lost in translation or deliberate falsification? Genetic analyses reveal erroneous museum data for historic penguin specimens. Proceedings Royal Society Series B, 277: 1057–1064.

Kruckenhauser L, Haring E. 2010. Advantages and limits of DNA analyses of specimens from scientific museum collections. 5th Biennial European Bird Curators Meeting, 225-235.

Analize starodavne in muzejske DNA (Analysis of ancient and museum DNA):

Allentoft ME, Collins M, Harker D, et al. 2012. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B: Biological Sciences, 279(1748): 4724-33.

Burrell AS, Disotell TR, Bergey CM. 2014. The use of museum specimens with high-throughput DNA sequencers. Journal of Human Evolution, 79: 35–44.

Cappellini E, Welker F, Pandolfi L et al. 2019. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature, 574: 103–107.

Evolucija človeka (Human evolution):
https://www.nobelprize.org/prizes/medicine/2022/press-release/

Meyer M, Kircher M, Gansauge MT. 2012. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science, 338 (6104): 222-226.

Prüfer K, Racimo F, Patterson N, Jay F. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481): 43-9.

2. Izumrtja (Extinctions):

Feigin CY, Newton AH, Doronina L. et al. 2018. Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore. Nature Ecology and Evolution, 2: 182–192.

Rogers RL, Slatkin M. 2017. Excess of genomic defects in a woolly mammoth on Wrangel island. Plos Genetics, 13(3): e1006601.

Shapiro B, Sibthorpe, Rambaut A et. Al. 2002. Flight of the Dodo. Science, 295: 1683.

3. Klimatske spremembe (Climate change):

Hadly EA, Ramakrishnan U, Chan YL, et al. 2004. Genetic response to climatic change: insights from ancient DNA and phylochronology. PLoS Biology, 2(10): e290.

4. Invazivne vrste (Invasive species):

Palandačić A, Kruckenhauser L, Ahnelt H, Mikschi E. 2020. European minnows through time: museum collections aid genetic assessment of species introductions in freshwater fishes (Cyprinidae: Phoxinus species complex). Heredity, 124: 410–422.

5. Jurassic Park:

Bailleul AM, Zheng W, Horner JR, Hall BK, Holliday CM, Schweitzer MH. 2020. Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage National Science Review: 7(4): 815–822.