Extracting ancient DNA
Museums worldwide hold large collections of preserved specimens of living things. In well preserved specimens, the cell nucleus contains DNA that scientists can extract and use for experimentation. This DNA is known as ancient DNA.
Why are we interested in extracting ancient DNA?
Ancient DNA gives us a snapshot of the molecular make-up of an individual in a species at a certain point in time. It’s particularly useful for molecular evolutionary studies where questions about speciation or phylogenetics are being investigated.
Find out about the research that looked at barcoding New Zealand swamp hens.
Where can we find ancient DNA?
Ancient DNA can be extracted from a wide range of source material. Much of this source material is found in museums. This material includes archaeological specimens, fossils, historical skeletal material, mummified tissues, medical specimen archives and preserved plant remains.
Extracting ancient DNA from bone samples
Centrifugation of samples
DNA samples in Eppendorf tubes are placed into a microcentrifuge for centrifugation.
The DNA extraction process varies according to the source material. These are the steps for a bone sample:
Take a small sample (0.5–1.0g) of bone.
Grind this into powder.
Decalcify by suspending the sample in EDTA overnight at room temperature.
Centrifuge to collect the sediment.
Digest the sediment with proteinase K and DTT (dithiothreitol) overnight at 50–55°C.
Extract the samples twice with phenol and once with chloroform.
Centrifuge to recover the DNA.
Make multiple copies of the DNA using polymerase chain reaction (PCR). (Source: Leonard, J., Wayne, R.K. and Cooper, A. (2000). ‘ Population genetics of Ice Age brown bearsPNAS, 97 (4): 1651–1654.)
Find out more about polymerase chain reaction (PCR).
DNA contamination is a problem
Working with ancient DNA presents a number of challenges for scientists. In particular, because the amount of ancient DNA is so small, scientists need to avoid contamination from other sources of DNA. In the lab, they use several procedures to ensure results are authentic and reproducible:
Using a ‘clean’ lab where no other DNA is handled and wearing protective clothing.
Adding negative controls to monitor for introduction of contaminating DNA, for example, including PCR blanks.
Reproducing the results, for example, by using the same PCR primers on different DNA extracts from the same source material.
DNA quality is lower
Unlike DNA extracted from fresh samples, ancient DNA is mostly low-quality DNA. Ancient DNA is of low average molecular size and is often damaged over time by exposure to air. This makes cloning ancient DNA difficult. Most molecular analyses of ancient DNA use PCR to amplify the number of copies of the DNA. Generally, ancient DNA cloning is restricted to high copy number mitochondrial DNA sequences.
What is extracted ancient DNA used for?
Scientists are using ancient DNA to investigate:
evolutionary relationships between species
how new species arise (speciation)
how species became extinct
impacts of climate change on species
DNA barcoding.
Read the article DNA barcoding to find out more.
New techniques
In From the smallest bones come the biggest secrets read about the work of former University of Otago Masters student Lachie Scarsbrook. He developed a specialised technique that allows scientists to non-destructively extract ancient DNA from tiny precious remains and sequence their genomes without damaging the original fossil.
Read Lachie’s 2022 paper Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus.
New genetic research using palaeogenetic techniques has shed new light on another iconic species – the takahē. It has not only uncovered the significant impact of humans and past climate change on the takahē but has also led to new theories on their evolutionary history.
