From million-year-old dinosaur remains to ‘resurrecting’ mammoths, stories in the news about ancient DNA make it seem as though Jurassic Park is just around the corner.
But ancient DNA is also an important tool for viewing the past. The only problem is that it’s not quite as abundant or easy to use as some think.
What is ancient DNA?
Ancient DNA can be isolated from the bone or tissue of a museum specimen or other types of preserved remains.
While there isn’t a hard and fast rule about what is considered ancient, it can be anywhere between decades to millennia old.
The first ancient DNA sample was extracted from a 150-year-old museum specimen of a quagga in 1984, but now samples have been isolated from remains that are hundreds of thousands of years old.
Why do we need to learn about ancient DNA?
Knowing the genetics of ancient people and animals gives us insight into how their genes were adapted to their environment, and therefore how we have changed to adapt to ours.
“It provides a very accurate snapshot of genetic diversity in a particular point in time, at a particular location,” says Bastien Llamas, an ancient DNA expert at the Australian Centre for Ancient DNA at the University of Adelaide.
“You can go straight into the past and say ‘this is the most accurate picture that we can have from the past’.”
It also provides data that fossils can’t give us, such as family relations. (In fossils, minerals replace the once-living parts of the body like bone and tissue, so DNA isn’t preserved.)
“[With] humans, plants, other animals and microbes, there are a number of questions that can only be answered with DNA and not with a fossil record,” says Llamas.
“For example, if you found humans and [the remains] seem to be a man, a woman and some children, do we know it is a mum and dad and their children? From the fossil record, it’s going to be hard to know. You can’t be 100% sure that you have a family.
“But genetic is going to be able to tell you that.”
How is ancient DNA extracted?
Originally, extracting, amplifying and sequencing DNA was a laborious process, but the method became a lot easier when the polymerase chain reaction (PCR) method was invented.
DNA is only in the nucleus of the cell, so if the nucleus is damaged there probably won’t be any DNA left to extract. But if there is a nucleus, there’s a chance that DNA inside.
DNA extraction follows a few common steps, which change slightly depending on the type of DNA.
- Take a small sample of bone or tissue
- Break open the cells by grinding or squashing
- Remove the fats from the sample with a special detergent
- Separate the DNA from the proteins using an enzyme that degrades protein
- Pull the DNA out of the solution using precipitation – this is sometimes done with phenol and/or chloroform
- Centrifuge the sample so that the undissolved DNA collects at the bottom of the tube
- Clean the DNA
- Make copies of the DNA using PCR
Voila! You have just extracted and made copies of ancient DNA.
The extraction process might seem simple on paper, but it actually takes a long time and requires absolutely sterile conditions. It is quite easy to lose the sample due to a small error, so fastidious precision is essential.
Are there other challenges?
“Low quantity, degraded and fragmented DNA, and contamination are the four issues that we have with ancient DNA,” says Llamas.
DNA is a long molecule made of units called base pairs. Each of these is a pair of smaller molecules connected in a long chain. However, like a real chain, those links can be broken.
Overtime, the DNA of a dead body breaks down into smaller and smaller units until it disappears altogether. The older a sample is, the more degraded the DNA is, unless something like extreme cold slows down the process.
“There’s not much DNA that survives and DNA decays with time,” says Llamas. “It becomes extremely fragmented and damaged… So much so that the sequence can be slightly modified.”
That’s because the base pair molecules break down and cause mutations that weren’t present in the living organism. This might cause errors in the code that don’t reflect the DNA of the original organism.
Finally, when remains sit around for literally thousands of years, they are likely be contaminated by another organism – especially microbial DNA.
“For example, if you have a bone from a human, you will retrieve some human DNA, but also a lot of DNA from the bacteria that invaded the body after death,” says Llamas.
“And then there is [DNA from] bacteria living in the soil around the bone, plants and other animals [that touch it] – like if an animal chewed on the bone.”
There is usually so little ancient DNA left that it must be extracted under strictly sterile conditions, so it won’t degrade further or be accidentally contaminated in the lab. If this happens, the whole sample could be lost.
What is the oldest ancient DNA?
“DNA survives a maximum of one to 1.5 million years, so forget about dinosaurs!” says Llamas.
To date, the oldest DNA found and extracted was from mammoth specimen that was potentially up to 1.6 million years old. The DNA was better preserved than other ancient mammoth specimens because the north-eastern Siberian permafrost stopped it from degrading quickly. The extreme cold slowed down the process of degradation.
This shows that, with the right preservation conditions and new technologies, we might be able to extract and isolate DNA that is even older.
But when you’re getting excited about resurrecting mammoths, just remember – extracting ancient DNA is still extremely rare and very hard to do!
Originally published by Cosmos as Can we really extract ancient DNA from dinosaurs?
Deborah Devis is a science journalist at Cosmos. She has a Bachelor of Liberal Arts and Science (Honours) in biology and philosophy from the University of Sydney, and a PhD in plant molecular genetics from the University of Adelaide.
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