Over the past few months, we've seen a lot of stories about prehistoric DNA, from cave lions to mammoths to Tasmanian tigers and more. It was only a few decades ago that the idea of extracting DNA from fossils was a scientific fantasy, but nowadays the study of ancient genetic material is a common and essential part of palaeontology.

Jurassic Park may be the first thing that comes to your mind when you hear about this subject – any time an ancient DNA news story surfaces, comments sections are sure to include questions about cloning or resurrecting extinct species – but there's more to this science than dreams of de-extinction (more on that topic later!): ancient DNA opens doors to answering many of palaeontology's perplexing questions, and has dramatically changed how scientists investigate the past.

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It might never give us Jurassic Park, but ancient DNA has already dramatically changed how scientists investigate the ancient past.

Long-held secrets

Last summer, a study triumphantly announced that ancient DNA had solved the mystery of Macrauchenia, a bizarre South American mammal whose place on the mammal family tree had been a palaeontological puzzle ever since the days of Darwin. Several months later, another group of palaeo-geneticists presented a new name for the curiously stilt-legged extinct horses of the ancient Americas: Haringtonhippus.

If you follow palaeontology news, these are familiar sorts of stories. Most of what we know about fossil animals comes from skeletons, but bones and teeth aren't always enough to answer our questions about prehistoric life. Over the years, ancient DNA has built up a bit of a reputation for revealing secrets that bones alone could not.

"Bone morphology can be influenced by environment and behaviour," explained Leigha Lynch of Oklahoma State University over the phone. This variability is great for adaptable animals, but it can also make for a confusing time trying to discern the true identities and relationships of ancient species.

In her own research, Lynch turns to DNA for assistance. She studies North American martens – small carnivores related to weasels – ranging in age from several decades to 15,000 years old. Not only does their DNA help her sort out the relationships between the animals' various ancient populations, but by constructing the extended marten genealogy, she can also identify the location and timing at which new populations arose and new traits evolved. Combining this evolutionary info with the geologic record, she can then piece together how the animals responded to environmental changes such as Ice Age glacial cycles.

Left: The 150-year-old skull of an American pine marten from Alaska. Right: In the lab at Oklahoma State University, Leigha Lynch prepares to amplify, sequence and study DNA from those 150-year-old martens. Images: Leigha Lynch

Animals' bodies also change as they grow, which can be another potential source of confusion when examining fossils. "[Sometimes] we don't know if we're looking at an adult or a juvenile or a new species. So being able to get the DNA to clarify that is really helpful."

A creature's chromosomes can also reveal its sex, a boon in those cases where males and females are so physically different they might be mistaken for separate species (think elephant seals!).

Ancient DNA can even help us understand extinction. A recent study of Tasmanian tigers found unexpectedly low genetic diversity in these animals going back thousands of years – a tell-tale sign of a long-term population decline that may have set the species up for its eventual human-induced disappearance.

(Fun fact: we can even get DNA from fossilised poop! One group of scientists, for example, was able to determine the diet of giant flightless moas from New Zealand in part by testing the DNA of the plants in their droppings!)

Faded genes

"Ancient DNA gets degraded over time," explained Viviane Slon of the Max Planck Institute for Evolutionary Anthropology in a phone call, "so not every fossil will yield DNA, and not every fossil will yield enough DNA to reconstruct a full genome." (A genome is the complete set of genes of an organism.)

A dead cell is a hostile environment for DNA, full of enzymes whose very job is to break down genetic material. In a still-living organism, this is important for DNA replication, repair and recycling, but once the whole organism dies, it means that DNA begins to deteriorate very quickly. The best environments for preserving DNA tend to be cold, dry and stable over long time periods, including permafrost, some caves, and – for more recent specimens – environmentally controlled museum collections.

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Genetic information inside these pieces of bone allowed scientists to decipher the complete genome of an extinct prehistoric horse that lived in what is now Canada some 700,000 years ago. Image: Ludovic Orlando

The oldest DNA sequence ever recovered comes from a 700,000-year-old horse from the frozen soil of northern Canada, and this might be about as old as we can hope for. Research indicates that DNA degrades to a non-usable point after one or two million years, even under perfect conditions (which are rare or non-existent in nature).

One-million-year-old DNA is extremely impressive ... although it leaves out the vast majority of the 3,500-million-year history of life on Earth.

So, no Jurassic Park. The last of the non-bird dinosaurs went extinct 66 million years ago. And yes, even the scientists are disappointed.

"I love the idea – in theory, I could have a little Triceratops hanging out in my backyard," Lynch said. "[But] I find it very hard to picture any scenario in which DNA was preserved in something that old."

Even in relatively young fossils, DNA can disappear very quickly in an unfriendly environment. The cold, dry Arctic is great for its preservation, but the warm, wet tropics are just the opposite, typically preserving very little genetic material. So the fossil record of ancient DNA is much more likely to give us information about, say, woolly mammoths than about island tortoises.

But when conditions are right, DNA can preserve spectacularly well. In fact, one of the biggest challenges facing researchers is that there's often too much of it: a fossil horse bone might retain some original horse genes, but it's likely to also have DNA from the bacteria and insects that have gotten into the bones, or the plants and fungi that grew around it (and it will pretty much always end up with DNA from the humans who excavated it). That means researchers have to pick through a lot of "noise" to get out the specific DNA they want.

For Slon, this is especially tricky: she studies ancient humans (and our relatives like Neanderthals), so her fossils include both ancient and recent human DNA. "You're always going to get contaminant. The trick is to be able to tell them apart," she explained. "And you're going to do that by taking advantage of a particular type of chemical damage [called deamination] that accumulates over time in DNA." Knowing how to identify this damage helps scientists separate the old DNA from the new.

Left: Excavations in this cave in El Sidrón, Spain are conducted with a special protocol to prevent accidental contamination of the ancient human DNA in the sediment. Image: Group of Paleoanthropology MNCN-CSIC).
Right: In the lab, Viviane Slon prepares a small bit of cave sediment for the extraction of ancient DNA tens of thousands of years old. Image: Sylvio Tüpke, Max Planck Institute for Evolutionary Anthropology.

Slon and her colleagues have also found a way to take advantage of DNA's tendency to contaminate its surroundings. She recently led a study that discovered ancient human DNA in cave sediment. Studies like this are very encouraging for palaeontologists because they suggest that we can explore the DNA of ancient organisms without even needing their fossils!

The take-home point here is this: ancient DNA has limits. It comes with a host of challenges, it only lasts so long, and only in certain environments. But when researchers do find it, modern techniques allow them to piece together an astonishingly complete picture. "In a fossil that is well-preserved," Slon said, "we can get a genome that is equal in quality to genomes that we get today, if you put enough sequencing effort into it."

Is extinction truly forever?

In 1990, Michael Crichton published the novel Jurassic Park, but he was not the first to explore the idea of bringing ancient species back from the dead using DNA. In fact, the idea has been bouncing around for a long time, and there are some scientists today who are working on doing something very much like that.

In Jurassic Park, the dinosaurs were essentially cloned from ancient DNA, but real-life cloning – such as in the case of Dolly the sheep or the recent monkey twins – only works with viable cells, which the fossil record doesn't preserve. (Famously, preserved cells of the recently extinct bucardo, a wild goat native to the Pyrenees, were used to create a short-lived revenant in 2003.)

"The technology that lets us preserve viable cells in a freezer is only about 50 years old," said Ben Novak, lead researcher at Revive & Restore, over the phone. "Anything that goes extinct prior to that, we have nothing viable from."

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Revive & Restore wants to bring back the passenger pigeon with the help of its closest living relative: the band-tailed pigeon (pictured). Image: Alan Vernon/Wikimedia Commons 

Revive & Restore is an organisation that aims to use genetic technology to aid struggling species and ecosystems, from collapsing coral reefs to unhealthy black-footed ferrets. Among their most ambitious missions is the de-extinction of the passenger pigeon.

Before their extinction due to human activity in the early 1900s, passenger pigeons soared over eastern North America in flocks billions strong. Research has shown that these birds were major environmental influencers; a visiting flock of pigeons would cause a huge disturbance in a forest, creating a similar rejuvenating effect to that of a forest fire. Their disappearance left the forest ecosystems far less able to maintain healthy and stable conditions.

Novak and his colleagues want to bring those populations back with some help from the passenger pigeon's closest living relative: the band-tailed pigeon.

"Ninety-seven percent of the passenger pigeon's genome is still alive in the band-tailed pigeon, because that's how identical they are," Novak explained. The plan is to peruse the passenger pigeon genome for the features that made the species unique – those traits that allowed them to maintain huge flocks across North America – and edit them into the band-tailed pigeon, ultimately engineering a population of birds that can serve the same role as their extinct predecessors. 

This is de-extinction, but it's not exactly bringing a species back from the dead. "If we're going to get really technical, it [would be] a bird that is the genetic offspring of band-tailed pigeons and passenger pigeons," Novak said. "If that had been produced through natural breeding, we would call it a hybrid."

The goal here isn't to resurrect exactly what existed before, but to restore ecosystems to a healthy state by replacing a lost keystone species. Novak likens it to the reintroduction of wolves to Yellowstone: the predators had disappeared from this area, and a new wolf population was introduced to fill in that missing piece of local ecology. The passenger pigeon project simply takes more genetic innovation.

Left: Ben Novak prepares ancient DNA for sequencing, wearing special garb to prevent his own human DNA from contaminating the sample; Right: The toe of a passenger pigeon from the Royal Ontario Museum. The tiny bit of tissue next to the toe is the sample size Novak typically uses to extract DNA. Images: University of California, Santa Cruz Paleogenomics Lab.

There are other species on the de-extinction radar, including the heath hen, which went extinct in the northeastern United States in 1932, and more famously the woolly mammoth, which has been extinct for thousands of years. These projects are in the exciting early stages, and may eventually play major roles in environmental conservation, but researchers are keen to remind us that we can never fully recreate the past.

"There's inevitably always something lost in extinction," Novak said, "things we don't know; things we can never know."

Our own past and future

"I think for me," said Slon, "the most amazing discovery of the last few years was the Denisovans."

In 2010, researchers sequenced the DNA of a very human-like finger bone in Denisova Cave in Siberia. The results were a surprise. It wasn't Homo sapiens and it wasn't Neanderthal; it was a closely related group that no one had ever seen. To this day, the only fossil remains known from this population – known as the Denisovans – are three teeth and one finger bone, and without ancient DNA we never would have realised they came from a totally separate lineage of ancient people.

From those bones, Slon and her colleagues have learned an immense amount of information about the Denisovans and their relationships. We know now, for example, that modern humans carry traces of not only Neanderthal DNA, but also that of the Denisovans.

"We know that Denisovans and Neanderthals must have mixed," Slon said, "and also Denisovans and modern humans mixed." More than perhaps any other species on Earth, the science of ancient DNA has taught us about ourselves.

Ancient DNA is an amazing resource for scientists aiming to learn about – and learn from – the past, and researchers are looking forward to a future filled with untold possibilities. Right now there are labs all over the world working at refining, improving and advancing the science of pulling DNA out of the past.