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Mapping a Woolly Mammoth’s DNA

Fictional depictions of the woolly-mammoth-like Snuffleupagus and Manny, the shy mammoth in the movie Ice Age, as well as museum displays of reconstructed woolly mammoth skeletons, may be the closest humans come to seeing the extinct animal in action. Although scientists say that the chances of bringing the woolly mammoth back to life, à la Jurassic Park, are slim, if not impossible, they do point to the wealth of other benefits they can reap from mapping mammoth DNA.

Mammoths are but one of a growing list of extinct organisms for which researchers have sequenced small snippets of DNA over the past decade and a half, including fossilized plants, cave bears and ancient humans. Using DNA to sequence parts of organisms’ genomes has revealed much about their evolutionary history, including when and where they moved and their population sizes. Researchers hope to more specifically understand what leads some creatures to go extinct and what allows others to evolve and survive, given climatic and other environmental changes.

Geneticist Evgeny Rogaev analyzes DNA extracted from muscle tissue of a woolly mammoth, as well as an African elephant and an Asian elephant, to learn more about to which animal the extinct mammoths were most closely related. Image is courtesy of Vera Nikishina.

Sequencing the genome of an organism that is still living is no easy task, much less one that has been dead tens of thousands of years, says Alan Cooper, director of the Australian Centre for Ancient DNA in Adelaide. Such sequencing is especially difficult because DNA begins degrading the minute an organism dies. Unless an organism is exceptionally preserved, through freezing, for example, researchers are likely to be left with only minute amounts of DNA.

Additionally, everything that comes into contact with the sample (including the humans extracting the DNA) leaves its mark, and over thousands of years, the contamination levels can be immense. Aside from those issues, however, the basic DNA extraction process for extinct animals is similar to what geneticists use to map out the genomes of modern organisms, including people.

All DNA is composed of the same four “bases” lined up in an exact sequential order that determines the unique characteristics of any given organism. Genomics researchers can sequence either the “mitochondrial” DNA or the “nuclear” DNA, referring to the part of the cell in which the DNA is located.

Sequencing each type of DNA has its benefits, says Hendrik Poinar, a paleogeneticist at McMaster University in Hamilton, Ontario. Mitochondrial DNA can be used effectively to determine who an organism is related to and where it came from, and what the population structure looked like, he says, whereas nuclear DNA explains the biology of an organism — characteristics such as what makes a person have blond hair or a mammoth have tusks, for example. But because cells contain many more copies of mitochondrial DNA than nuclear, it is generally far easier to extract and sequence them.

Recent DNA studies of the woolly mammoth genome illustrate some of these differences. While two teams determined the mitochondrial sequences to better understand the mammoth’s ancestral relationship to modern African and Asian elephants, another team analyzed the nuclear genome to learn more about mammoth’s environmental conditions, as well as specific physical traits of the beast.

In one of the mitochondrial studies, published Feb. 3 in PLoS Biology, a team led by Evgeny Rogaev, a geneticist at the University of Massachusetts Medical School in Amherst and Academy of Sciences in Moscow, reconstructed a complete sequence of 16,842 base pairs of mitochondrial DNA of a woolly mammoth, as well as the mitochondrial genome of the African and Asian elephant. They radiocarbon dated the exceptionally well-preserved mammoth (found in permafrost in northeastern Siberia) to about 32,000 years before present. The researchers had an abundance of ancient material to work with and were able to use DNA from the muscle tissue to compare to the modern animals.

In another independent study published in the Dec. 18 Nature online, a team led by Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, extracted 16,770 base pairs from a mitochondrial sequence of a younger mammoth, radiocarbon dated to about 12,000 years before present. Also found in Siberian permafrost, this mammoth was less well-preserved, and the team isolated DNA from a bone.

As the mitochondrial sequence (passed down from the mother to offspring) does not undergo nearly the amount of gene mixing that nuclear DNA undergoes, researchers can trace a fairly linear path from an ancestor to a more recent species, and can compare DNA sequences to tell when one species split off from another. Rogaev says their research suggests that sometime around 4 million years ago, a group of mammoth and elephant ancestors wandered out of Africa, while Krause’s team puts that ancestral split at about 6 million years ago.

Both studies, however, point to a quick evolution: Those animals that stayed in Africa evolved into the modern African elephant, and those that wandered out evolved into two separate species — the woolly mammoth and the Asian elephant — within 500,000 years or so, Rogaev says, a blink of an eye in evolutionary time. “Clearly, we still can’t precisely determine when they split off,” Rogaev says, but that will come with further research, as will other evolutionary history information.

But while mitochondrial DNA studies have worked well and will continue to provide insight in determining organisms’ evolutionary history, the future of ancient DNA research is in nuclear DNA studies, Cooper says. Still, while nuclear studies show promise, they are more complicated.

Indeed, the third recent woolly mammoth genome project, which involves nuclear DNA, is still a work in progress. From the small portion of nuclear DNA already mapped, researchers found a similar ancestral divergence around 5 million to 6 million years ago. But this group hopes to learn even more about the woolly mammoth.

The team, led by Poinar of McMaster, took a sample of 28,000-year-old bone from a Siberian mammoth and sequenced everything that was part of the sample, from microbes and bacteria to humans and the mammoth, in an approach called metagenomics. Even a tiny sample of bone will contain millions of fragments of “contaminants” as well as those that the researchers are hoping to map, so “the idea is to get all of the DNA out of everything in the sample” and to map it all, Poinar says.

It’s basically a brute-force solution, he says: If you can’t separate out what you want, you sequence it all and then separate it later. The group sequenced about 28 million base pairs in the sample, about half of which came from the mammoth.

Researchers have already mapped parts of the genomes of thousands of bacteria, microbes, plants and animals and created a “library” filled with the genomic data. Powerful computer algorithms can sort through the mass of metagenomic data to match sequences.

The brute force of the metagenomics approach can deal with contamination better than more traditional methods of DNA studies, Cooper says. However, “the method can be very wasteful, depending on the quality and purity of the sample,” as alongside the genome that scientists are interested in may be a very large percentage of other sequences — as high as 99 percent in a metagenomic cave bear study published in Science last year — that will go unstudied.

Metagenomics is also currently expensive. Running a single plate of DNA, which can yield 40 million base pairs, through the sequencing machine costs about $6,000, Poinar says. Although “this is cheaper per base than standard current technologies,” he says, it is nonselective, meaning “you have to sequence everything,” which can be wasteful. But it will get less expensive and more effective, he says, as mitochondrial DNA sequencing has done.

Of further interest, says Matthew Collins, a specialist in bioarchaeology at the University of York in the United Kingdom, is that in the near future, metagenomics “may allow you to do paleontologic research without the fossils.” Researchers are finding that proteins and DNA can persist in soil for hundreds of thousands of years, if not millions, he says. Mapping all the sequences of DNA or proteins that are found in a particular location, “you can tell when a creature or plant had been there.” As fossils are rare, especially in low-preservation environments such as warm, temperate climates, this might be an “interesting path forward,” he says.

Even under the best preservation systems, however, researchers suggest that readable DNA does not likely exist beyond a couple of million years. And so far, sequences haven’t been reputably reproduced back further than 500,000 years old, researchers say. So for all the kids out there hoping for a real-life Jurassic Park with dinosaurs returning to life, Cooper chuckles, saying “I don’t think so.”

In theory, however, Poinar says, the possibility might someday exist to create “hybrid organisms” from younger extinct animals and their closest relatives — such as Asian elephants and a woolly mammoth, for example. This “Pleistocene Park” is in theory possible, he says, but the “more important question is ‘should it be done?’”

Megan Sever

Links:
Australian Centre for Ancient DNA at the University of Adelaide
McMaster Ancient DNA Center
Joint Genome Institute at Lawrence Berkeley National Laboratory


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