Human evolution: The Neanderthal in the family

Photo Adapted from: Tetra Images/Alamy

Before ancient DNA exposed the sexual proclivities of Neanderthals or the ancestry of the first Americans, there was the quagga.

An equine oddity with the head of a zebra and the rump of a donkey, the last quagga (Equus quagga quagga) died in 1883. A century later, researchers published1 around 200 nucleotides sequenced from a 140-year-old piece of quagga muscle. Those scraps of DNA the first genetic secrets pulled from a long-dead organism revealed that the quagga was distinct from the mountain zebra (Equus zebra).

More significantly, the research showed that from then on, examining fossils would no longer be the only way to probe extinct life. If the long-term survival of DNA proves to be a general phenomenon, geneticists Russell Higuchi and Allan Wilson of the University of California, Berkeley, and their colleagues noted in their quagga paper1, several fields including palaeontology, evolutionary biology, archaeology and forensic science may benefit.

At first, progress was fitful. Concerns over the authenticity of ancient-DNA research fuelled schisms in the field and deep scepticism outside it. But this has faded, thanks to laboratory rigour that borders on paranoia and sequencing techniques that help researchers to identify and exclude contaminating modern DNA.

These advances have fostered an ancient-genomics boom. In the past year, researchers have unveiled the two oldest genomes on record: those of a horse that had been buried in Canadian permafrost for around 700,000 years2, and of a roughly 400,000-year-old human relative from a Spanish cavern3. A Neanderthal sequence every bit as complete and accurate as a contemporary human genome has been released4, as has the genome of a Siberian child connecting Native Americans to Europeans5.

Enabling this rush are technological improvements in isolating, sequencing and interpreting the time-ravaged DNA strands in ancient remains such as bones, teeth and hair. Pioneers are obtaining DNA from ever older and more degraded remains, and gleaning insight about long-dead humans and other creatures. And now ancient DNA is set to move from the clean-rooms of specialists to the labs of archaeologists, population geneticists and others. Thirty years after the quagga led the way, Nature looks to the field's future.

Ludovic Orlando, an evolutionary biologist at the University of Copenhagen, had low expectations when he started sequencing DNA from a 560,000-to-780,000-year-old horse leg bone. His colleague, Eske Willerslev, had discovered the bone buried in the permafrost of the Canadian Yukon in 2003. Then he had chucked it into a freezer, waiting for technological improvements that would allow the bone's degraded DNA to be read. (Freezers in ancient-DNA labs brim with such 'wait and see' samples.)

On a Sunday evening in 2010, Willerslev called Orlando to say that the time had come. Orlando was unconvinced: I started the project with the firm intention of proving that it was not possible, he says.

Sequencing ancient DNA is a battle against time. After an organism dies, the long strands of its DNA fissure into ever shorter pieces, helped along by DNA-munching enzymes. Low temperatures slow this process, but eventually the strands become so short that they contain little information.

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Human evolution: The Neanderthal in the family