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).
A few years ago, David Reich discovered a ghost. Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts, and his team were reconstructing the history of Europe using genomes from modern people, when they found a connection between northern Europeans and Native Americans. They proposed that a now-extinct population in northern Eurasia had interbred with both the ancestors of Europeans and a Siberian group that later migrated to the Americas6.
Reich calls such groups ghost populations, because they are identified by the echoes that they leave in genomes — not by bones or ancient DNA.
Ghost populations are the product of statistical models, and as such should be handled with care when genetic data from fossils are lacking, says Carlos Bustamante, a population geneticist at Stanford University in California. “When are we reifying something that's a statistical artefact, versus when are we understanding something that's a true biological event?”
An international team had sequenced the genome of Ötzi, a 5,300-year-old frozen corpse found in the Tyrolean Alps of Italy in 1991. The researchers wondered if Bustamante could help them to make sense of the ice-man's ancestry. Together, they showed that Ötzi was more closely related to humans who now live in Sardinia and Corsica than those in central Europe, evidence that the population of Europe when he was alive looked very different to how it does today9.
Bustamante has since plunged into the world of ancient DNA. His team is sequencing samples that chart the arrival of farming in Bulgaria, the transatlantic slave trade in the Americas and dog domestication. The group is developing tools to make sequencing ancient DNA cheaper and easier. “We want to democratize the field,” says Bustamante.
These discoveries are only the beginning. The Akey and Reich teams found that the genomes of east Asians possess, on average, slightly more Neanderthal DNA than do people of European ancestry. Akey sees this as possible evidence that Neanderthals interbred with ancient humans on at least two separate occasions: once with the ancestors of all Eurasians, and later with a population ancestral only to east Asians. And Akey believes that humans are likely to bear genetic scraps from other extinct species, including some that interbred with the ancestors of humans in sub-Saharan Africa.