New genetic evidence shows our ancestors interbred with now-extinct species.

Although only three fossils of Denisovans have been found so far (the finger bone and two molars in the same cave), the girl belonged to a group that left its mark on living people today in Southeast Asia. In follow-up studies, researchers identified people who had inherited about 3 percent of their DNA from the Denisovans, as well as 4 percent to 6 percent of their DNA from Neanderthals. These people are found in a patchwork quilt of populations on islands of Southeast Asia, including Melanesians in Papua New Guinea, aboriginals in Australia, and Negritos in the Philippines. Researchers are searching for new fossils of Denisovans in Asia. But for now, they’re in the curious position of having a genome in search of a substantive fossil record of this new kind of human.

Finding out the overall fraction of our DNA derived from Denisovans or Neanderthals is only the beginning. Researchers are trying to mine as much information as possible from the Neanderthal and Denisovan genomes to find out as much as they can about these archaic peoples’ identities—and what set them apart from us. In August, Pääbo announced in the journal Science that his group had sequenced the genome of the Denisovan girl 31 times over, using a new method to get as sharp a picture of this ancient genome as of a living person’s. The girl’s genome already has given researchers a better look at her: It reveals, for example, that her eyes, hair, and skin were brown.

The research is also giving us a new way to know ourselves. By comparing the girl’s genome to those of living people and Neanderthals, researchers are producing a near-complete catalog of the small number of genetic changes that make us different today from Denisovans and Neanderthals. “This is the genetic recipe for being a modern human,” says Pääbo, whose team also is at work to produce a high-quality copy of the Neanderthal genome.

We three groups were all enough alike that some of our ancestors could interbreed and produce fertile offspring. But the differences in the genomes of Denisovans, Neanderthals, and modern humans are also revealing the genetic traits that set us apart from them—the traits that made us human. “I've been comparing it to the pictures of Earth that came back from Apollo 8. The Neanderthal genome gives us a picture of ourselves, from the outside looking in,” says paleoanthropologist John Hawks of the University of Wisconsin in Madison, in his blog on paleoanthropology, genetics, and evolution. “We can see, and now learn about, the essential genetic changes that make us human—the things that made our emergence as a global species possible.”

Already, researchers have identified differences in genes associated with the wiring of the nervous system, including those involved in the growth of axons and dendrites—the threadlike branches of neurons that transmit signals and connect different parts of the brain. They’ve spotted differences in 34 genes associated with disease in humans, including autism and speech disorders. This doesn’t mean that Denisovans or Neanderthals had those disorders, but changes in those genes during our ancestors’ evolution led to variants that can cause disease.

The next step is to uncover exactly which parts of our genomes have come from Neanderthals and Denisovans. Did we inherit genes from them that helped our ancestors adapt to frigid climates where Neanderthals had lived longer—or to withstand disease or digest different foods? “What, if anything, are those Denisovan genes doing in modern-day Melanesians?” asks paleoanthropologist Chris Stringer of the Natural History Museum in London. “Could they have picked up useful defenses against some of the disease endemic to Southeast Asia?”

Soon we'll be able to specify which parts of our own genes came from Neanderthals and Denisovans. At 23andMe, some customers already are downloading their DNA data and plugging it into search engines to identify which DNA markers they have inherited from Neanderthals—and discussing it on the Spittoon blog. It’s fun to speculate whether you inherited a version of a gene that gives you red hair or a pronounced brow ridge from a Neanderthal, but the quality of the genomic data for Neanderthals is not good enough yet for the comparisons to be reliable, says population geneticist Joanna Mountain, senior director of research at 23andMe.

The Denisovan genome is of high enough quality, however, and it will be a short time before people like me can scan our own genomes data for specific Denisova markers. (Sadly, I’m unlikely to have any Denisovan DNA since my ancestors were not from Melanesia or island Southeast Asia—at least that I know of.) For now, I’m waiting for higher-quality data on the Neanderthal genome, which will be coming, according to Pääbo. In the meantime, we should think twice before we call people Neanderthals. They may not be as fortunate in their inheritance of such an ancient and distinguished bloodline.