Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past

by David Reich

some experts designating Neanderthals as a distinct species of the genus Homo (Homo neanderthalensis), and others as a subgroup of modern humans (Homo sapiens neanderthalensis). The designation of two living groups as distinct species is often based on the supposition that the two do not in practice interbreed.

whether extinct populations are distinct enough to merit designation as different species are traditionally made based on the shapes of skeletons, and for Denisovans there are very few physical remains, providing even more reason to be cautious.

These teeth were enormous, beyond the range of nearly all teeth previously reported in the genus Homo. Large molars are thought to be biological adaptations to a diet that includes lots of tough uncooked plants. Prior to the Denisovans, the humans closest to us who were known to have had teeth of this size were the primarily plant-eating australopithecenes, like the famous “Lucy,” whose skeleton, dating to more than three million years ago, was found in the Awash Valley of Ethiopia.

Denisovans were genetically a little closer to New Guineans than they were to any population from mainland Eurasia, suggesting that New Guinean ancestors had interbred with Denisovans. Yet the distance from Denisova Cave to New Guinea is around nine thousand kilometers, and New Guinea is, of course, separated by sea from the Asian mainland.

In New Guinean genomes today we were able to measure the size of intact archaic ancestry segments, and found that the ones related to Denisovans were about 12 percent longer than the ones related to Neanderthals, implying that the Denisovan-related segments had been introduced that much more recently on average.

Based on how much longer the Denisovan segments were than the Neanderthal segments in New Guineans, we could conclude that the interbreeding between Denisovan and New Guinean ancestors occurred fifty-nine to forty-four thousand years ago.

5 to 8 percent of New Guinean ancestry comes from archaic humans. This is the largest known contribution of archaic humans to any present-day human population.

We found the largest amounts of ancestry in indigenous populations in the islands off Southeast Asia and especially in the Philippines and the very large islands of New Guinea and Australia

The populations in question are largely east of Huxley’s Line, a natural boundary that separates New Guinea, Australia, and the Philippines from the western parts of Indonesia and the Asian mainland. This line was described by the nineteenth-century British naturalist Alfred Russel Wallace, and adapted by his contemporary the biologist Thomas Henry Huxley to highlight differences in the animals living on either side, for example, it roughly forms the boundary between placental mammals to the west and marsupials to the east. It corresponds to deep ocean trenches that have formed geographical barriers to the crossing of animals and plants, even in ice ages when sea levels were up to one hundred meters lower. It is remarkable that modern humans after fifty thousand years ago made it across this barrier.

Had the interbreeding occurred in mainland Asia, and modern humans carrying Denisovan-related ancestry then spread all over, multiple populations of the region as well as ancient humans from East Asia would be expected to carry Denisovan-related ancestry in amounts comparable to what is seen in New Guineans. But this is not what we observe.

it is more likely that interbreeding occurred in southern China or mainland Southeast Asia.

An archaic human from Narmada in central India may date to around seventy-five thousand years ago.

Chinese and Indian government rules complicate the export of skeletal material, but world-class ancient DNA labs have now been established in China and are beginning to be built in India. DNA from these samples could lead to extraordinary insights.

the archaic people who interbred with the ancestors of New Guineans were not close relatives of the Siberian Denisovans.

the ancestors of the Siberian Denisovans separated from the Denisovan lineage that contributed ancestry to New Guineans two-thirds of the way back to the separation of the ancestors of Denisovans from Neanderthals.

Most likely there are other Denisovan populations as well that we haven’t sampled at all. Maybe we should even consider Neanderthals as part of this broad Denisovan family.

I like to call them “Australo-Denisovans” to highlight their likely southern geographical distribution. Anthropologist Chris Stringer prefers “Sunda Denisovans” after the landmass that joined most of the Indonesian islands to the Southeast Asian mainland.14 But this would not be an accurate name if the interbreeding occurred in what is now mainland Southeast Asia, China, or India.

A big-skulled skeleton found near Heidelberg in Germany in 1907 and dated to around six hundred thousand years ago15 was plausibly from a species that was ancestral to modern humans and Neanderthals,16 and by implication, Denisovans

the tiny humans of Flores island in present-day Indonesia—the “hobbits” who likely descend from early Homo erectus whose descendants arrived at Flores island before seven hundred thousand years ago and became isolated there by deep waters.

Seventy thousand years ago, the world was populated by very diverse human forms, and we have genomes from an increasing number of them, allowing us to peer back to a time when humanity was much more variable than it is today.

Denisovan-related ancestry in East Asians is about a twenty-fifth of that seen in New Guineans—it comprises about 0.2 percent of East Asians’ genomes, rising to up to 0.3–0.6 percent in parts of South Asia.20 We have not yet been able to determine if the Denisovan-related ancestry in mainland Asia and the islands off Southeast Asia comes from the same archaic population or from different ones.

One of the most striking genomic discoveries of the past few years is a mutation in a gene that is active in red blood cells and that allows people who live in high-altitude Tibet to thrive in their oxygen-poor environment.

some Denisovan relatives in mainland Asia may have harbored an adaptation to high altitude, which the ancestors of Tibetans inherited through Denisovan interbreeding. Archaeological evidence shows that the first inhabitants of the Tibetan high plateau began living there seasonally after eleven thousand years ago, and that permanent occupation based on agriculture began around thirty-six hundred years ago.

at genes associated with the biology of keratin proteins, present-day Europeans and East Asians have inherited much more Neanderthal ancestry on average than is the case for most other groups of genes.

keratin is an essential ingredient of skin and hair, which are important for providing protection from the elements in cold environments such as the ones that modern humans were moving into and to which Neanderthals were already adapted.

sub-Saharan Africans to be slightly more closely related to Neanderthals than to Denisovans.24 This must reflect another example of interbreeding we didn’t know about. The pattern we observed could only be explained by Denisovan interbreeding with a deeply divergent, still unknown archaic population—one from which Africans and Neanderthals have little or no DNA, and which separated from the common ancestors of modern humans, Neanderthals, and Denisovans well before their separation from each other.

the unknown archaic population that interbred into Denisovans first split off from the lineage leading to modern humans 1.4 to 0.9 million years ago and that this unknown archaic population contributed at least 3 to 6 percent of Denisovan-related ancestry.

think of this group as “superarchaic” humans, as they represent a more deeply splitting lineage than Denisovans. They are what I call a “ghost” population, a population we do not have data from in unmixed form, but whose past existence can be detected from its genetic contributions to later people.

the first important spread of humans to Eurasia occurred at least 1.8 million years ago, bringing Homo erectus from Africa. The genetic evidence suggests that a second lineage split from the one leading to modern humans around 1.4 to 0.9 million years ago, giving rise to the superarchaic group

Genetics also suggests a third major split 770,000 to 550,000 years ago when the ancestors of modern humans separated from Denisovans and Neanderthals, followed by Denisovans and Neanderthals from each other 470,000 to 380,000 years ago.

The argument that modern humans radiated from Africa comes from the observation that the most deeply divergent branches among present-day humans are most strongly represented in African hunter-gatherers (such as San from southern Africa and central African Pygmies).

the genetic comparisons of present-day populations that point to an origin in Africa can only probe the population structure that has arisen in the last couple of hundred thousand years, the time frame of the diversification of the ancestors of present-day populations.

the ancestral population of modern humans, Neanderthals, and Denisovans actually lived in Eurasia, descending from the original Homo erectus spread out of Africa.

what of the intervening period between two million years ago and about three hundred thousand years ago? In a large part of this time, the human skeletons we have from Africa are not obviously more closely related to modern humans than are the human skeletons of Eurasia.25 Over

María Martinón-Torres and Robin Dennell.

humans they call Homo antecessor, found in Atapuerca, Spain, and dating to around one million years ago, show a mix of traits indicating that they are from a population ancestral to modern humans and Neanderthals.

Martinón-Torres and Dennell argue for the possibility of continuous Eurasian habitation from at least 1.4 million years ago until the most recent common ancestor of humans and Neanderthals after eight hundred thousand years ago, at which point one lineage migrated back to Africa to become the lineage that evolved into modern humans.

Two years after Meyer and Pääbo published mitochondrial DNA data from Sima de los Huesos, they published genome-wide data.29 Their analysis not only confirmed that the Sima humans were on the Neanderthal lineage, but went further in showing that the Sima humans were more closely related to Neanderthals than they are to Denisovans. These results provided direct evidence that Neanderthal ancestors were already evolving in Europe at least four hundred thousand years ago, and that the separation of the Neanderthal and Denisovan lineages had already begun by that time.

patterns suggest that Denisovans and Neanderthals both had ancestry from the same superarchaic population, with just a larger proportion present in the Denisovans.

Eurasia was a locus of human evolution that rivaled Africa.

Europe is a peninsula, a modest-sized tip of Eurasia.

The significance of the tree is that once a population separates, it does not remix, as fusions of branches cannot occur.

how wrong the tree metaphor is for summarizing the relationship among modern human populations.

If a set of four populations is described by a tree, then the frequencies of their mutations are expected to have a simple relationship.2

at mutations not shared with sub-Saharan Africans, Europeans are more closely related to Native Americans than they are to East Asians.

we found the same pattern in every Native American population we studied, including those we could prove had no European admixture. The scenario of Native Americans and Europeans descending from a common population that split earlier from East Asians was also contradicted by the data.

the patterns reflect an episode of mixture deep in the ancestry of Native Americans: a coming together of people related to Europeans and people related to East Asians prior to crossing the Bering land bridge between Asia and the Americas.

the Three Population Test, which evaluates a “test” population for evidence of mixture. If the test population is a mixture of lineages related to the comparison populations in two different ways—as African Americans are a mixture of Europeans and West Africans—then the frequencies of the test population’s mutations are expected to be intermediate between those of the two comparison populations. In contrast, if mixture did not occur, there is no reason to expect the frequencies of mutations in the population to be intermediate. Thus the scenarios of mixture and no mixture yield two qualitatively very different patterns.

people in northern Europe, such as the French, are descended from a mixture of populations, one of which shared more ancestry with present-day Native Americans than with any other population living today.

more than fifteen thousand years ago, there was a population living in northern Eurasia that was not the primary ancestral population of the present-day inhabitants of the region. Some people from this population migrated east across Siberia and contributed to the population that crossed the Bering land bridge and gave rise to Native Americans. Others migrated west and contributed to Europeans. This would explain why today, the evidence of mixture in Europeans is strong when using Native Americans as a surrogate for the ancestral population and not as strong in indigenous Siberians, who plausibly descend from more recent, post–ice age migrations into Siberia from more southern parts of East Asia.