2017's “Greatest Hits” in Human Population Genetics

Over the past 10 years human population genetics has undergone a major revision from where it was a decade before. To a great extent the field as we understand it existed in a relatively “flat,” incomplete sense at the turn of the century.

Why? Because inferences were made based on patterns of variation in present populations, as opposed to past populations. It turns out that to truly understand the past, one must obtain results from the past.

But how can we make inferences from the past? After all, it’s dead and gone. And yet between the years of 2005 — 2010, geneticists working in the previously abstruse field of ancient DNA refined and improved their techniques so that analyses could be routinely brought to bear upon remains, human and otherwise, which had been lost to prehistory.

Because questions related to human population genetics have to do with tens of thousands (rather than millions) of years, and younger fossils on this time scale are not entirely mineralized, salvageable DNA could be extracted. Out of this previously obscure discipline have emerged some of the most revolutionary population genetic results of the 21st century, and this year has been no different.

Anatomically modern humans may be hundreds of thousands of years more ancient than we’d thought. In September, Science published Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Using an ancient genome from South Africa, the researchers re-calibrated the divergence date between the Khoisan people of the region and other modern humans. Prior to this, a 200,000 year-old anatomically modern human fossil from Ethiopia had been “pegged” the common ancestor of our species. Because the Khoisan were (and are) the most genetically distant modern human population in relation to other lineages, it was presumed that their divergence dated to this period.

It turns out, though, that the Khoisan have had gene flow from other Africans in the last 2,000 years. The ancient genome was even more distant from other humans than the modern samples! Combined with the fossil discovery of a modern human from Morocco that dates to over 300,000 years ago, “modern human” just got a whole lot more ancient in 2017.

Sub-Saharan Africa has been demographically transformed in the past 4,000 years. The ethno-linguistic landscape of Africa south and east of Nigeria is dominated by the interplay of Bantu-speaking peoples with other groups, such as the Nilotic peoples or the Khoisan, as bit players. But ancient DNA tells us that this is a recent phenomenon. In the ancient past, African hunter-gatherers from the Cape of Good Hope northward toward Ethiopia were part of a distinct genetic continuum, which seems to have left little genetic imprint on the modern peoples of East Africa.

At least that’s the major finding a new paper, Reconstructing Prehistoric African Population Structure. Looking at ancient genomes from Malawi and Tanzania the researchers found that the ancient hunter-gatherers contributed no ancestry to modern Bantu farmers, while farmers from the ancient Near East were already mixing with local African populations.

Much of human genetic variation in pigmentation was present before modern humans left Africa. It is well known that most of the genetic variation found in modern humans can be found within Africa. That is due to the fact that 50,000 years ago the ancestors of non-Africans went through a bottleneck as they were leaving the continent and lost much of their ancestral variation. But another fact discovered in 2017 is that most of the variation in skin color in modern humans derives from our ancient African forebears.

The paper, in Science, has the unassuming title of Loci associated with skin pigmentation identified in African populations. There has been a lot of research on the genetics of skin color in humans, in part because the trait is important to us. Using a large sample from African populations, the authors found that most of the genetic variation found outside of Africa controlling the range of complexions we see around the world today was already present within Africa — 50,000 years ago!

Though arguably 2017 was the year when Africa finally came to center stage, presaging a shift in human population genomics in the next few years, other parts of the world also had major finds. The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe is a curious title about something quite significant: the people who are most closely associated with Stonehenge were not the same people who created Stonehenge.

Stonehenge was constructed around 3100 B.C. by a farming people with affinities to modern Sardinians, and ultimate origins in the ancient Near East. What the latest ancient DNA results indicate is that a massive demographic disruption occurred around 2400 B.C., and these British farmers were replaced by people who brought with them the “Bell Beaker culture.” Originating in Iberia, and named after their distinctively-shaped pottery, the Bell Beaker culture spread through Northern Europe. Around 2400 B.C. massive numbers of these Northern European Bell Beaker people seem to have migrated to Britain, replacing the people and culture who had lived there previously.

As we near the writing of the final chapters of the story of the ancient population genetic history of Northern Europe, 2017 witnessed the prologue of what is to come for Asia. Published in Current Biology, 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia, is understated in the way that only scientific paper titles can be. With the first reasonably complete ancient genome from East Asia, the authors have now established that the divergence between West and East Eurasians dates to more than 40,000 years before the present, not too far after our emergence out of Africa ~50,000 years ago. Why? Because the 40,000 year old individual that they analyzed from China is genetically closer to modern East Eurasians than it is to West Eurasians.

And yet, just as one fact is clarified, another mystery emerges: the 40,000 year old individual was likely not the ancestor of modern East Asians, just related to them. It exhibits genetic distinct affinities to peoples in Oceania and the Amazon, and hints at a startlingly surprising and novel genomic landscape in Pleistocene Asia. The story whose first chapters are only now coming into focus….

Finally, a new Neanderthal genome was sequenced and analyzed. But isn’t a Neanderthal just a Neanderthal? Not at all, and our understanding of Neanderthal genetic diversity is still developing. Neanderthals lived for hundreds of thousands of years from the Atlantic to the Altai mountains of Siberia. There’s no reason why they shouldn’t be a diverse and varied lot.

The first blockbuster of ancient human genomics landed in 2010: Neanderthals seem to have contributed to the ancestry of most modern non-Africans, at the level of a few percent. But generalizing from one Neanderthal genome to all Neanderthals is like generalizing from the whole genome of Craig Venter to all humans. You’ll learn something, but not everything.

The new genome from Vindija Cave in Croatia ~50,000 years ago, is exactly when modern humans seem to have obtained their Neanderthal ancestry. It turns out that this individual’s genome is more similar to non-Africans than the earlier genome. We’re actually 10–20% more Neanderthal than we had thought!

As 2017 has come and gone some things are obvious when it comes to the utilization of genomics for inference of human history: much has been learned, but much will be learned. Europe has been so well-studied that little of an earth-shaking nature was or will be produced. On the other hand, even a single good quality whole genome from Asia is notable. Africa occupies a position in the middle, as ancient genomes and better sampling are already giving us a better understanding of the cradle of modern humanity.

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