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Human origins becoming more complex

“Neo” skull of Homo naledi, on exhibit at Maropeng. John Hawks CC-BY.

John Hawks, Three new discoveries in a month rock our African origins, Medium, June 2017

The evolutionary story of modern humans just got more complicated

Four years ago, the story of modern human origins seemed fairly simple. Modern humans originated in Africa sometime around 200,000 years ago. Some modern people spread into other parts of the world sometime after 100,000 years ago, mixing a bit with archaic human groups they met along the way.

New discoveries have shown just how oversimplified this picture was. The common ancestors of today’s modern humans lived a lot earlier than we thought, and we can’t connect them to the fossil record. They were far from alone: Africa was full of other groups, now extinct, and some of them mixed Neanderthal-like into living populations.

The last month has seen more shake-ups to the modern human origins story than any time I can remember. Here’s what we have learned in the last few weeks about this key time period in Africa.

The deepest split

Modern humans share a lot with each other. We’re 99.9% genetically the same, and that impressive genetic similarity comes from inbreeding.

When geneticists first started measuring genetic differences between people, they realized that the population must have once been a lot smaller. They came up with the idea of a genetic “bottleneck”, a period in which the human population might have been very small.

But the last few years have added a lot of complications to this simple picture.

A result from PSMC studies of human genomes from different populations (indicated). The French underwent a clear bottleneck, starting between 100,000 and 50,000 years ago, which was actually shared by all other people outside Africa. But the African populations here had no strong bottleneck.

One problem is that the “bottleneck” concept applies mostly to people outside of Africa. They have inherited most of their genes from a small population that grew and dispersed throughout the world. That dispersal carried that signal of a “founder effect” along with it. Those people further mixed a small fraction with archaic humans, the Neanderthals and, for a few, the Denisovans. That founder effect unfolded within the last 100,000 years.

The story of the rest of the world during the last 100,000 years is not the story of Africa. Most humans continued to live in Africa and didn’t share the bottleneck. They preserve a pattern of diversity that goes much earlier back in time, meaning that today they are much more diverse in their genes.

In all the world, genetic diversity is greatest today among the Khoe-San peoples of southern Africa. Until this week, geneticists have thought that their ancestral lineage has existed for as long as 200,000 years. That origin, the deepest split between human populations that still exist, points to the stem population of all living people. It doesn’t divide Africans from non-Africans, it reflects a deep history of diversity among African populations — the founder effect leading to non-African peoples was much later.

That stem population, in genetic terms, is the origin of modern humans.

This week, Carina Schlebusch and colleagues posted a preprint that reports on the ancient genome of a boy who lived at Ballito Bay, South Africa, around 2000 years ago. His genome connects him to the Khoe-San peoples of today. But there’s an important difference. By comparing his genome with the genes of living people, Schlebusch and her coworkers found that today’s Khoe-San have received a lot of genetic mixture from other populations during the last 2000 years.

That’s not a surprise. Humans mix with each other, and that mixture has increased in recent times. Very ancient peoples mixed too, but migration and mixing were less in the distant past than in recent history.

What this means is that today’s Khoe-San people share many genes with people in other parts of Africa, and with people in Eurasia, from recent mixing. If we use today’s genetic diversity to try to work out the original ancestors of modern humans, we’re going to come up with an answer that is too recent, because of these recently shared genes.

Schlebusch and her team used the 2000-year-old genome to come up with a better estimate of when the stem population of modern humans lived. The answer was a lot older, around 260,000 years ago. Modern populations, the ancestors of living people, have been diversifying from each other within Africa for at least that long.

It’s a good reminder that within humans, a genetic “split” is not really a split. Populations of humans mix. That’s what we do. So when we look back into the past, we are looking at populations that reticulated with each other.

Who were these early modern humans?

Genetics tells us that the ancestry of African groups is like a river delta, spreading from some 260,000 years ago up to the present. But anthropologists really disagree about how to identify “modern humans” in the fossil record. A fossil that shares some human traits might be part of that delta network leading to some living populations. But just as easily, it might instead be off on its own branch, flowing until it disappears into the desert sands.

Archaic people in Africa — all the humans who were not part of that river delta — were not Neanderthals. So they didn’t share the features of Neanderthals, certainly not all of them. Many of them would have shared features with modern people. So how can we recognize them? And how many groups of them were there?

One big clue has been published just this week, by Jean-Jacques Hublin and his colleagues. They conducted new excavations at a site in Morocco called Jebel Irhoud. Old excavations carried out in the 1960s had produced parts of three skulls and some other human bones. Previous scholars had tried to work out the geological age of these remains, ultimately deciding they were around 150,000 years old.

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