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Image of a forest-covered island.
Enlarge / The home territory of New Guinea highland populations.

The inhabitants of the Pacific came in waves. Aboriginal Australians were the first to cross the area, and they were followed by separate populations that inhabited New Guinea and nearby island chains. Later still, the Polynesians, descendants of early East Asians, spread through the distant islands of the Pacific.

While modern genetics has made these rough outlines clear, it has also made it clear that these different populations sometimes interacted, sharing DNA along with technology and trade goods. Paleontology finds have made it clear that at least three distinct hominin species had occupied some of these islands before modern humans arrived, including the enigmatic Hobbits of Indonesia and a similarly diminutive species in the Philippines.

A recent study of the genomes of Pacific island populations provides a map of some of the major interactions that took place in the Pacific. And it suggests at least one of these involved the introduction of additional Denisovan DNA.

New genomes

The work started with the sequencing of over 300 genomes volunteered by individuals from 20 different populations throughout the Pacific. The research team grouped these populations according to whether they came from Near Oceania (Indonesia, New Guinea, and the Philippines) or more distant islands of the Pacific (collectively Far Oceania). The latter is largely populated by the Polynesians, who arrived relatively late and had a distinct genetic history. But there were clearly interactions between the two groups, and the border between the areas each occupies is fuzzy in locations.

By comparing the genome sequences with each other and ancestral populations, it’s possible to make estimates of which groups are related to which others, as well as the time at which the different populations branched off. In addition, it’s possible to detect interbreeding among the populations, based on the appearance of stretches of DNA that are found in one population but are more similar to those from another.

The people who live in the highlands of Papua New Guinea have the earliest split, separating from the populations of other islands about 40,000 years ago. The branches of that lineage who inhabit the Bismarck and Solomon Islands separated from each other about 20,000 years ago.

But things get much less neat in Vanuatu, a group of islands out past the eastern end of the Solomons. About a third of their genome comes from Bismarck islanders, and that was a recent arrival, the result of interactions that took place only about 3,000 years ago. The rest comes from a group that started out in Papua but interbred with the Solomon Islands population en route. All of that means that Vanuatu is like a melting pot of near oceanic populations.

Then there are the Polynesians. They seem to have interbred with both the Bismarck and Solomon islanders. The best fit to the data involves one interaction right as the Polynesians arrived in the area about 3,500 years ago and a second interaction that occurred a thousand years later.

Premodern humans

All of the populations sampled seem to have roughly similar amounts of Neanderthal DNA, present in similar locations in the genome, suggesting there was nothing unusual about their genetic history compared to other groups in the region. But that was not the case with the Denisovans. The amount of Denisovan DNA varied considerably among the populations, with the highest percentage found in those from the New Guinea highlanders.

Analysis of the Denisovan DNA segments was used to determine two things. The length of the DNA provided a measure of how long ago the interbreeding took place, as the Denisovan DNA segments would get shorter over time thanks to recombination. The sequence itself could be compared to the genome of a Denisovan bone in Siberia, which tells us a bit about how diverse the Denisovan population was.

East Asian populations and the Polynesians appear to have had two different periods of interbreeding with Denisovans, both of which were reasonably closely related to the Siberian population.

The people of Papua New Guinea also showed signs of two periods of interbreeding. But, rather critically, they weren’t the same ones seen in East Asians. The first involved interbreeding around 45,000 years ago with a population that had separated from the Siberian Denisovans by roughly 200,000 years—a genetic contribution shared with the East Asians and Polynesians. But the second interbreeding event took place about 25,000 years ago—after the point where the population was out in the Pacific.

And that’s a bit strange. In terms of fossil evidence, we know that Homo erectus was in the area before modern humans arrived, but its DNA would be substantially different from that of Denisovans. There are two other species—the Hobbits of Flores and an equally odd hominin from the island of Luzon. While these look very different from modern humans (having some traits shared with the earlier Australopiths), we can’t rule out that they are closely related to the Denisovans, which would explain the origin of this DNA.

The researchers checked, and the only signs of distantly related DNA can be accounted for by Neanderthals and Denisovans. So if these island species aren’t Denisovans, then it appears we didn’t interbreed with them in a way that left its mark on modern genomes.

What this tells us

Modern humans reached places that required travel across the open ocean very early during their expansion out of Africa. That would seem to suggest that ocean-going voyages were well within our abilities. But these data indicate that most populations remained relatively isolated from each other once they were established. That suggests that, even though the technology was available to manage this travel, it wasn’t widely used—certainly, there’s no indication of longstanding trade until the Polynesians arrive.

Once the Polynesians did arrive, however, there are indications that they interacted at least twice with the inhabitants of the islands near New Guinea. And Vanuatu, at the border between Near Oceania and Polynesia, seems to have an exceedingly complicated history.

To an extent, it seems that, outside of Vanuatu, these people groups interacted with each other about as often as their ancestors interacted with the Denisovans. The genomic data provides evidence of several distinct periods of interbreeding, including one that for now appears specific to a group that is native to the Philippines. This indicates that some of the interbreeding likely went on after modern humans had migrated out into the Pacific islands.

Since we don’t know of any Denisovan remains in the region, it suggests two possibilities. One is that the Denisovans were in the area undetected—not a huge surprise, given how long their presence in Asia went undetected. But the more intriguing prospect is that one of the species we’re aware of from skeletal remains—Homo luzonensis or Homo floresiensis—represents a branch of the Denisovan lineage. So far, all attempts at extracting DNA from these skeletons have failed, so it’s not clear if or how we’d be able to figure this out.

Nature, 2021. DOI: 10.1038/s41586-021-03236-5  (About DOIs).

Image of a skull partially buried in sediments.
Enlarge / One of the remarkably intact Dmanisi skulls at the time of its discovery.

We have an extensive collection of fossils from the lineages that produced us humans. A large number of Australopithecus and early Homo skeletons track the transition to bipedal walking and the appearance of features that mark our present anatomy. But it’s much harder to figure out what led to the mental capabilities—complex language, the near-constant use of tools, and so on—that help set humans apart.

Much harder—but not entirely impossible. Remains of skulls can help us figure out the likely cranial capacity of extinct species. And the brain actually leaves its mark on the interior of skulls, allowing some aspects of the brain’s anatomy to be pieced together. Now, an international team has done this sort of analysis on a set of Homo erectus from a critical point in our species’ past. They have found that some earlier brain species persisted well into the history of our genus Homo, but that didn’t stop those ancestors from migrating out of Africa.

Reconstructing brains

How do you figure out what a brain once looked like? You need a reasonably intact skull, which is relatively rare, given the fragility of the bones. Once the skull is reconstructed, it’s possible to make what’s called an “endocast” of the interior of the skull, capturing the details of its features, including where it conformed to the underlying brain. In some cases, endocasts form naturally during the deposition of material around a fossil. They could also be made after discovery and now can be done virtually thanks to our ability to scan and reconstruct 3D volumes.

Obviously, there’s a lot going on in the brain that isn’t near its interface with the skull, and endocasts aren’t going to be able to tell us about those changes. But if you look at endocasts of the brains of humans and our closest simian relatives, there are some clear diagnostic differences. One of the more significant ones is in an area called Broca’s cap, which is associated with language abilities.

Lots of endocasts have been made over the years, and they show a pretty clear pattern. Early relatives like Australopiths retained the ape-like arrangement of the forebrain. More recent ancestors, like Homo erectus had an arrangement that looked much more like what we have today. This led to the assumption that the modern arrangement evolved at the same time as our genus Homo appeared.

The new work extends our collection of endocasts to some critical skeletons: the Dmanisi hominins, which date to about 1.8 million years ago and were discovered in the Republic of Georgia. These are generally classified as members of Homo erectus, but they retain enough features of earlier species that this label remains controversial. The Dmanisi skeletons are interpreted as indications that Homo erectus expanded out of Africa very early, perhaps while its features were still in flux.

Redrawing the tree

The results are pretty clear: all five Dmanisi skulls show the earlier pattern of brain structure. That has a number of significant implications. It clearly means that the present-day brain structure did not originate with the genus Homo but only evolved after we’d been around for nearly a million years. In addition, the Dmanisi skeletons were found with a variety of stone tools, so we can infer that the modern brain structure wasn’t a prerequisite for their development.

Finally, it also shows that our ancestors didn’t need the present-day brain structure in order to spread far beyond their point of origin in Africa. In fact, it suggests that the relationship between our brains and migrations is extremely complicated because previous data, when incorporated into this analysis, indicates that the modern arrangement of the brain was in place by 1.5 million years ago—and appeared almost contemporaneously from Africa to Southeast Asia.

This suggests that our ancestors left Africa in multiple waves, some not separated by very much time, at least in evolutionary terms. And before this critical time period, the size of the brain (as opposed to its arrangement) was increasing gradually and steadily. (Albeit with some severe outliers like the Indonesian hobbits and Homo naledi, which were small-brained but very recent.)

Complicating matters further, the researchers note that there were much larger changes going on in facial morphology during this time, probably driven largely by diet. But there’s no clear correlation between what was going on with the face and jaw and what was happening with the brain structure.

So while the new study clarifies a lot of questions and overturns a major assumption, there are limits to how much it can tell us. Although the brain region looked at here is associated with language, there’s no way to tell if its appearance correlated with the use of language. Tool technologies changed at around the same time as the transition between brain structures, but it’s impossible to tell if the two were related. And we can only guess at the selective pressures that drove the changes in the brain.

But one thing is clear: our ancestors’ ability and desire to roam the world was present long before our current brain structure was in place.

Science, 2021. DOI: 10.1126/science.aaz0032  (About DOIs).

Sex with Neanderthals was common for early Eurasian Homo sapiens, DNA says
Hajdinjak et al. 2020

DNA from the earliest Homo sapiens in Europe adds more detail to the story of our species’ expansion into Eurasia—and our complicated 5,000-year relationship with Neanderthals.

The earliest traces of our species in Eurasia are a lower molar and a few fragments of bone from Bacho Kiro Cave in Bulgaria, dating to between 46,000 and 42,000 years old. A recent paper describes DNA from those fossils, as well as a 42,000- to 37,000-year-old jawbone from the Oase site in Romania. The results suggest that the early waves of Homo sapiens in Eurasia included several genetically distinct groups, only some of which eventually passed their genes on to modern people. Most of those early Eurasians mingled with Neanderthals fairly often.

Paleolithic and ready to mingle

Neanderthals had lived in Europe and Asia for at least 350,000 years (and had a complicated population history of their own) when the first groups of Homo sapiens expanded northward from eastern Africa and the Levant. Today, many populations of modern humans still carry tiny fragments of Neanderthal DNA in our genomes as souvenirs from the mingling of two hominin species 45,000 years ago. But we still don’t know much about how often Neanderthals and Homo sapiens got together during the few millennia when they shared a continent.

When Max Planck Institute for Evolutionary Anthropology geneticist Mateja Hadjinjak and her colleagues sequenced DNA from the Homo sapiens bones at Bacho Kiro Cave in Bulgaria, one lower molar and a small scrap of bone were all that remained of a man who died at the site around 45,900 years ago. But that’s enough to get us genetic data these days. His genome contained fragments of the Neanderthal versions of some genes, which had been split up and rearranged in a way that suggested they’d been passed down through about six generations. In other words, one of his great-great-great-great grandparents was a Neanderthal.

Two other pieces of bone at Bacho Kiro Cave were the sole remains of two men who died around 45,000 to 42,000 years ago, and both of them had Neanderthal ancestors seven generations back. Meanwhile, at the Oase site in Romania, DNA from a man who died between 42,000 and 37,000 years ago revealed that one of his direct relatives—a parent or grandparent—was a Neanderthal.

That’s a rare glimpse of a specific, very human story: direct evidence that a Neanderthal and a Homo sapiens had sex and produced a child. A tooth from Denisova Cave in the Altai Mountains of Siberia tells a similar story about a Neanderthal, a Denisovan, and their daughter 90,000 years ago. Those moments are rare in a genetic and archaeological record, which usually only reveals big, sweeping populations trends.

While we don’t have direct evidence of individual relationships—whatever form they took, and whatever they meant to the people involved—the relationships themselves probably were anything but rare.

“It is striking that all four of the European individuals who overlapped in time with late Neanderthals and from whom genome-wide data have been retrieved had close Neanderthal relatives in their family histories,” wrote Hadjinjak and her colleagues in their paper. “This suggests that mixing between Neanderthals and the first modern humans that arrived into Europe was perhaps more common than is often assumed.”

Neanderthal deserts

If Neanderthals and Homo sapiens were really having sex—and offspring—that often, it may sound like modern people with European and Asian ancestry should be carrying around a lot more Neanderthal DNA. But on average, it’s only about two percent. But Hadjinjak’s study suggests that most Neanderthal genes got weeded out by the process of natural selection very quickly. Within just a few generations, the three men from Bacho Kiro Cave only had between 3.0 and 3.8 percent Neanderthal DNA.

In modern people, Neanderthal DNA is scattered throughout the genome, but Neanderthal versions of genes are more common in some parts of the genome than others. And in some areas, called “Neanderthal deserts,” there are no Neanderthal genes. When Hadjinjak and her colleagues examined the DNA from the three Bacho Kiro men and the one from Oase, they found that although a few Neanderthal alleles still lingered in those sections of the genome, the “Neanderthal deserts” were already starting to form. In other words, the Homo sapiens versions of certain genes offered such an evolutionary advantage that they had already out-competed the Neanderthal versions within just a few generations.

In fact, a younger bone fragment from Bacho Kiro dating to around 35,000 years ago came from a person who had just 1.9 percent Neanderthal DNA, similar to the levels seen in most modern non-African people. However, Hadjinjak and her colleagues acknowledged that “additional individuals with recent Neanderthal ancestry will be needed to fully resolve this question.”

A complicated relationship history

Before this pair of recent studies, we had DNA from just three individuals older than 45,000 years. Now we have DNA from seven, and that drastically improves our view. Still, as always in archaeology, the more data we get, the more questions we can ask.

And there are some questions we may never be able to answer. When Homo sapiens and Neanderthals had offspring, were those pairings the result of illicit relationships, intergroup marriages, or something more violent? It’s hard to imagine what kind of archaeological evidence could provide those details, and the genetic evidence records only the bare biological facts. But because people have always been people, the answer is likely “all of the above, at different times and places.”

Another recent study supports the suggestion that the story wasn’t the same everywhere. DNA from the bones of a 45,000-year-old member of our species, from the Ust’Ishim site in Siberia, suggested that this person’s most recent Neanderthal ancestor was 80 to 95 generations back in the family tree.

And when anthropologist Kay Prüfer, also of the Max Planck Institute, sequenced the DNA of a woman who died at Zlatý kůň in the Czech Republic, her mitochondrial DNA (DNA outside the cell nucleus that is passed directly from mother to child) suggested that she was about 43,000 years old. And based on the length of the segments of Neanderthal DNA in her nuclear genome, her last Neanderthal ancestor lived about 64 to 80 generations before she did. This could mean that interactions varied as different groups of humans and Neanderthals moved around and potentially interacted in different ways.

Who’s related to who?

The DNA from both recent studies sheds some light on how those different groups moved around and how some of them are related to groups of modern people in central and eastern Asia. Both Hadjinjak and her colleagues and Prüfer and her colleagues compared DNA from their specimens to genomes from other ancient and modern people, looking to see how many alleles they shared in common and using computer modeling to see how they might be related.

In Prüfer and her colleagues’ study, the woman from Zlatý kůň belonged to a group of people who apparently didn’t contribute much to the ancestry of later Eurasian people. And DNA from Oase 1, the son of a Neanderthal and a Homo sapiens, suggested that his population also hadn’t “contributed detectably to later populations.” In other words, he was part of a lineage that had died out.

On the other hand, the earliest known Homo sapiens remains in Europe, at Bacho Kiro Cave, belonged to a group that shared noticeably more alleles with modern people in eastern and central Asia than with the people now living in Bulgaria (or anywhere else in Europe or western Asia). The Bacho Kiro population also seems to have been related to another group, which included the ancestors of a 40,000-year-old person unearthed at Tiayuan, in China.

That “provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia,” as Hadjinjak and her colleagues put it, but it’s also clear that several of the first Homo sapiens groups to reach Europe eventually faded away without leaving much of a genetic mark.

The tooth and bone fragments at Bacho Kiro Cave were found buried in a layer of sediment that also contained the remains of a culture known to archaeologists as the Initial Upper Paleolithic. Based on a common style of making stone tools, Initial Upper Paleolithic, or IUP, artifacts have turned up at sites from central and eastern Europe all the way to Mongolia, and it’s possible that some may be waiting to be discovered even further east.

Archaeologists are still debating whether the IUP spans such a wide area because one group of people managed to spread that far or because ideas spread between groups. But both archaeological and genetic evidence now suggest connections between the first Homo sapiens to gain a foothold in Europe and those who lived in Asia just a few thousand years later.

Nature, 2021 DOI: 10.1038/s41586-021-03335-3  (About DOIs).