Another Mystery Ancestor Joins The Group

Science Daily has a story on genetic work done by researchers at Cornell University and Cold Spring Harbor Laboratory that suggests that there is, as yet, another unnamed ancestor to the modern human line. They write:

In the new paper, the researchers developed an algorithm for analyzing genomes that can identify segments of DNA that came from other species, even if that gene flow occurred thousands of years ago and came from an unknown source. They used the algorithm to look at genomes from two Neanderthals, a Denisovan and two African humans. The researchers found evidence that 3 percent of the Neanderthal genome came from ancient humans, and estimate that the interbreeding occurred between 200,000 and 300,000 years ago. Furthermore, 1 percent of the Denisovan genome likely came from an unknown and more distant relative, possibly Homo erectus, and about 15% of these "super-archaic" regions may have been passed down to modern humans who are alive today.

The paper is available in PLoS Genetics, which means that it is free to the public.  The above-description makes it sound like bootstrapping on stilts.  Here is a paragraph from the paper, itself, that describes the process:

In this paper, we describe a powerful and highly general new method, called ARGweaver-D, that samples ancestral recombination graphs (ARGs) [18–20] conditional on a generic demographic model, including population divergence times, size changes, and migration events. After introducing ARGweaver-D, we present simulation studies showing it can successfully detect Nea→Hum introgression, even when using a limited number of genomes, and that it also has power for older migration events, including Hum→Nea, Sup→Den, and Sup→Afr events. Finally, we apply this method to modern-day Africans and ancient hominins, and characterize both new and previously reported cases of introgression between humans and archaic hominins.

Okay, it still sounds like bootstrapping on stilts.  I am not sure how you can do a simulation to detect older migration events when that is what you are looking for in the first place.  What exactly is an ancestral recombination graph, you ask?  From a previous paper on this subject:

It is possible to capture these complex relationships using a representation called the ancestral recombination graph (ARG), which provides a complete description of coalescence and recombination events in the history of the sample. However, previous methods for ARG inference have not been adequately fast and accurate for practical use with large-scale genomic sequence data. In this article, we introduce a new algorithm for ARG inference that has vastly improved scaling properties. Our algorithm is implemented in a computer program called ARGweaver, which is fast enough to be applied to sequences megabases in length. With the aid of a large computer cluster, ARGweaver can be used to sample full ARGs for entire mammalian genome sequences.

The best data we have suggests that Neandertals and African archaics split some 600 ky ago when a group of Homo ergaster migrated out of Africa and took up residence in western Europe, leading to branching events that eventually included H. antecessor and the Neandertals.  This is supported by this research, which found about 7% introgression into the Neandertal genome of archaic H. sapiens.  The surprise was that 1% of the Denisovan genome likely came from an, as yet, undiscovered hominin.  

Increasingly, there is evidence that considerable interbreeding occurred throughout the middle to late Pleistocene, continuing through the interbreeding that occurred in China and Europe.  As I wrote about the 105-130 ky old Chinese Xuchang skulls:

These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”

This likely represents only a small part of the vast scope of population mixing. I will be curious to see where the ARG research leads.

Neandertal/Denisovan Ancestors Interbred With Unknown Hominin

As if the tangle of early archaic Homo sapiens relationships couldn't get any more confusing, evidence has now surfaced that the ancestors of both the Neandertals and Denisovans interbred with a hominin only known from its DNA signature.  From the University of Utah, through Science Daily:

For three years, anthropologist Alan Rogers has attempted to solve an evolutionary puzzle. His research untangles millions of years of human evolution by analyzing DNA strands from ancient human species known as hominins. Like many evolutionary geneticists, Rogers compares hominin genomes looking for genetic patterns such as mutations and shared genes. He develops statistical methods that infer the history of ancient human populations.

According to the article, Rogers performed a study that argued that Neandertals and Denisovans separated earlier than has previously been suggested but that his evidence for this was thin.

The new study has solved that puzzle and in doing so, it has documented the earliest known interbreeding event between ancient human populations -- a group known as the "super-archaics" in Eurasia interbred with a Neanderthal-Denisovan ancestor about 700,000 years ago. The event was between two populations that were more distantly related than any other recorded. The authors also proposed a revised timeline for human migration out of Africa and into Eurasia. The method for analyzing ancient DNA provides a new way to look farther back into the human lineage than ever before.

"We've never known about this episode of interbreeding and we've never been able to estimate the size of the super-archaic population," said Rogers, lead author of the study. "We're just shedding light on an interval on human evolutionary history that was previously completely dark."

According the Rogers, the DNA evidence puts the final nail in the coffin of the complete Out-of-Africa replacement model of modern human origins:

The researchers also proposed there were three waves of human migration into Eurasia. The first was two million years ago when the super-archaics migrated into Eurasia and expanded into a large population. Then 700,000 years ago, Neanderthal-Denisovan ancestors migrated into Eurasia and quickly interbred with the descendants of the super-archaics. Finally, modern humans expanded to Eurasia 50,000 years ago where we know they interbred with other ancient humans, including with the Neanderthals.

This was likely something like Homo antecessor.  As is also true with the Chinese evidence, this evidence suggests that throughout human evolutionary history, there has never/rarely been a time when these groups of archaic and early modern Homo sapiens could not/did not interbreed. As J. Lawrence Angel once said “When two groups of people meet, they may fight, but they will always mate.”

The Science Advances article is open access. 

http://dx.doi.org/10.1126/sciadv.aay5483

BBC: How Did the Last Neanderthals Live

The BBC has a post on some archaeological discoveries that have illuminated how the Neandertals lived.  Melissa Hogenboom writes:

For the most part, Neanderthals were a resilient group. They existed for about 200,000 years longer than we modern humans (Homo sapiens) have been alive. Evidence of their existence vanishes around 28,000 years ago – giving us an estimate for when they may, finally, have died off.

Fossil evidence shows that, towards the end, the final few were clinging onto survival in places like Gibraltar. Findings from this British overseas territory, located at the southern tip of the Iberian peninsula, are helping us to understand more about what these last living Neanderthals were really like. And new insights reveal that they were much more like us than we once believed.

It always seems to strike these writers as odd that Neandertals were capable of culture roughly equivalent to our own.  The last group of Neandertals lived at a time that was much harsher, climate-wise, than today, with the tundra line being equivalent in latitude, to Vienna.

The original Gibraltar skull was discovered in 1848 (eight years before the type specimen was discovered in the Neander Valley, in Germany).  Clive Finlayson, the Director of the Gibraltar Museum has been part of a team that has been excavating the set of caves there and four caves have been identified.

“It was in some way Neanderthal city,” he says. “This was the place with the highest concentration of Neanderthals anywhere in Europe.” It’s not known if this might amount to only dozens of people, or a few families, since genetic evidence also suggests that Neanderthals lived in “many small subpopulations.”

There is still considerable mystery surrounding just why the Neandertals faded out. The best theory going at the moment is gene swamping. Given that the Neandertal and early modern human genomes were both probably pretty stable, Neandertal/modern human mating could very well have resulted in hybrid depression. Eventually, the Neandertal genes, facing negative selection, dropped out of the genome.

More Information About the Denisovans

Discover Magazine has an article on new finds at Denisova and their context in early modern human evolution.  Bridget Alex writes:

Nestled in foothills of Russia’s Altai Mountains, Denisova Cave has been a research mecca since 2010, when fossil DNA from the site revealed a previously unknown human lineage, now called the Denisovans. Scientists have been working hard to reconstruct the cave’s history, through ongoing excavations as well as new analyses of materials recovered years ago.

First, what everyone wants to know: Yes, they found more human remains. In addition to the four Denisovan specimens (one pinky finger, two adult molars and a baby tooth), the cave has yielded 12 fossils from ancient humans, including teeth, toes, fingers and unclassifiable fragments.

Based on their genomes, proteins and physical appearance, the collection contains four Denisovans, three Neanderthals and one hybrid cross between the two human types. Excavators have also found four more fossils that belong to the Homo genus, but haven’t yet been assigned to a particular human species. Additional DNA sequences, recovered directly from the dirt, suggest the presence of even more individuals.

As reported last year, Denisova 11 has been determined to be the offspring between a Neandertal mother and Denisovan father. As with other finds in Asia, we are finding that there appears to have been considerable population mixing over the course of at least 100 thousand years. Although the article indicates that the Neandertals were “sandwiched” in between two modern human occupations, that is difficult to square with any hybridization model. I suspect that the habitation patterns were more complex.

Chris Stringer: Meet the Relatives

Chris Stringer has a post in the Financial Times titled Meet the Relatives.  It is sort of a whirlwind tour through the evolution of the genus Homo.    He writes:

The discoveries of Homo floresiensis, Homo luzonensis, Denisovans and Homo naledi in the past 15 years remind us that the fossil record of humans is still very patchy — stone tools are scattered across much of Africa as a witness to widespread human occupation, yet fossil evidence has been recovered from less than 10 per cent of that continent’s area.

The percentage coverage for Asia is hardly any better: there is, for example, currently only one significant human fossil from the whole of the Indian subcontinent. The discoveries of the past few years underline just how much evolutionary history remains unknown, with other extinct lineages no doubt still to be revealed.

Many of the new finds challenge how we classify fossils in relation to Homo sapiens today. I continue to call the Neanderthals a different species from us, based on their distinctive skeletons and skulls; others feel that the recent evidence of interbreeding and increasing evidence of sophisticated behaviour mean that we should merge them, and the Denisovans, into our species.

I think that the discovery of the Xuchang hominins indicates that there has been considerable population mixing for several hundred thousand years.  As I wrote at the time:

These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”

Whether this represents such behavior at the peripheries of different species or that of one polytypic species is, as yet, unclear.  It is very clear that our understanding of how these populations interacted is rudimentary, at best. 

Neandertals Occupying Open-Air Site in Israel

There is evidence of Neandertal occupation at an open-air site in northern Israel called Ein Qashish.  From the researchers:

Whereas many open-air settlements are thought to be short-lived and chosen for specialized tasks, 'Ein Qashish appears to be the site of repeated occupations each of which hosted a range of general activities, indicating a stable and consistent settlement system. The authors suggest that within a complex settlement system, open-air sites may have been more important for prehistoric humans than previously thought.

The vast majority of Neandertal sites in France and the Levant are cave sites so this represents a sharp contrast in societal behavioral patterns.  The site appears to have been repeatedly occupied by Neandertals from around 70 to possibly 54 thousand years ago, representing potentially an 18 thousand year span, although the span is probably 70-60 kya.  Although the hominin remains at the site are fragmentary,  a designation of Neandertal was made based on the morphology of a third molar and a complete femur. 

This is more evidence that Neandertal society and life-styles were much more complex and advanced than most researchers have allowed.

Here is a link to the open-access PLoS ONE paper, Persistent Neanderthal occupation of the open-air site of ‘Ein Qashish, Israel.

The Ancient History of Neanderthals in Europe

The Max Planck Society has a post in PhysOrg, a highly-regarded science site, on the history of Neandertals (they have used the old spelling). 

Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have retrieved nuclear genome sequences from the femur of a male Neanderthal discovered in 1937 in Hohlenstein-Stadel Cave, Germany, and from the maxillary bone of a Neanderthal girl found in 1993 in Scladina Cave, Belgium. Both Neanderthals lived around 120,000 years ago, and therefore predate most of the Neanderthals whose genomes have been sequenced to date.

Perhaps the most interesting aspect of the research was how much evolution within Neandertals was revealed:

Intriguingly, unlike the nuclear genome, the mitochondrial genome of the Neanderthal from Hohlenstein-Stadel Cave in Germany is quite different from that of later Neanderthals—a previous report showed that more than 70 mutations distinguish it from the mitochondrial genomes of other Neanderthals. The researchers suggest that early European Neanderthals may have inherited DNA from a yet undescribed population.

As with what is going on in human fossil research in China, it seems as though there is a tangled web of relationships between human populations extending through both time and space.  Whatever complexity we envision for these groups, it is probably far more so.  As I wrote about the Chinese material:

The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well.  As Chris Davis of China Daily News put it: “One big happy family.”

It is becoming increasingly clear that our simplistic notions of population replacement and regional continuity are probably wrong. Is evolution occurring in these human groups? It absolutely is. Just how these puzzle pieces relate to each other is the question.

Large Denisovan Fossil Discovered

Nature News is reporting on a jaw fragment that has been discovered on the Tibetan Plateau that is close to 160,000 years old. From the story:

The research marks the first time an ancient human has been identified solely through the analysis of proteins. With no usable DNA, scientists examined proteins in the specimen’s teeth, raising hopes that more fossils could be identified even when DNA is not preserved...

Until now, everything scientists have learnt about Denisovans has come from a handful of teeth and bone fragments from Denisova Cave in Russia’s Altai Mountains. DNA from these remains revealed that the Denisovans were a sister group to Neanderthals, both descending from a population that split away from modern humans about 550,00–765,000 years ago. And at Denisova Cave, the two groups seem to have met and interbred: a bone fragment described last year belonged an ancient-human hybrid individual who had a Denisovan father and Neanderthal mother.

One of the most important aspects of the study is that it opens the door to answering questions of other fossils through protein analysis:

Previous research identified Neanderthal remains using both proteins and DNA — but the success of the latest study could lead to a greater emphasis on getting ancient proteins out of fossils that haven’t yielded DNA, says Chris Stringer, a palaeoanthropologist at the Natural History Museum in London. The method could prove particularly useful for older samples or those from southeast Asia and other warm climates, where DNA degrades quickest.

On the Heels of the Discovery of Homo luzonensis...

A new study from the journal Cell suggests that there were multiple migrations of individuals into Southeast Asia with the Denisovan genome.  Here is the summary from Cell.

Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

These data, in combination with the new Luzon material further suggest that the population interrelationships in Southeast Asia were complex, with considerable mixing between Denisovans, archaic Homo sapiens, eastward-migrating Neandertals and who knows how many other groups. We know from the material in China that the fossil material of even 100 thousand years back exhibits multiple origins.  As I noted about the Xuchang hominins at the time:

These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”

The presence of the hominins in Luzon, as well as the new research reported here suggests that this complexity comprised all of East Asia.

More Information From Denisova

Nature News is reporting about some more evidence from Denisova, following up on the bombshell news last year that bones discovered there belonged to a person (who they named “Denny”) who's father was a Denisovan and mother a Neandertal. From the story:

In the years that followed the discovery of Denisovans, scientists used DNA sequencing to attribute a few molar teeth from the cave to the same group4. They have also found other remains that harboured Neanderthal DNA. The analysis of Denny fills in some important details about the two groups. “We knew that Denisovans and Neanderthals had been there. We just didn’t think they interacted this intimately,” says [Svante] Pääbo. “It was so amazing to find direct proof — to find these people in the act, almost, of mixing.”

Denny’s discovery has also convinced Pääbo and other scientists that the remains of similar individuals, with recent ancestry from two groups of hominin, will be found — perhaps also in Denisova Cave. Researchers who analysed Denny’s genome found signs that the chromosome set that was contributed by her father, although clearly Denisovan, harboured some Neanderthal ancestry, which hints at earlier encounters between the groups2. “We should be able to pick up these individuals,” says [Katerina] Douka.

The Denisova cave appears to have been occupied for several hundred thousand years, being originally settled by either Denisovans or Neandertals, no one is sure which. Subsequent to this, it is unclear how much interbreeding actually occurred. 

“It’s still a head scratcher,” adds Tom Higham, an archaeological scientist at the University of Oxford, UK, who works with Douka and Brown. “It’s either an incredible piece of luck, or interbreeding happens so frequently that we might expect to find these types of occurrence in the archaeological record.”

One thing becomes increasingly clear with each new discovery, however: the complete replacement model of modern human origins, as espoused by Stringer and Andrews, is dead.

Neandertals Had Same Gait as Modern Humans

A virtual reconstruction of the skeleton of the La Chapelle Neandertal has revealed that Neandertals had exactly the same bipedal pattern that modern humans had.  From the ScienceDaily article:

Since the 1950s, scientists have known that the image of the Neanderthal as a hunched over caveman is not an accurate one. Their similarities to ourselves -- both in evolutionary and behavioral terms -- have also long been known, but in recent years the pendulum has swung in the opposite direction. "Focusing on the differences is back in fashion," says Martin Haeusler, UZH specialist in evolutionary medicine. For instance, recent studies have used a few isolated vertebrae to conclude that Neanderthals did not yet possess a well-developed double S-shaped spine.

However, a virtual reconstruction of the skeleton from La Chapelle-aux-Saints has now delivered evidence to the contrary. This computer-generated anatomical model was created by the research group led by Martin Haeusler from the University of Zurich and included Erik Trinkaus from Washington University in St. Louis. The researchers were able to show that both the individual in question as well as Neanderthals in general had a curved lumbar region and neck -- just like the humans of today.

This is the final nail in the coffin of the absolutely atrocious report that came out in 1913, written by Marcelin Boule¹, in which he described the skeleton of the La Chapelle Neandertal as stooped over and primitive, doing his best to derail any possibility that Neandertals were related to modern humans.  Boule's work is an object lesson in how an, otherwise, respected scientist can let personal opinions completely cloud their scientific judgement. 


¹Boule M (1911-13) L’homme fossile de La Chapelle-aux-Saints. Ann Paléontol 6:111–172, 7:21–56, 85–192, 8:1–70

'Swiss Army knife of prehistoric tools' Found in China

Science Daily is on a roll.  This came out a bit back during the late semester crunch and I didn't get a chance to post about it.  Stone tools have been found in south China that appear to be made using the Levallois technology, which originated during the Middle Stone Age, in Africa.  They write:

A study by an international team of researchers, including from the University of Washington, determines that carved stone tools, also known as Levallois cores, were used in Asia 80,000 to 170,000 years ago. Developed in Africa and Western Europe as far back as 300,000 years ago, the cores are a sign of more-advanced toolmaking -- the "multi-tool" of the prehistoric world -- but, until now, were not believed to have emerged in East Asia until 30,000 to 40,000 years ago.

And now the, somewhat, startling conclusion:

With the find -- and absent human fossils linking the tools to migrating populations -- researchers believe people in Asia developed the technology independently, evidence of similar sets of skills evolving throughout different parts of the ancient world.

This particular conclusion seems somewhat ignorant of the fossil record, which clearly has hominins in the area that have distinct Neandertal traits.  The authors, in fact, even mention the possibility that the appearance of the tools might be tied to these earlier migrations, then seem to dismiss this for reasons that are, in my mind, not clear. 

The site, itself, Guanyindong Cave in Guizhou Province, is not new, having been excavated in the 1960s and 1970s.What is new is the date of 80-170 kya.  Levallois tools were thought to have arrived in the area around 30-40 kya and are seen as the artifacts of a late migration.  This re-dating of the sediments of Guanyindong Cave means that these kinds of tools were in the area some 100 ky earlier than was originally thought.  I do, however, think their evidence for independent origin is sparse. 

New Data on Neandertal Anatomy

Anatomists have reconstructed the rib cage of the Kebara 2 Neandertal to get a better understanding of the trunk of our nearest relatives.  Science Daily has the story:

An international team of scientists has completed the first 3D virtual reconstruction of the ribcage of the most complete Neanderthal skeleton unearthed to date, potentially shedding new light on how this ancient human moved and breathed.

The team, which included researchers from universities in Spain, Israel, and the United States, including the University of Washington, focused on the thorax -- the area of the body containing the rib cage and upper spine, which forms a cavity to house the heart and lungs.

What did they find?

The reconstruction of the thorax, coupled with the team's earlier finding, shows ribs that connect to the spine in an inward direction, forcing the chest cavity outward and allowing the spine to tilt slightly back, with little of the lumbar curve that is part of the modern human skeletal structure. "The differences between a Neanderthal and modern human thorax are striking," said Markus Bastir, senior research scientist at the Laboratory of Virtual Anthropology at the National Museum of Natural History in Spain.

"The Neanderthal spine is located more inside the thorax, which provides more stability," said Gomez-Olivencia. "Also, the thorax is wider in its lower part." This shape of the rib cage suggests a larger diaphragm and thus, greater lung capacity.

In my anthropology class, I teach about the effects of Bergmann's and Allen's rules of body morphology. In the case of Neandertals, the adaptations to the cold were shortened distal limb segments, a large, projecting mid-face and a tendency toward barrel-chestedness. The new study reinforces these ideas.

Interestingly, it should be noted that the Kebara Neandertal is found in Israel, not known for its cold climate.  It is hypothesized that the Neandertal population came down from Eastern Europe to escape the cold (the tundra line was at Vienna).  What is peculiar about the Kebara 2 Neandertal is that it consists only of a body.  Whether he died and his head fell in a stream or some animal carried it off, there is no cranium.  Oddly, what we do have is one of the bones that is preserved least in the fossil record: a hyoid.  It is this that has given us the most information about the Neandertal vocal tract.

Fun stuff.

Neandertal Teeth 450Ky Old Found in Italy

The Smithsonian is reporting that excavations in Italy have uncovered teeth dated to 450 thousand years ago that have Neandertal characteristics.

A fossil tooth study published today in the journal PLOS ONE analyzes some of the oldest human remains ever found on the Italian Peninsula. The teeth, which are some 450,000 years old, have some telltale features of the Neanderthal lineage of ancient humans. Dating back to the Middle Pleistocene, the fossils help to fill in gaps in an intriguingly complex part of the hominid family tree.

The species Homo neanderthalensis shares an unknown common ancestor with our own species, Homo sapiens, but it’s unclear exactly when the lineages diverged. Homo sapiens evolved perhaps 300,000 years ago, according to the fossil record, while Neanderthals’ evolutionary timeline has proven even trickier to pin down. Some genetic studies suggest that their lineage split from our own as long as 650,000 years ago, but the oldest definitive fossil evidence for Neanderthals extends back only about 400,000 years.

Conventional wisdom is that Neandertals emerged around 200 thousand years ago, in Europe. The Atapuerca Sima de Los Huesos remains, which show pre-Neandertal characteristics, are about the same age as the Italian remains. It has been suggested that Homo heidelbergensis is the common ancestor to both Neandertals and modern humans but this is far from clear. The genetics suggests that Neandertals and modern humans split around 600 thousand years ago but interacted as recently as 60 to 70 thousand years ago and interbred.Modern Europeans have between 3 and 6% Neandertal genes. 

This pushes back the origins of Neandertals and further muddies the picture of when and where these groups were and how they interacted.  More puzzle pieces. 

Neandertal/Denisovan Hybrid?

As J. Lawrence Angel once said: “When two groups of people meet, they may fight, but they will always mate.”  A story is now coming out of Russia describing more research at the Denisova Cave, in the Altai Mountain region that recounts exactly what Angel was talking about.  From Richard Coniff, at Scientific American:

In a remarkable twist in the story line of early human evolution, scientists have announced the discovery of “Denisova 11”—a female who was at least 13 years old, lived more than 50,000 years ago and was a child of mixed parentage. Her parents were not just of different races, but two different and now-extinct early human types. Their exact taxonomic designations—whether they were separate species or subspecies—is still a matter of scientific debate. But the bottom line for Denisova 11 is that mom was a Neandertal and dad a Denisovan.

This is a remarkable claim, similar to the one that Erik Trinkaus made about the Lagar Velho child discovered in Portugal that is thought to be a Neandertal/modern human offspring. What evidence has been marshalled to support this claim?  In a word: genetics.  The evidence is taken from another bone fragment from the site.  From the abstract:

The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave. The mother came from a population more closely related to Neanderthals who lived later in Europe than to an earlier Neanderthal found in Denisova Cave, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal–Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.

So, if they interbred regularly (or regularly enough, anyway), why aren't they just one species?  Svante Paabo argues that it is because they simply did not come together very often.  To this, I would argue that they probably also had fairly distinct cultures. 

If this kind of information had come out a few decades back, there would have been quite a few squawks and naysayers but as the evidence piles up for hybridization between many different groups throughout the Pleistocene, researchers have become more accepting of it.  It is pretty clear that the evolutionary picture was a whole lot more complex than we thought. 

New Homo sapiens Fossil Found in Arabia

A new fossil finger has been unearthed as Arabia that purports to be 87 ky old.  UPI is on it.

The fossil was found buried beneath the sands of the Nefud Desert, which today stretches across the Northern Arabia Peninsula. The site where the fossil was found was once home to a freshwater lake.

Around the time humans showed up, a climatic shift brought monsoons to the region, spawning grasslands. Animal fossils suggest antelope grazed the land and hippos swam in the ancient lake.

Researchers measured ratios of radioactive elements in the finger bone and compared the ratios to those found in animal fossils with confirmed dates. The analysis confirmed the age of the human fossil, the oldest found in Arabia.

"This discovery for the first time conclusively shows that early members of our species colonized an expansive region of southwest Asia and were not just restricted to the Levant," Huw Groucutt, a researcher with the University of Oxford and the Max Planck Institute for the Science of Human History, said in a news release.

How do we know it was from Homo sapiens?

Among these finds was a well preserved and small fossil, just 3.2 cm long, which was immediately recognized as a human finger bone. The bone was scanned in three dimensions and its shape compared to various other finger bones, both of recent Homo sapiens individuals and bones from other species of primates and other forms of early humans, such as Neanderthals. The results conclusively showed that the finger bone, the first ancient human fossil found in Arabia, belonged to our own species.

I do not have access to this article as neither the lab nor UT has a subscription to Nature: Ecology & Evolution. Aside: Given our focus on materials science and computing, I kind of get why ORNL does not have a subscription.  UT, not so much.  This journal should be in their wheelhouse.  According to the abstract, the find is securely dated and:

The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna.

Maddenly, there is no information in the abstract about the morphology of the find, especially given that Neandertal and early anatomically modern phalanges are remarkably similar. I am sure they were able to differentiate it, but I would sure like to know how.

Modern Humans Interbred with Two Groups of Denisovans

There is now more evidence that were were “one big happy family.”  Here is a short recap:

Beginning around 1.8 million years ago, a hominin form called Homo erectus left Africa for points east, eventually settling in Indonesia and China. These early humans were characterized by having heads roughly ¾ the size of modern humans with very large brow ridges and with their widest point just above the ears. They were also the first humans to conquer fire and perfect hunting.

Then, at some point, between 300 and 500 thousand years ago, a population group migrated from North Africa into Europe and, eventually into East Asia. The European branch became the Neandertals, between 200 and 250 thousand years ago, and the East Asian group eventually became the Denisovans. The Denisovans then spread east and south, eventually mixing with other populations, some of which were the precursors of the Melanesians and native Australians. The bulk of the Neandertals hunkered down in Europe and tried to outlast the bitter cold of not one but two glaciations.  Despite this, while often pilloried in cultural literature as being half-witted brutes, Neandertals were a very complex society, with advanced weaponry and hunting behavior, grave goods, habitation structures and who practiced ritual behavior. Some populations of Neandertals eventually  expanded their range into Western Asia and steppic Russia and interbred with the Denisovans.  Unfortunately, as a culture, we know next to nothing about the Denisovans. 

Roughly 100 thousand years after this, there was yet another wave of migration, between 100 and 60 thousand years ago, of early modern humans from North Africa, who moved north and East mixing with both the Neandertals in Europe and, perhaps, Western Asia and the Denisovans in East Asia.

And now we learn that the modern humans arriving from Africa interbred with not one but two groups of Denisovans.  From Gizmodo:

We know so little about the Denisovans that they don’t even have a formal scientific name, though scientists are considering Homo sp. Altai or Homo sapiens ssp. Denisova. Indeed, as these names suggest, Denisovans were a branch of humans, having diverged from Neanderthals some 200,000 years ago. We know this because the Altai fossil yielded a near-complete genome, which scientists have been poring over since it was first sequenced in 2010.

But in addition to the Neanderthal ancestry, genetic anthropologists also learned that Denisovan DNA lives on in modern humans, especially among Oceanians and East and South Asians. This means anatomically modern humans, or Homo sapiens, must’ve interbred with a population of Denisovans. But as new research published today in the science journal Cell points out, our ancestors mated with Denisovans on at least two different historical occasions. So the traces of Denisovan DNA embedded in the genomes of some people living today originated from at least two distinct Denisovan populations.

Given Palaeolithic population densities, this is not surprising.The research seems to indicate that there were early modern human/Denisovan mixes in both Asia and Oceania.  What this means is that, once the Denisovans and Neandertals split, the Denisovans migrated east and northeast (as humans will do) and established population centers in these areas.  When the modern humans came (Huh.  I wonder what is over that hill?  Oh look, humans...sort of.) it made sense to intermingle with them.  We already know that Neandertals and modern humans could, and did, mix.  It is, absent any knowledge to the contrary, reasonable to assume that the Denisovans looked mostly modern human. 

Interestingly, the research seems to indicate that the rate of interbreeding of Neandertals to early moderns was much more limited than with moderns and Denisovans.  This is at variance with other studies (and fossil material) which seems to indicate more sustained contact.  It would be nice if we could find a bit more fossil evidence to get a handle on what at least one Denisovan looked like. 

Indian Site of Attirampakkam Pushes Middle Palaeolithic of India Back to 385 Kya

Great Googlymoogly!  Fresh on the heels of the discovery of the Misliya site (upcoming BioLogos post) that the Middle Palaeolithic Levallois technology was present in Israel as early as 194 thousand years ago, we now have news from India that places the emergence of the same technology as early as 385 thousand years ago.  From Malcolm Ritter at the site PhysOrg:

Homo sapiens arose in Africa at least 300,000 years ago and left to colonize the globe. Scientists think there were several dispersals from Africa, not all equally successful. Last week's report of a human jaw showed some members of our species had reached Israel by 177,000 to 194,000 years ago.

Now comes a discovery in India of stone tools, showing a style that has been associated elsewhere with our species. They were fashioned from 385,000 years ago to 172,000 years ago, showing evidence of continuity and development over that time. That starting point is a lot earlier than scientists generally think Homo sapiens left Africa.

This tool style has also been attributed to Neanderthals and possibly other species. So it's impossible to say whether the tools were made by Homo sapiens or some evolutionary cousin, say researchers who reported the finding Wednesday in the journal Nature.

Nowhere is there any indication that modern humans are associated with the tools at Attirampakkam (ATM). In fact, there are no hominin remains whatsoever at ATM. The Indian subcontinent has always had a paucity of human remains, the most notable of which is the Narmada Homo erectus cranium.  In Europe, the Levallois technology, which also shows up at ATM, is almost exclusively associated with Neandertals and in the Levant, at the Skhul, Qafzeh, Tabun and Amud sites in the Mt. Carmel region, it is used by both Neandertals and early moderns. Consequently, while someone was using early Middle Palaeolithic tools at ATM, we don't know who.

What is incredibly striking about the ATM site is that, from 385 ky down to 172 ky, there is continuous technological evolution, beginning with what the describers call the “terminal Acheulean,” through a punch flake industry with points, to knives.  Another point made by the authors is that this Middle Palaeolithic industry appears and flourishes during a time where other sites in India are still using Acheulean technology.  This suggests “that spatial variability among Palaeolithic cultural sequences is larger than previously thought.”  From the Nature article¹:

The behavioural transformations that mark the advent of the Indian Middle Palaeolithic at ATM are summarized by the following diagnostic features: the obsolescence of Acheulian large-flake reduction sequences, with a directional shift towards smaller tool components; the adoption and continuance of Levallois recurrent and preferential strategies; a gradual intensification of blade reduction; and an increased use of finer grained quartzite during phase II than during A gradual discontinuation of biface use—which becomes definite at ATM after approximately 172 ± 41 ka—has been reported at other Middle Palaeolithic and Middle Stone Age sites worldwide (see Supplementary Information and references therein).

This is an astounding find for so many reasons. It establishes the appearance of the Levallois technology, one we know originated in Africa, outside Africa over 150 thousand years earlier than we thought. This is a technology that was considered to have originated some 400 thousand years ago. We may now have to revise this date further into the past.

It shows a clear progression of human cultural evolution, from the late Acheulean hand axes, through Middle Palaeolithic Levallois technology to a more blade-oriented technology.  Sadly, it appears as though the site began to fall into disuse and the sequence stops cold around 74 kya.  This is not surprising since it coincides with the Toba supervolcano eruption in Indonesia.  Nonetheless, as the authors point out, it suggests multiple migrations out of Africa of first archaic Homo sapiens, then modern Homo sapiens, such as those in Misliya and that these groups interacted with the Archaic hominins they encountered along the way.

¹Akhilesh, K., Pappu, S., Rajapara, H. M., Gunnell, Y., Shukla, A. D., & Singhvi, A. K. (2018). Early Middle Palaeolithic culture in India around 385–172 ka reframes Out of Africa models. Nature, 554, 97. https://doi.org/10.1038/nature25444

Modern Humans Came Out of Africa Earlier Than Thought and Did So Multiple Times

If you have been studying human evolution, this story is not new.We have suspected for some time that humans migrated out of Africa in waves, beginning with Homo heidelbergensis, up through archaic Homo sapiens and, now, modern Homo sapiens.  As the story notes, there have likely been multiple migrations of Homo sapiens, as well. 

From the story in Science Daily:

A review of recent research on dispersals by early modern humans from Africa to Asia by researchers from the Max Planck Institute for the Science of Human History and the University of Hawai'i at Manoa confirms that the traditional view of a single dispersal of anatomically modern humans out of Africa around 60,000 years ago can no longer be seen as the full story. The analysis, published in the journal Science, reviews the plethora of new discoveries being reported from Asia over the past decade, which were made possible by technological advances and interdisciplinary collaborations, and shows that Homo sapiens reached distant parts of the Asian continent, as well as Near Oceania, much earlier than previously thought. Additionally, evidence that modern humans interbred with other hominins already present in Asia, such as Neanderthals and Denisovans, complicates the evolutionary history of our species.

Here is the graphic from the story:

 
What is only hinted at in the article is that when these waves of moderns came out of Africa, they interbred with the archaic hominins that they encountered. Further, this genome was remarkably stable, since there is genetic evidence that there was at least 500 thousand years of separation between them.Also missing from the story is the range of variation that these hybridizations display.  For example, as noted by the triangle on the map, the Xuchang fossils from China seem to show a mix of modern, Neandertal and late Homo erectus morphologies.  As I noted at the time:

The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well.

The other peculiar thing about the graphic is that there seems to be no migration pattern through the strait of Gibraltar. This seems odd since this is likely at least one of the routes that were taken by H. ergaster between 1.5 and 2.0 mya, and since it is thought that the Levallois tool technology comes from the Middle Stone Age of Africa, this would have been a likely route of introduction.  There may have been a barrier of sorts, suggested by the fact that the latest surviving Neandertals are from Spain. 

New Jebel Irhoud Date Causes Rethink of Chinese Dali Skull

Newsweek (Yes, that Newsweek) has a story on the reexamination of the Chinese Dali cranium, in light of the revised dates for the Jebel Irhoud skulls.  Kastalia Medrano writes:

Known as the Dali skull, it was discovered nearly 40 years ago in China’s Shaanxi province. It belonged to a member of the early hominin species Homo erectus. Its facial structure and brain case are intact, despite being dated to around 260,000 years ago. The Dali skull is so old that archaeologists initially didn’t believe it could share features with the modern Homo sapiens.

But Xinzhi Wu of the Chinese Academy of Sciences in Beijing believed that due to the overwhelming physical similarities, Homo erectus must have shared DNA with Homo sapiens. After decades of this idea being dismissed by mainstream academia, Wu and a colleague, Sheela Athreya of Texas A&M University, recently reanalyzed the Dali skull and found it may force us to rewrite our evolutionary history after all. It’s incredibly similar to two separate Homo sapiens skulls previously found in Morocco. “I really wasn’t expecting that,” Athreya told New Scientist.

If we’d found only the Moroccan skulls, and not the Dali skull, it would make sense to keep believing all modern humans evolved in Africa. But the similarities show that early modern humans may not have been genetically isolated from other parts of the world, like what we know today as China.

“I think gene flow could have been multidirectional, so some of the traits seen in Europe or Africa could have originated in Asia,” Athreya told New Scientist.

Okay, now the nuts and bolts.Dali has always been thought to occupy that rarified space between Homo erectus  and early modern Homo sapiens.  It was always thought to be between 200 and 250 kya, and optically-stimulated luminescence dating (a variant of thermoluminescence) places it between 258 and 267 kya.  My analyses of the skull suggested that it was, in no way, shape or form, a modern human but it did not tend to cluster with the Neandertals in terms of head shape.  Athreya and Wu have done an extensive multivariate analysis and conclude (from the article, likely behind a paywall:

When just the facial skeleton is considered, Dali aligns with Middle Paleolithic H. sapiens and is clearly more derived than African or Eurasian Middle Pleistocene Homo. When just the neurocranium is considered, Dali is most similar to African and Eastern Eurasian but not Western European Middle Pleistocene Homo. When both sets of variables are considered together, Dali exhibits a unique morphology that is most closely aligned with the earliest H. sapiens from North Africa and the Levant.

These results add perspective to our previous view of as Dali a “transitional” form between Chinese H. erectus and H. sapiens. Athough no taxonomic allocation is appropriate at this time for Dali, it appears to represent a population that played a more central role in the origin of Chinese H. sapiens. Dali's affinities can be understood in the context of Wu's Continuity with Hybridization scenario and a braided-stream network model of gene flow. Specifically, we propose that Pleistocene populations in China were shaped by periods of isolated evolutionary change within local lineages at certain times, and gene flow between local lineages or between Eastern and Western Eurasia, and Africa at other times, resulting in contributions being made in different capacities to different regions at different times.

In combination with the Xuchang remains, the reanalysis of this skull suggests that, indeed, there is a long and complex interrelationship between different hominin groups that dates back some 400 thousand years. From the paper:

In the braided-stream network model, evolutionary change in China was the result of a shifting network of gene flow among distinct regional Chinese populations, as well as between Chinese and Western Eurasian populations. These were not isolated evolutionary lineages; gene flow both within China and between Eastern Eurasia, Western Eurasia and Africa was intermittent and could explain the similarities in aspects of the neurocranium found here between Dali and Western Eurasian Middle Pleistocene humans. Gene flow would best be described as a braided stream network with periods of isolated evolutionary change within a local lineage at times, and periods of gene flow between local lineages or paleo-demes at other times, resulting in contributions being made in different capacities to different regions at different times.

It is pretty clear that our simplistic models of Recent African Replacement and Multiregional Evolution need to be reworked. It is becoming more apparent that what we are looking at either a polytypic species with a huge geographical range or a syngamion of related species that intermixed regularly. The Xuchang skulls were, apparently, not unique.