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

EarthSky: Twenty years of discoveries changing story of human evolution

EarthSky has an interesting article that summarizes twenty years of human evolution discoveries.  They write:

Perspectives on our own species have also changed. Archaeologists previously thought Homo sapiens evolved in Africa around 200,000 years ago, but the story has become more complicated. Fossils discovered in Morocco have pushed that date back to 300,000 years ago, consistent with ancient DNA evidence. This raises doubts that our species emerged in any single place.

This century has also brought unexpected discoveries from Europe and Asia. From enigmatic “hobbits” on the Indonesian island of Flores to the Denisovans in Siberia, our ancestors may have encountered a variety of other hominins when they spread out of Africa. Just this year, researchers reported a new species from the Philippines.

All of these discoveries point to the idea that there was considerable population mixing throughout the Middle to Late Pleistocene not just in Africa but throughout the Old World. We know that it took place in China around 120,000 years ago by the evidence from Linjing.  These particular hominins have characteristics found in modern humans, Neandertals and Homo erectus.

Interestingly, the idea that our species did not originate in any single place was an idea pursued by Rachel Caspari almost two decades ago, at a paper given at one of the American Association of Physical Anthropologists conventions.  At the time, it was still thought that the “Out of Africa” replacement model was still the best explanation for modern human origins.We now know that it is not.

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. 

Earliest Art Made By Humans?

Artnet News has a post on a discovery in Henan Province, China that purports to be the oldest indications of consciously-created art.  From Sarah Gascone:

Abstract patterns carved on bone fragments discovered in China could be the oldest art ever made, dating back to between 105,000 and 125,000 years ago.

The marks on two bones were found at a site in Henan Province thought to be populated by Denisovans, an extinct species or subspecies of ancient humans, according to a new study in the Cambridge University Press journal Antiquity. The markings on the weathered rib bones contain traces of ochre on one specimen, the earliest evidence of pigment’s use for decorative purposes.

The newly discovered artworks pre-date even the 73,000-year-old markings—thought by some to be abstract drawings—found last year on a rock excavated from a South African cave, and previously thought to be the earliest-known example of human artistic activity.

Here is an image of the markings:

Photo Credit: Francesco d’Errico and Luc Doyon.

There seems to be a persistent thought that people of this age simply could not make art of this kind. I think it more stems from the fact that this kind of representation rarely survives in the fossil record. We know that as far back as 300k, there was division of labor and that there was quite a bit of population mixing this far back.  There is also a record of Neandertal cave paintings at 65k.  It is nice to find this kind of artistic expression but it ought not to surprise us. 

DNA Proteins Revealing Information About Human Evolution

Since the advent of population genetics and modern techniques to examine DNA, research has focused on, first, Mitochondrial DNA and then nuclear DNA.  Now we have another weapon in our arsenal.  Matthew Warren of Nature News relates new research done on palaeoproteomics.  This is the study of proteins found in fossilized human ancestors.  How is this possible, you ask?

Some time in the past 160,000 years or so, the remains of an ancient human ended up in a cave high on the Tibetan Plateau in China. Perhaps the individual died there, or parts were taken there by its kin or an animal scavenger. In just a few years, the flesh disappeared and the bones started to deteriorate. Then millennia dripped by. Glaciers retreated and then returned and retreated again, and all that was left behind was a bit of jawbone with some teeth. The bone gradually became coated in a mineral crust, and the DNA from this ancient ancestor was lost to time and weather. But some signal from the past persisted.

Deep in the hominin’s teeth, proteins lingered, degraded but still identifiable. When scientists analysed them earlier this year, they detected collagen, a structural support protein found in bone and other tissues. And in its chemical signature was a single amino-acid variant that isn’t present in the collagen of modern humans or Neanderthals — instead, it flagged the jawbone as belonging to a member of the mysterious hominin group called Denisovans. The discovery of a Denisovan in China was a major landmark. It was the first individual found outside Denisova Cave in Siberia, where all other remains of its kind had previously been identified. And the site’s location on the Tibetan Plateau — more than 3,000 metres above sea level — suggested that Denisovans had been able to live in very cold, low-oxygen environments.

As the author notes, this kind of research has opened many other doors that, up until now, have been shut to researchers. The realization that proteins have much longer staying power than DNA could radically reshape our understanding of human evolution:

Previously, scientists had recovered proteins from 1.8-million-year-old animal teeth and a 3.8-million-year-old eggshell. Now, they hope that palaeoproteomics could be used to provide insights about other ancient hominin fossils that have lost all traces of DNA — from Homo erectus, which roamed parts of the world from about 1.9 million to 140,000 years ago, to Homo floresiensis, the diminutive ‘hobbit’ species that lived in Indonesia as recently as 60,000 years ago. By looking at variations in these proteins, scientists hope to answer long-standing questions about the evolution of ancient human groups, such as which lineages were direct ancestors of Homo sapiens.

Whether that level of resolution will ever be possible remains to be seen, especially given that the modus operandi of modern palaeontology is focused on clade relationships. It will be interesting to see.

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.

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. 

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. 

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 DNA Analysis Allows for Greater Understanding of Modern Human Prehistory

From Science Daily:

A University of Utah-led team developed a new method for analyzing DNA sequence data to reconstruct the early history of the archaic human populations. They revealed an evolutionary story that contradicts conventional wisdom about modern humans, Neanderthals and Denisovans.

The study¹ found that the Neanderthal-Denisovan lineage nearly went extinct after separating from modern humans. Just 300 generations later, Neanderthals and Denisovans diverged from each other around 744,000 years ago. Then, the global Neanderthal population grew to tens of thousands of individuals living in fragmented, isolated populations scattered across Eurasia.

"This hypothesis is against conventional wisdom, but it makes more sense than the conventional wisdom." said Alan Rogers, professor in the Department of Anthropology and lead author of the study that will publish online on August 7, 2017 in the Proceedings of the National Academy of Sciences.

As the authors note, there is mounting evidence of a migration from Africa to Europe, likely by way of the Strait of Gibraltar, in which Acheulean stone tools are introduced by a group which became known as Homo heidelbergensis.  This group, subsequently, split, likely gave rise to the Neandertals  and the Denisovans a bit later.  Then, a second wave of migrations around 90 to 100 ky happened, during which there was hybridization between Neandertals, moderns and Denisovans.

We live in a time where we now have the genomes of archaic Africans, Eurasians, Neandertals, Denisovans and early moderns and can compare them using site pattern analysis.  These authors found that

• In contrast to previous studies, this one indicates that Neandertal population size was large, on the order of tens of thousands of people, in isolated populations
• The split between the Neandertals and Denisovans was early, on the order of 744 thousand years ago.  
• By the time you find these hominins in the fossil record, they had already split from the Denisovans, which explains why the Atapuerca Sima De Los Huesos hominins resemble Neandertals more than Denisovans.
• Therefore, Neandertal features are thought to have emerged over a long period of time in Europe. 

This analysis will help us rethink our understanding of the fossil material from Gran Dolina, which now likely represents a population from which both the Denisovans and Neandertals split.  This makes sense, given the general, non-derived nature of the fossil material from there.  Things are slowly (maybe?) falling into place.

¹Alan R. Rogers, Ryan J. Bohlender, and Chad D. Huff. Early history of Neanderthals and Denisovans. PNAS, August 2017 DOI: 10.1073/pnas.1706426114

Genetic Data Indicates Another Migration of Archaic Homo sapiens Out of Africa

Ars Technica is running a story based off of a Nature Communications article about a migration of archaic Homo sapiens out of Africa that took place more recently than the one at c. 650 kya that was hypothesized to have given rise to the Neandertals. Cathleen O'Grady writes:

The picture painted by nuclear DNA (nDNA) is that, between 765,000 and 550,000 years ago, our ancestors in Africa diverged into two groups. One group would eventually lead to our own species, although we wouldn't make an appearance until around 200,000 years ago. The other group would lead to Neanderthals and the closely related Denisovans. This proto-Neanderthal/Denisovan group left Africa for Eurasia at some point; sometime around 430,000 years ago, they diverged into distinct Neanderthals and Denisovans.

But the picture painted by mtDNA is different. Neanderthal mtDNA is more similar to modern humans than it is to Denisovan mtDNA. And the divergence date between us and them, when estimated based on mtDNA, is much more recent—between 498,000 and 295,000 years ago.

Some researchers have suggested that you can explain this mixed genetic evidence if Neanderthals interbred with another, more recent African group of humans. This would provide them with different mtDNA after they split from Denisovans. And that, in turn, means that there must have been humans, closely related to our own species, who left Africa for Europe far earlier than previously suspected.

It is not such a stretch to suggest that the recent finds from Jebel Irhoud may be a population related to this mystery population.  The Jebel Irhoud crania show modern characteristics in the face and have been placed in the modern Homo sapiens clade (if provisionally).  Whether or not they have enough traits found in later humans to be the stem group of anatomically modern Homo sapiens is not currently known.  Jebel Irhoud is a hop, skip and a jump to Gibraltar, which we know had already provided an avenue of migration for earlier populations of early Homo which gave rise to Homo heidelbergensis in Europe.

As the story notes, there are remarkable similarities in stone tool technologies between the northern  African Middle Stone Age and the European late Acheulean and early Mousterian tools.  There are Levallois flakes found in both areas, as well as similarly-made knives and points.  This suggests that populations in North Africa had some contact with those of southern Europe.  As we push the age of the modern human clade back in time, these discoveries help to frame the appearance of modern humans and how they interacted with the populations around them.  Exciting times!

The Nature Communications article, Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals can be found here and was free when I read it.