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.

Homo erectus 200,000 Years Older Than We Thought

UPI has a story about a discovery in South Africa of a Homo erectus infant that is 200 ky older than the oldest known specimen currently in existence.  From the original Science article: 

Fossil hominins from South Africa are enriching the story of early human evolution and dispersal. Herries et al. describe the geological context and dating of the hominin-bearing infilled cave, or palaeocave, at a site called Drimolen in South Africa (see the Perspective by Antón). They focus on the age and context of a recently discovered Homo erectus sensu lato fossil and a Paranthropus robustus fossil, which they dated to ∼2.04 million to 1.95 million years ago. This makes Drimolen one of the best-dated sites in South Africa and establishes these fossils as the oldest definitive specimens of their respective species ever discovered. The age confirms that species of Australopithecus, Paranthropus, and early Homo overlapped in the karst of South Africa ∼2 million years ago

The goofy thing about this is that, in East Africa,  early Homo was still running around and out-competing the robust australopithecines (Paranthropus).  The fossil was uncovered and described over a five year period at the site of Drimolen, which is part of the UNESCO World Heritage Site in South Africa that contains the important fossil sites of Swartkrans and Sterkfontein. 

From the UPI story:

“One of the questions that interests us is what role changing habitats, resources, and the unique biological adaptations of early Homo erectus may have played in the eventual extinction of Australopithecus sediba in South Africa,” said study co-author Justin Adams, researcher at Monash University's Biomedicine Discovery Institute.
“Similar trends are also seen in other mammal species at this time. For example, there are more than one species of false sabre tooth cat, Dinofelis, at the site -- one of which became extinct after two million years,” Adams said. “Our data reinforces the fact that South Africa represented a truly unique mixture of evolutionary lineages -- a blended community of ancient and modern mammal species that was transitioning as climates and ecosystems changed.”

Just a few short years ago, it was thought that Australopithecus sediba might be ancestral to early Homo based on the characteristics of its hands, pelvis and the proximity of stone tools to the Rising Star Cave.  This was an idea championed by Lee Berger, but it now seems likely that it was another, earlier form that gave rise to Homo erectus. 

Here is the photo of DNH134, taken by Jesse Martin, Reanud Joannes-Boyau, and Andy I. R. Herries

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

The Ghost of an Unknown Hominin

Science Alert has a story about the Ghost of an Unknown Hominin in Africa.  Carly Cassella writes:

The gene pool of modern West Africans contains the 'ghost' of a mysterious hominin, unlike any we've detected so far. Similar to how humans and Neanderthals once mated, new research suggests this ancient long-lost species may have once mingled with our ancestors on the African continent.

Using whole-genome data from present-day West Africans, scientists have found a small portion of genetic material that appears to come from this mysterious lineage, which is thought to have split off from the human family tree even before Neanderthals.

It is not clear to me that these necessarily represent different species. This may reflect an inter-related group of populations from a very genetically diverse population. As my advisor Fred Smith once upon a time said: “If two species interbreed on a regular basis, is it reasonable to call them different species?”

BTW, the  “Unrelated” skull in the page is the Kabwe skull from What was once Rhodesia, discovered in 1925, 400 feet down, in a mine.

Todd Wood's Take on Danuvius

Todd Wood is always interesting to read, even if I don't share his chronological leanings.  He has thoughts on the new Miocene ape from Bavaria, Danuvius:

Based on the fragmentary remains, we make some really interesting observations about the anatomy of Danuvius. These apes had strongly opposed big toes, which would allow them to effectively grip things with their feet. Their tibiae (shinbones) have the kinds of joints that would allow them to walk upright, and their femora (thighbones) support that conclusion. These apes might have been in some way bipedal. The arm bones they found have traits that are associated with suspensory locomotion, like hanging from tree branches. The body size was fairly small, about the mass of a bonobo.

As I mentioned in my post, I think the evidence for bipedalism is vastly over-stated and, even if it can be shown that this “Extended Limb Clambering” is shared by other fossil ape finds from the region, there is no particular reason to think that these critters were ancestral to later hominins. It is entirely likely that they exhibited a separate adaptation to this particular style of locomotion.  Todd raises some other questions, though, that are not answered in the paper:

So why not address similarities of Danuvius to later fossil hominins? The authors are trying to establish a new means of locomotion that they call Extended Limb Clambering (ELC). So they compare Danuvius to living primates (where the authors know how they get around), and they're interested in comparing it to contemporary Miocene apes of Europe. But they're not all that excited about other comparisons to later fossil forms like Ardipithecus, Australopithecus, or Orrorin. They also don't relate their findings to later fossil apes in Europe like Graecopithecus or the Trachilos tracks, both of which have been linked to hominins or bipedality. Perhaps they don't think those things are worth talking about (maybe because they're skeptical of Graecopithecus like I am), but I guess I just don't agree.

I think that part of the reason that these questions are not raised is because there is so much of a gap between these finds, chronologically and geographically. There is simply with which to relate them. As Todd points out, the hominin status of Graecopithecus is dubious, at best, and, even if the Trachilos tracks are hominin, they are still quite a distance from Bavaria and six million years later in time.

For now, this fossil ape stands on its own.  If we find other evidence of incipient bipedality in other forms in the area and can relate them to later forms, then the picture might change.  For now, though, Danuvius is a very interesting, odd Miocene ape. 

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.

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.

New Species of Hominin Found in Phillipines

From a story in UPI:

At the completion of excavations on the island of Luzon, scientists had unearthed several teeth, part of a thigh bone, and a few hand and foot bones. The fossils comprise the "the earliest direct evidence of a human presence in the Philippines," according to the latest study.

The fossilized bones, dated to between 67,000 and 50,000 years ago, feature a mix of anatomical characteristics, some that recall more primitive hominins and others similar to those of more modern human species.

Callao Cave is toward the northern tip of Luzon. The corresponding article from Nature seems to indicate that the fossil remains from this cave are “all over the map.”  The premolars indicate size and shape affinities to later Homo, while some of the characteristics are australopithecine (!).  This is also true of the hand elements. 

Although we have found human fossil remains in East Asia for some time (1896 on), there are large gaps in our knowledge, especially from the first appearance of Homo erectus to the advent of modern humans.  These fossils, while giving us more  information than we had, muddy the waters a bit.  Once upon a time, Grover Kranz (RIP) tried to convince me that australopithecines could be found in East Asia, but his evidence was based on a badly crushed occipital bone. 

It is clear from the presence of H. floresiensis and the current evidence that primitive traits were being retained in some groups but, as the authors point out, we need quite a bit more fossil material to make any definitive assessments. 

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.

More Evidence For Bipedality at 4.5 MYA

Out of Case Western Reserve comes a study of some new fossil material that sheds like on early human bipedal adaptation.  From ScienceDaily:

Scott W. Simpson, PhD, led an analysis of a 4.5 million-year-old fragmentary female skeleton of the human ancestor Ardipithecus ramidus that was discovered in the Gona Project study area in the Afar Regional State of Ethiopia.

The newly analyzed fossils document a greater, but far from perfect, adaptation to bipedalism in the Ar. ramidus ankle and hallux (big toe) than previously recognized. "Our research shows that while Ardipithecus was a lousy biped, she was somewhat better than we thought before," said Simpson.

While the weight of evidence has always a bit more than slightly favored the facultative bipedality of Ardipithecus ramidus, this research provides greater support for this hypothesis.  In my class, I stress the difference between facultative bipedality (practiced by Ardipithecus) and obligate bipedality (practiced by every other hominin).  Additionally, from the article¹:

The more complete adoption of bipedality in the australopiths resulted in the loss of functionally critical adaptations to arboreality present in Ardipithecus such as a grasping, opposable hallux, an antero-posteriorly broad pelvis with reorganization of the origin (and most likely function) of the hamstring muscles, and a more derived humero-femoral ratio. The changes in the size and structure of the dentition in the subsequent australopiths (larger molar and premolar crowns, increased enamel thickness, more robust mandibles) indicates a major behavioral and dietary shift for most hominins (perhaps excluding the species indicated by the Burtele foot) that occurred about 4.2 Ma with the earliest appearance of Australopithecus (Leakey et al., 1995, White et al., 2006).

Many of these changes, then, appear to have occurred somewhat rapidly, once the early hominins moved away from the forest and into the fringe.  Once we thought that bipedality originated in the forest/fringe.  The Ardipithecus data have killed this hypothesis. 


¹Scott W. Simpson, Naomi E. Levin, Jay Quade, Michael J. Rogers, Sileshi Semaw. Ardipithecus ramidus postcrania from the Gona Project area, Afar Regional State, Ethiopia. Journal of Human Evolution, 2019; 129: 1 DOI: 10.1016/j.jhevol.2018.12.005

Mutation Rate in Humans Has Slowed Down

I am not quite sure what this means, yet. Researchers at the Aarhus University, Denmark, and the Copenhagen Zoo have discovered that, when compared to our nearest taxonomic relatives, our mutation rates have slowed down. Science Daily has the scoop:

"Over the past six years, several large studies have done this for humans, so we have extensive knowledge about the number of new mutations that occur in humans every year. Until now, however, there have not been any good estimates of mutation rates in our closest primate relatives," says Søren Besenbacher from Aarhus University.

The study has looked at ten families with father, mother and offspring: seven chimpanzee-families, two gorilla families and one orangutan family. In all the families, researchers found more mutations than would be expected on the basis of the number of mutations that would typically arise in human families with parents of similar age. This means that the annual mutation rate is now about one-third lower in humans than in apes.

Why is this important for the study of human origins?

The higher rates in apes have an impact on the length of time estimated to have passed since the common ancestor of humans and chimpanzees lived. This is because a higher mutation rate means that the number of genetic differences between humans and chimpanzees will accumulate over a shorter period.

If the new mutation rates for apes are applied, the researchers estimate that the species formation (speciation) that separated humans from chimpanzees took place around 6.6 million years ago. If the mutation rate for humans is applied, speciation should have been around 10 million years ago.

The six-to-eight million year point for the LCA never made a whole lot of sense to me. If the fossil material from Orrorin, at 6 mya really does reflect bipedality, then the split has to have been much earlier.  The material from Ardipithecus kadabba is very sketchy with regard to bipedalism (one toe bone found ten miles away), but the fragmentary post-cranial bones can be confidently identified as being hominin, in nature.  Furthermore, the fossil material is dated to between 5.6 and 5.8 mya.  That would leave a very short period of time.  It cannot be pre-split because the fossil material exhibits derivations in the hominin direction, rather than the modern ape direction. 

If this study holds up, it will change how we view the search for the LCA. 

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 Chinese Material Pushes the Exit From Africa to 2.1 mya

Nature is reporting research on new Chinese material that strongly suggests that the Georgian site of Dmanisi is not the earliest location to which migration out of Africa went.  Here is the abstract:

Considerable attention has been paid to dating the earliest appearance of hominins outside Africa. The earliest skeletal and artefactual evidence for the genus Homo in Asia currently comes from Dmanisi, Georgia, and is dated to approximately 1.77–1.85 million years ago (Ma)1. Two incisors that may belong to Homo erectus come from Yuanmou, south China, and are dated to 1.7 Ma2; the next-oldest evidence is an H. erectus cranium from Lantian (Gongwangling)—which has recently been dated to 1.63 Ma3—and the earliest hominin fossils from the Sangiran dome in Java, which are dated to about 1.5–1.6 Ma4. Artefacts from Majuangou III5 and Shangshazui6 in the Nihewan basin, north China, have also been dated to 1.6–1.7 Ma. Here we report an Early Pleistocene and largely continuous artefact sequence from Shangchen, which is a newly discovered Palaeolithic locality of the southern Chinese Loess Plateau, near Gongwangling in Lantian county. The site contains 17 artefact layers that extend from palaeosol S15—dated to approximately 1.26 Ma—to loess L28, which we date to about 2.12 Ma. This discovery implies that hominins left Africa earlier than indicated by the evidence from Dmanisi.

For the new site sequence data, we don't have any hominin remains so we don't know exactly what these folks looked like but the tools are very primitive.  A section from a companion piece reads thus:

The identity of their makers is, for now, unclear: no hominin bones have been recovered at Shangchen. “We would all love to find a hominin — preferably one with a tool in its hand,” says Dennell. Homo erectus is one possibility, because some of the earliest members of this species were found at Dmanisi. But Dennell thinks that the Shangchen toolmakers belonged to an earlier species in the genus Homo.

Petraglia and Rezek both say that the age of the tools — not to mention the possibility that hominins arrived in China even earlier than the 2.12-million-year mark — suggests that the toolmaker was a species such as Homo habilis. This relatively small-brained hominin is thought to have been confined to Africa between around 2.4 million to 1.4 million years ago.

Jungers holds open the possibility that the Shangchen toolmaker was a species of Australopithecus, a group of more ape-like hominins to which the iconic fossil Lucy belongs. So far, all Australopithecus fossils have been discovered in Africa.

Before his death, Grover Krantz argued for the presence of Australopithecus in East Asia but could never get anyone to come on board with him. Everyone was pretty content to label what was coming out of the ground as Homo erectus.I think it would be a stretch if the hominins from Shangchen were australopithecines since we don't see any advanced species of Australopithecus in East or North Africa between 2 and 2.5 mya.  In fact, Au. boisei drops out around 2.1, likely out-competed by early Homo.

Nonetheless, something was making stone tools in China at 2.1 mya and that is “Yuuuuge” news. 

How Intelligent Was Homo naledi?

Discover Magazine (and other outlets) are running a story which questions how important cranial size is to overall intelligence.  The focus of this inquiry is Homo naledi, the small-brained hominin that is now thought to be no more than 200ky old.  Lee Berger, who was on the team that discovered Homo naledi has always argued that, because of the comparative difficulty of navigating the cave, that she was placed in the Rising Star Chamber intentionally.  At issue is the brain size:

When it comes to brain volume, previous research established that Homo naledi‘s was 465-560 milliliters. (In today’s study, the authors acknowledge those earlier numbers, based on virtual reconstructions, but also perform their own physical reconstructions and measure the volume with a water displacement method, arriving at a similar range of 460-555 mL.)

This is very small. As the authors note, contemporary hominins possessed brains well over 1000 cc at this point. It was the complexity of H. naledi's brain that surprised people:

Homo naledi‘s inferior frontal and lateral orbital gyri were organized notably more like that of other members of the genus Homo than that of australopiths. These are parts of the brain associated with complex behaviors, such as communication, planning and tool-making, that are particularly important in our lineage.

Finding Homo naledi‘s brain was structurally similar to that of larger-brained members of the genus tells us two important things. First, it means Homo naledi itself was likely capable of more complex behavior than australopiths with a similar brain volume but different brain structure. Second, it torpedoes the old notion that Homo brains grew steadily in size and complexity until reaching the evolutionary pinnacle that is Homo sapiens (/sarcasm, just a touch).

As we discover that early Homo was behaviorally more complex than we thought, it also forces us to rethink what went on later in hominin evolution and re-evaluate evidence of complexity in H. erectus and archaic H. sapiens. 
 

New Laetoli Footprints Demonstrate Full Bipedality

A story running in Newsweek and the Washington Post (and other outlets, presumably), details research into the newly discovered fossil footprints at Laetoli dated to 3.6 mya that clearly show a modern human gait.

Two sites in Laetoli, Tanzania, feature footprints of human ancestors who lived about 3.6 million years ago. They were members of the genus Australopithecus. That's the genus of “Lucy,” the 3.2 million-year-old human ancestor whose fossilized bones were discovered in Ethiopia in 1974.

David Raichlen, an evolutionary anthropologist at the University of Arizona, has studied the Laetoli footprints and compared them to footprints made by human volunteers in laboratory settings. He examined footprints of individuals walking normally and also those walking with bent knees and bent hips. (Scientists who study locomotion use the acronym BKBH). The Laetoli footprints more closely match modern human footprints.

“Upright, humanlike bipedal walking goes back 4 to 5 million years,” Raichlen told The Washington Post in advance of a symposium on the evolution of human locomotion, which took place Sunday at the Experimental Biology 2018 conference in San Diego.

This dovetails with the recent findings that Ardipithecus, a hominin dated to around 4.4 mya, likely could travel equally well on the ground or in the trees.  Oddly, the WaPo article doesn't mention this.  

Ardipithecus May Not Have Been Entirely a Facultative Biped After All

In a new article in the Proceedings of the National Academy of Sciences, several researchers have concluded, using 3D morphometric analysis have discovered that Ardipithecus ramidus, while still having facultative (didn't have to but could) bipedalism, when it did walk, its bipedal gait was nearly human.  From the abstract:

We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by the relative length and orientation of the ischium. Ape pelves permit greater extensor moments at the hip, enhancing climbing capability, but limit their range of hip extension, resulting in a crouched gait. Human pelves reduce hip extensor moments but permit a greater degree of hip extension, which greatly improves walking economy (i.e., distance traveled/energy consumed). Applying these results to fossil pelves suggests that early hominins differed from both humans and extant apes in having an economical walking gait without sacrificing climbing capability. Ardipithecus was capable of nearly human-like hip extension during bipedal walking, but retained the capacity for powerful, ape-like hip extension during vertical climbing. Hip extension capability was essentially human-like in Australopithecus afarensis and Australopithecus africanus, suggesting an economical walking gait but reduced mechanical advantage for powered hip extension during climbing.

This positions Ardipithecus as the classic intermediate in terms of bipedal locomotion.Although there are many traits in Australopithecus afarensis that are still transitional in terms of the rib cage, dentition and aspects of the hip, it is clear that the major adaptations for bipedalism were in place nearly a million years earlier.  This also suggests that it is not out of the realm of possibility that the fossil footprints in Crete really do reflect a bipedal hominin.  At the risk of positing heresy, the fact remains that we really don't know exactly where hominins first appeared.  This study also reinforced the distinct separation between apes and humans in terms of iliac shape, and that this split must have taken place even further back in time that we have supposed.

The Independent has a news story on this here.  One of the authors, Herman Pontzer remarks:

“It kicks us out of this old paradigm of thinking about human evolution,”...“In that old picture that is everywhere where you have the evolution of man going from crouching thing to upright thing to a human – as much as we have known that is not right, I still think people have it in their heads.”

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. 

Daniel Everett: Homo erectus Could Speak and Make Boats

Bentley University Global Studies professor Daniel Everett argues that Homo erectus could speak and had the ability to make ocean-going vessels.  The Guardian has the story:

“Oceans were never a barrier to the travels of Erectus. He travelled all over the world, travelled to the island of Flores, across one of the greatest ocean currents in the world,” said Daniel Everett, professor of global studies at Bentley University, and author of How Language Began. “They sailed to the island of Crete and various other islands. It was intentional: they needed craft and they needed to take groups of twenty or so at least to get to those places.”

While Everett is not the first to raise the controversial possibility that H. erectus might have fashioned some sort of seagoing vessel, he believes that such capabilities mean that H. erectus must also have had another skill: language.

“Erectus needed language when they were sailing to the island of Flores. They couldn’t have simply caught a ride on a floating log because then they would have been washed out to sea when they hit the current,” said Everett, presenting his thesis at the meeting of the American Association for the Advancement of Science in Austin. “They needed to be able to paddle. And if they paddled they needed to be able to say ‘paddle there’ or ‘don’t paddle.’ You need communication with symbols not just grunts.”

It is pretty clear that Homo erectus hunted, at least in some fashion, could control fire and evidence seems to be accumulating that they hafted spears and, at least late in the range, the European variant set up rudimentary complex settlements.

There is, naturally, skepticism that any hominin form prior to Neandertals were sea-going: 

But others say that there is little evidence that H. erectus was a sophisticated seafarer, let alone had a language. “I don’t accept that, for example, [Homo] erectus must have had boats to get to Flores,” said Chris Stringer, head of human origins at the Natural History Museum in London. “Tsunamis could have moved early humans on rafts of vegetation.”

Before dismissing that idea out of hand, remember that it is the best one going to explain how the New World Monkeys got where they are, since Africa and South America had parted ways some 180 million years prior to their arrival.

I think there is likely not enough evidence to know one way or another if Homo erectus could sail the high seas and had speech, although the only skeletal evidence that we have for that part of the anatomy suggests not. 

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

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.