Genetic study reveals hidden chapter in human evolution

Modern humans descended from not one, but at least two ancestral populations that drifted apart and later reconnected, long before modern humans spread across the globe.

Using advanced analysis based on full genome sequences, researchers from the University of Cambridge have found evidence that modern humans are the result of a genetic mixing event between two ancient populations that diverged around 1.5 million years ago. About 300,000 years ago, these groups came back together, with one group contributing 80% of the genetic makeup of modern humans and the other contributing 20%.

For the last two decades, the prevailing view in human evolutionary genetics has been that Homo sapiens first appeared in Africa around 200,000 to 300,000 years ago, and descended from a single lineage. However, these latest results, reported in the journal Nature Genetics, suggest a more complex story.

“The question of where we come from is one that has fascinated humans for centuries,” said first author Dr Trevor Cousins from Cambridge’s Department of Genetics. “For a long time, it’s been assumed that we evolved from a single continuous ancestral lineage, but the exact details of our origins are uncertain.”

“Our research shows clear signs that our evolutionary origins are more complex, involving different groups that developed separately for more than a million years, then came back to form the modern human species,” said co-author Professor Richard Durbin, also from the Department of Genetics.

While earlier research has already shown that Neanderthals and Denisovans – two now-extinct human relatives – interbred with Homo sapiens around 50,000 years ago, this new research suggests that long before those interactions – around 300,000 years ago – a much more substantial genetic mixing took place. Unlike Neanderthal DNA, which makes up roughly 2% of the genome of non-African modern humans, this ancient mixing event contributed as much as 10 times that amount and is found in all modern humans.

The team’s method relied on analysing modern human DNA, rather than extracting genetic material from ancient bones, and enabled them to infer the presence of ancestral populations that may have otherwise left no physical trace. The data used in the study is from the 1000 Genomes Project, a global initiative that sequenced DNA from populations across Africa, Asia, Europe, and the Americas.

The team developed a computational algorithm called cobraa that models how ancient human populations split apart and later merged back together. They tested the algorithm using simulated data and applied it to real human genetic data from the 1000 Genomes Project.

While the researchers were able to identify these two ancestral populations, they also identified some striking changes that happened after the two populations initially broke apart.

“Immediately after the two ancestral populations split, we see a severe bottleneck in one of them—suggesting it shrank to a very small size before slowly growing over a period of one million years,” said co-author Professor Aylwyn Scally, also from the Department of Genetics. “This population would later contribute about 80% of the genetic material of modern humans, and also seems to have been the ancestral population from which Neanderthals and Denisovans diverged.”

“However, some of the genes from the population which contributed a minority of our genetic material, particularly those related to brain function and neural processing, may have played a crucial role in human evolution,” said Cousins.

The study also found that genes inherited from the second population were often located away from regions of the genome linked to gene functions, suggesting that they may have been less compatible with the majority genetic background. This hints at a process known as purifying selection, where natural selection removes harmful mutations over time.

Beyond human ancestry, the researchers say their method could help to transform how scientists study the evolution of other species. In addition to their analysis of human evolutionary history, they applied the cobraa model to genetic data from bats, dolphins, chimpanzees, and gorillas, finding evidence of ancestral population structure in some but not all of these.

“What’s becoming clear is that the idea of species evolving in clean, distinct lineages is too simplistic,” said Cousins. “Interbreeding and genetic exchange have likely played a major role in the emergence of new species repeatedly across the animal kingdom.”

So who were our mysterious human ancestors? Fossil evidence suggests that species such as Homo erectus and Homo heidelbergensis lived both in Africa and other regions during this period, making them potential candidates for these ancestral populations, although more research (and perhaps more evidence) will be needed to identify which genetic ancestors corresponded to which fossil group.

Looking ahead, the team hopes to refine their model to account for more gradual genetic exchanges between populations, rather than sharp splits and reunions. They also plan to explore how their findings relate to other discoveries in anthropology, such as fossil evidence from Africa that suggests early humans may have been far more diverse than previously thought.

“The fact that we can reconstruct events from hundreds of thousands or millions of years ago just by looking at DNA today is astonishing,” said Scally. “And it tells us that our history is far richer and more complex than we imagined.”

When did human language emerge?

 

A new analysis suggests our language capacity existed at least 135,000 years ago, with language used widely perhaps 35,000 years after that.

Peer-Reviewed Publication

Massachusetts Institute of Technology

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It is a deep question, from deep in our history: When did human language as we know it emerge? A new survey of genomic evidence suggests our unique language capacity was present at least 135,000 years ago. Subsequently, language might have entered social use 100,000 years ago.

Our species, Homo sapiens, is about 230,000 years old. Estimates of when language originated vary widely, based on different forms of evidence, from fossils to cultural artifacts. The authors of the new analysis took a different approach. They reasoned that since all human languages likely have a common origin — as the researchers strongly think — the key question is how far back in time regional groups began spreading around the world. 

“The logic is very simple,” says Shigeru Miyagawa, an MIT professor and co-author of a new paper summarizing the results. “Every population branching across the globe has human language, and all languages are related.” Based on what the genomics data indicate about the geographic divergence of early human populations, he adds, “I think we can say with a fair amount of certainty that the first split occurred about 135,000 years ago, so human language capacity must have been present by then, or before.”

The paper, “Linguistic capacity was present in the Homo sapiens population 135 thousand years ago,” appears in Frontiers in Psychology. The co-authors are Miyagawa, who is a professor emeritus of linguistics and the Kochi-Manjiro Professor of Japanese Language and Culture at MIT; Rob DeSalle, a principal investigator at the American Museum of Natural History’s Institute for Comparative Genomics; Vitor Augusto Nóbrega, a faculty member in linguistics at the University of São Paolo; Remo Nitschke, of the University of Zurich, who worked on the project while at the University of Arizona linguistics department; Mercedes Okumura of the Department of Genetics and Evolutionary Biology at the University of São Paulo; and Ian Tattersall, curator emeritus of human origins at the American Museum of Natural History. 

The new paper examines 15 genetic studies of different varieties, published over the past 18 years: Three used data about the inherited Y chromosome, three examined mitochondrial DNA, and nine were whole-genome studies. 

All told, the data from these studies suggest an initial regional branching of humans about 135,000 years ago. That is, after the emergence of Homo sapiens, groups of people subsequently moved apart geographically, and some resulting genetic variations have developed, over time, among the different regional subpopulations. The amount of genetic variation shown in the studies allows researchers to estimate the point in time at which Homo sapiens was still one regionally undivided group. 

Miyagawa says the studies collectively provide increasingly converging evidence about when these geographic splits started taking place. The first survey of this type was performed by other scholars in 2017, but they had fewer existing genetic studies to draw upon. Now, there are much more published data available, which when considered together point to 135,000 years ago as the likely time of the first split.

The new meta-analysis was possible because “quantity-wise we have more studies, and quality-wise, it’s a narrower window [of time],” says Miyagawa, who also holds an appointment at the University of São Paolo. 

Like many linguists, Miyagawa believes all human languages are demonstrably related to each other, something he has examined in his own work. For instance, in his 2010 book, “Why Agree? Why Move?” he analyzed previously unexplored similarities between English, Japanese, and some of the Bantu languages. There are more than 7,000 identified human languages around the globe. 

Some scholars have proposed that language capacity dates back a couple of million years, based on the physiological characteristics of other primates. But to Miyagawa, the question is not when primates could utter certain sounds; it is when humans had the cognitive ability to develop language as we know it, combining vocabulary and grammar into a system generating an infinite amount of rules-based expression. 

“Human language is qualitatively different because there are two things, words and syntax, working together to create this very complex system,” Miyagawa says. “No other animal has a parallel structure in their communication system. And that gives us the ability to generate very sophisticated thoughts and to communicate them to others.”

This conception of human language origins also holds that humans had the cognitive capacity for language for some period of time before we constructed our first languages. 

“Language is both a cognitive system and a communication system,” Miyagawa says. “My guess is prior to 135,000 years ago, it did start out as a private cognitive system, but relatively quickly that turned into a communications system.”

So, how can we know when distinctively human language was first used? The archaeological record is invaluable in this regard. Roughly 100,000 years ago, the evidence shows, there was a widespread appearance of symbolic activity, from meaningful markings on objects to the use of fire to produce ochre, a decorative red color. 

Like our complex, highly generative language, these symbolic activities are engaged in by people, and no other creatures. As the paper notes, “behaviors compatible with language and the consistent exercise of symbolic thinking are detectable only in the archaeological record of H. sapiens.”

Among the co-authors, Tattersall has most prominently propounded the view that language served as a kind of ignition for symbolic thinking and other organized activities. 

“Language was the trigger for modern human behavior,” Miyagawa says. “Somehow it stimulated human thinking and helped create these kinds of behaviors. If we are right, people were learning from each other [due to language] and encouraging innovations of the types we saw 100,000 years ago.”

To be sure, as the authors acknowledge in the paper, other scholars believe there was a more incremental and broad-based development of new activities around 100,000 years ago, involving materials, tools, and social coordination, with language playing a role in this, but not necessarily being the central force.

For his part, Miyagawa recognizes that there is considerable room for further progress in this area of research, but thinks efforts like the current paper are at least steps toward filling out a more detailed picture of language’s emergence. 

“Our approach is very empirically based, grounded in the latest genetic understanding of early homo sapiens,” Miyagawa says. “I think we are on a good research arc, and I hope this will encourage people to look more at human language and evolution.”

This research was, in part, supported by the São Paolo Excellence Chair awarded to Miyagawa by the São Paolo Research Foundation.

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Written by Peter Dizikes, MIT News

Paper: “Linguistic capacity was present in the Homo sapiens population 135 thousand years ago”

https://www.frontiersin.org/journals/psychology/articles/10.3389/fpsyg.2025.1503900/full

 

The earliest human face of Western Europe

 

Who the first inhabitants of Western Europe were, what their physical characteristics were, and when and where they lived are some of the pending questions in the study of the settlement of Eurasia during the Early Pleistocene epoch. The available palaeoanthropological information from Western Europe is limited and confined to the Iberian Peninsula1,2. 

This study presents most of the midface of a hominin found at the TE7 level of the Sima del Elefante site (Sierra de Atapuerca, Spain), dated to between 1.4 million and 1.1 million years ago. 

This fossil (ATE7-1) represents the earliest human face of Western Europe identified thus far. Most of the morphological features of the midface of this hominin are primitive for the Homo clade and they do not display the modern-like aspect exhibited by Homo antecessor found at the neighbouring Gran Dolina site, also in the Sierra de Atapuerca, and dated to between 900,000 and 800,000 years ago3. Furthermore, ATE7-1 is more derived in the nasoalveolar region than the Dmanisi and other roughly contemporaneous hominins. 

On the basis of the available evidence, it is reasonable to assign the new human remains from TE7 level to Homo aff. erectus. The archaeological, palaeontological and palaeoanthropological information obtained in the lower levels of the Sima del Elefante and Gran Dolina sites4,5,6,7,8, suggests a turnover in the human population in Europe at the end of the Early Pleistocene.

First burials: Neanderthal and Homo sapiens interactions in the Mid-Middle Palaeolithic Levant

Peer-Reviewed Publication

The Hebrew University of Jerusalem

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image: 

Exposed section of archaeological sediments dated to to 110 thousand years ago at Tinshemet cave

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Credit: Credit- Yossi Zaidner

The first-ever published research on Tinshemet Cave reveals that Neanderthals and Homo sapiens in the mid-Middle Paleolithic Levant not only coexisted but actively interacted, sharing technology, lifestyles, and burial customs. These interactions fostered cultural exchange, social complexity, and behavioral innovations, such as formal burial practices and the symbolic use of ochre for decoration. The findings suggest that human connections, rather than isolation, were key drivers of technological and cultural advancements, highlighting the Levant as a crucial crossroads in early human history.

Link to the images: https://drive.google.com/drive/folders/19p__omKCSSPkGBI3b8beF1QXqeRahGk1?usp=drive_link

A new discovery at Tinshemet Cave in central Israel is reshaping our understanding of human interactions during the Middle Palaeolithic (MP) period in the Near East. The cave, remarkable for its wealth of archaeological and anthropological findings, has revealed several human burials—the first mid-MP burials unearthed in over fifty years.

This research, published in Nature Human Behaviour, marks the first publication on Tinshemet Cave and presents compelling evidence that Neanderthals and Homo sapiens in the region not only coexisted but also shared aspects of daily life, technology, and burial customs. These findings underscore the complexity of their interactions and hint at a more intertwined relationship than previously assumed.

The excavation of Tinshemet Cave, led by Prof. Yossi Zaidner of the Hebrew University of Jerusalem, Prof. Israel Hershkovitz of Tel Aviv University, and Dr. Marion Prévost of the Hebrew University of Jerusalem, has been ongoing since 2017. A primary goal of the research team is to determine the nature of Homo sapiens–Neanderthal relationships in the mid-Middle Palaeolithic Levant. Were they rivals competing for resources, peaceful neighbours, or even collaborators?

By integrating data from four key fields—stone tool production, hunting strategies, symbolic behaviour, and social complexity—the study argues that different human groups, including Neanderthals, pre-Neanderthals, and Homo sapiens, engaged in meaningful interactions. These exchanges facilitated knowledge transmission and led to the gradual cultural homogenization of populations. The research suggests that these interactions spurred social complexity and behavioural innovations. For instance, formal burial customs began to appear around 110,000 years ago in Israel for the first time worldwide, likely as a result of intensified social interactions. A striking discovery at Tinshemet Cave is the extensive use of mineral pigments, particularly ochre, which may have been used for body decoration. This practice could have served to define social identities and distinctions among groups.

The clustering of human burials at Tinshemet Cave raises intriguing questions about its role in MP society. Could the site have functioned as a dedicated burial ground or even a cemetery? If so, this would suggest the presence of shared rituals and strong communal bonds. The placement of significant artifacts—such as stone tools, animal bones, and ochre chunks—within the burial pits may further indicate early beliefs in the afterlife.

Prof. Zaidner describes Israel as a "melting pot" where different human groups met, interacted, and evolved together. “Our data show that human connections and population interactions have been fundamental in driving cultural and technological innovations throughout history,” he explains.

Dr. Prévost highlights the unique geographic position of the region at the crossroads of human dispersals. “During the mid-MP, climatic improvements increased the region’s carrying capacity, leading to demographic expansion and intensified contact between different Homo taxa.”

Prof. Hershkovitz adds that the interconnectedness of lifestyles among various human groups in the Levant suggests deep relationships and shared adaptation strategies. “These findings paint a picture of dynamic interactions shaped by both cooperation and competition.”

The discoveries at Tinshemet Cave offer a fascinating glimpse into the social structures, symbolic behaviours, and daily lives of early human groups. They reveal a period of profound demographic and cultural transformations, shedding new light on the complex web of interactions that shaped our ancestors’ world. As excavations continue, Tinshemet Cave promises to provide even deeper insights into the origins of human society.

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Journal

Nature Human Behaviour

DOI

10.1038/s41562-025-02110-y 

New fossil discovery of an early human ancestor reveals that it walked upright, just like humans

 

Remarkable new fossils from Swartkrans Cave reveal that a prehistoric relative of humans was also extremely small and vulnerable to predators.

Peer-Reviewed Publication

University of the Witwatersrand

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The new Paranthropus robustus thigh and shin bones, articulated at the knee joint. 

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Credit: Jason L. Heaton

Paranthropus robustus was a species of prehistoric human that lived in South Africa about two million years ago, alongside Homo ergaster, a direct ancestor of modern people. Fossils of Paranthropus robustus are found in abundance at Swartkrans Cave, situated about halfway between Johannesburg and Pretoria. Much has been revealed about the diet and social organisation of this extinct species based on studies of its many skulls and hundreds of teeth, which have been recovered from Swartkrans since scientific excavations began there in 1948. 

For instance, the extremely heavy jaws and thickly enameled teeth of Paranthropus robustus suggest that, when times were lean, it was capable of subsisting on low quality foods that were difficult to chew. Moreover, some of the skulls and teeth of Paranthropus robustus are exceptionally large, while others are robust but not as large as those in the first group. This suggests that Paranthropus robustus was characterised by larger males and smaller females, indicating a mating system called polygyny, in which a single dominant male mates with multiple females.

Unfortunately, Swartkrans has over the years yielded many fewer bones from the rest of the Paranthropus robustus skeleton, limiting our understanding of its stature, posture, and locomotion, essential characteristics related to finding food and mates. A major new find from Swartkrans, the first articulating hipbone, thigh bone, and shin bone of Paranthropus robustus, changes that. 

A team of international researchers affiliated to the Evolutionary Studies Institute at the University of the Witwatersrand (Wits University), in South Africa including Travis Pickering, Matthew Caruana, Marine Cazenave, Ron Clarke, Jason Heaton, A.J. Heile, Kathleen Kuman, and Dominic Stratford, indicates in new research that this group of fossils belong to a single, young adult Paranthropus robustus. The fossil not only demonstrates that the species was, like modern humans, a habitual upright walker, but also confirms it was also extremely small. The research was published in the Journal of Human Evolution.

“It is estimated that this individual, probably a female, was only about a meter tall and 27 kg when it died, making it even smaller than adults from other diminutive early human species, including those represented by the famous ‘Lucy’ (Australopithecus afarensis, about 3.2 million years old) and ‘Hobbit’ (Homo floresiensis, about 90,000 years old) skeletons, from Ethiopia and Indonesia, respectively,” says Professor Pickering from the Univesity of Wisconsin-Madison, who led the research. 

The small size of the new Paranthropus robustus individual would have made it vulnerable to predators — such as sabertooth cats and giant hyenas — known to have occupied the area around Swartkrans Cave. This notion is confirmed by the team’s investigation of damage on the surface of the fossils, which includes tooth marks and other chewing damage identical to that made by leopards on the bones of their prey. 

“Although it seems that this particular Paranthropus robustus individual was the unfortunate victim of predation, that conclusion does not mean that the entire species was inept. We know that Paranthropus robustus survived in South Africa for over a million years and is found invariably, and at various sites, in spatial association with stone and bone tools,” says Pickering. 

Those implements were used for a variety of purposes, including butchering animals for their meat and digging for edible roots and underground insects. It is a matter of current research whether Paranthropus robustus, contemporaneous Homo ergaster, or both, was the maker and user of those important tools—but the Swartkrans team believes that Paranthropus robustus very likely possessed the cognitive and physical capabilities to do both.

The team’s continued investigation of the fossils includes CT-scan analyses of internal bone structures, which will provide additional information on the growth and developmental patterns of Paranthropus robustus, as well as adding details to our growing appreciation of its locomotor behaviours.

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Journal

Journal of Human Evolution

Prehistoric bone tool ‘factory’ hints at early development of abstract reasoning in human ancestors

The oldest collection of mass-produced prehistoric bone tools reveal that human ancestors were likely capable of more advanced abstract reasoning one million years earlier than thought, finds a new study involving researchers at UCL and CSIC- Spanish National Research Council.

The paper, published in Nature, describes a collection of 27 now-fossilised bones that had been shaped into hand tools 1.5 million years ago by human ancestors.

It’s the earliest substantial collection of tools made from bone ever found, revealing that they were being systematically produced one million years earlier than archaeologists once thought.

Early human ancestors known as hominins (human ancestors who could walk upright) had already been making tools out of stone in some capacity for at least a million years, but there’s been scant evidence of widespread toolmaking out of bones before about 500,000 years ago.

The hominins who shaped the recently-discovered bone tools did so in a manner similar to how they made tools out of stone, by chipping away small flakes to create sharp edges – a process called ‘knapping’.

This transfer of techniques from one medium to another shows that the hominins who made the bone tools had an advanced understanding of toolmaking, and that they could adapt their techniques to different materials, a significant intellectual leap. It could indicate that human ancestors at that time possessed a greater level of cognitive skills and brain development than scientists thought.

Co-author Dr Renata F. Peters (UCL Archaeology) said: “The tools show evidence that their creators carefully worked the bones, chipping off flakes to create useful shapes. We were excited to find these bone tools from such an early timeframe. It means that human ancestors were capable of transferring skills from stone to bone, a level of complex cognition that we haven’t seen elsewhere for another million years.”

Lead author Dr Ignacio de la Torre of the CSIC-Spanish National Research Council added: “This discovery leads us to assume that early humans significantly expanded their technological options, which until then were limited to the production of stone tools and now allowed new raw materials to be incorporated into the repertoire of potential artifacts.

“At the same time, this expansion of technological potential indicates advances in the cognitive abilities and mental structures of these hominins, who knew how to incorporate technical innovations by adapting their knowledge of stone work to the manipulation of bone remains.”

The tools were discovered in Olduvai Gorge in Tanzania, a site renowned for its long history of important archaeological discoveries revealing the origins of humans.

The researchers found 27 bones that had been shaped into tools at the site. The bones mostly came from large mammals, mostly elephants and hippos. The tools are exclusively made from the animals’ limb bones, as these are the most dense and strong.

The tools originate from a time in prehistory where early hominin cultures were undergoing one of the first ever technological transitions.

The very earliest stone tools come from the “Oldowan” age which stretched from about 2.7 million years ago to 1.5 million years ago. It employs a simple method for making stone tools, by chipping one or a few flakes off a stone core using a hammerstone.

The bone tools reported in this study were from the time that the ancient human ancestors were progressing into the “Acheulean” age which began as far back as about 1.7 million years ago. The Acheulean technology is best characterised by the use of more intricate handaxes that were carefully shaped by knapping – allowing the production of tools through more standardised means. 

The bone tools show that these more advanced techniques were carried over and adopted for use on bones as well, something previously unseen in the fossil record for another million years, much later into the Acheulean age.

Prior to this find, bones shaped into tools had only been identified sporadically in rare, isolated instances in the fossil record and never in a manner that implied that human ancestors were systematically producing them.

Though it’s unclear precisely what the tools were used for, because of their overall shape, size and sharp edges, it’s likely that they may have been employed to process animal carcasses for food.

It’s also unclear which species of human ancestor crafted the tools. No hominin remains were found alongside the collection of bone artefacts, though it’s known that, at the time, our human ancestor Homo erectus and another hominin species known as Paranthropus boisei were inhabitants of the region.

Because these tools were such an unexpected discovery, the researchers hope that their findings will prompt archaeologists to re-examine bone discoveries around the world in case other evidence of bone tools has been missed.