IMAGE: ORIGINAL EXCAVATION PHOTOGRAPH OF TSUKUMO NO. 24, COURTESY OF THE LABORATORY OF PHYSICAL ANTHROPOLOGY, KYOTO UNIVERSITY. view more
CREDIT: KYOTO UNIVERSITY
Newspapers regularly carry stories of terrifying shark attacks, but in a paper published today, Oxford-led researchers reveal their discovery of a 3,000-year-old victim - attacked by a shark in the Seto Inland Sea of the Japanese archipelago.
The research in Journal of Archaeological Science: Reports, shows that this body is the earliest direct evidence for a shark attack on a human and an international research team has carefully recreated what happened - using a combination of archaeological science and forensic techniques.
The grim discovery of the victim was made by Oxford researchers, J. Alyssa White and Professor Rick Schulting, while investigating evidence for violent trauma on the skeletal remains of prehistoric hunter-gatherers at Kyoto University. They came upon No24, from the previously excavated site of Tsukumo, an adult male riddled with traumatic injuries.
'We were initially flummoxed by what could have caused at least 790 deep, serrated injuries to this man,' say the Oxford pair. 'There were so many injuries and yet he was buried in the community burial ground, the Tsukumo Shell-mound cemetery site.'
They continue, 'The injuries were mainly confined to the arms, legs, and front of the chest and abdomen. Through a process of elimination, we ruled out human conflict and more commonly-reported animal predators or scavengers.'
Since archaeological cases of shark reports are extremely rare, they turned to forensic shark attack cases for clues and worked with expert George Burgess, Director Emeritus of the Florida Program for Shark Research. And a reconstruction of the attack was put together by the international team.
The team concluded that the individual died more than 3,000 years ago, between 1370 to 1010 BC. The distribution of wounds strongly suggest the victim was alive at the time of attack; his left hand was sheared off, possibly a defence wound.
Individual No 24's body had been recovered soon after the attack and buried with his people at the cemetery. Excavation records showed he was also missing his right leg and his left leg was placed on top of his body in an inverted position.
According to the pair, 'Given the injuries, he was clearly the victim of a shark attack. The man may well have been fishing with companions at the time, since he was recovered quickly. And, based on the character and distribution of the tooth marks, the most likely species responsible was either a tiger or white shark.'
Co-author Dr Mark Hudson, a researcher with the Max Planck Institute, says, 'The Neolithic people of Jomon Japan exploited a range of marine resources... It's not clear if Tsukumo 24 was deliberately targeting sharks or if the shark was attracted by blood or bait from other fish. Either way, this find not only provides a new perspective on ancient Japan, but is also a rare example of archaeologists being able to reconstruct a dramatic episode in the life of a prehistoric community.'
VIDEO: AN INTERNATIONAL STUDY HAS DISCOVERED A CORONAVIRUS EPIDEMIC BROKE OUT IN THE EAST ASIA REGION MORE THAN 20,000 YEARS AGO, WITH TRACES OF THE OUTBREAK EVIDENT IN THE GENETIC MAKEUP... view more
CREDIT: QUT
Genome study reveals East Asian coronavirus epidemic 20,000 years ago
An international study has discovered a coronavirus epidemic broke out in the East Asia region more than 20,000 years ago, with traces of the outbreak evident in the genetic makeup of people from that area.
Professor Kirill Alexandrov from CSIRO-QUT Synthetic Biology Alliance and QUT's Centre for Genomics and Personalised Health, is part of a team of researchers from the University of Arizona, the University of California San Francisco, and the University of Adelaide who have published their findings in the journal Current Biology.
In the past 20 years, there have been three outbreaks of epidemic severe coronaviruses: SARS-CoV leading to Severe Acute Respiratory Syndrome, which originated in China in 2002 and killed more than 800 people; MERS-CoV leading to Middle East Respiratory Syndrome, which killed more than 850 people, and SARS-CoV-2 leading to COVID-19, which has killed 3.8 million people.
But this study of the evolution of the human genome has revealed another large coronavirus epidemic broke out thousands of years earlier.
"The modern human genome contains evolutionary information tracing back tens of thousands of years, like studying the rings of a tree gives us insight into the conditions it experienced as it grew," Professor Alexandrov said.
In the study, the researchers used data from the 1000 Genomes Project, which is the largest public catalogue of common human genetic variation, and looked at the changes in the human genes coding for SARS-CoV-2 interacting proteins.
They then synthetised both human and SARS-CoV-2 proteins, without using living cells, and showed that these interacted directly and specifically pointed to the conserved nature of the mechanism coronaviruses use for cell invasion.
"Computational scientists on the team applied evolutionary analysis to the human genomic dataset to discover evidence that the ancestors of East Asian people experienced an epidemic of a coronavirus-induced disease similar to COVID-19," Professor Alexandrov said.
East Asian people come from the area that is now China, Japan, Mongolia, North Korea, South Korea, and Taiwan.
"In the course of the epidemic, selection favoured variants of pathogenesis-related human genes with adaptive changes presumably leading to a less severe disease," Professor Alexandrov said.
"By developing greater insights into the ancient viral foes, we gain understanding of how genomes of different human populations adapted to the viruses that have been recently recognised as a significant driver of human evolution.
"Another important offshoot of this research is the ability to identify viruses that have caused epidemic in the distant past and may do so in the future.
"This, in principle, enables us to compile a list of potentially dangerous viruses and then develop diagnostics, vaccines and drugs for the event of their return."
In two companion studies, researchers reveal a previously unknown population of archaic hominin- the "Nesher Ramla Homo" - from a recently excavated site in Israel dated to roughly 140,000 to 120,000 years ago. Analysis of both the fossils and associated artifacts from the site suggests that the group represents a last surviving population of Middle Pleistocene Homo, characterized by a distinctive combination of Neanderthal and archaic human features and technology that until only recently was linked to more modern Homo lineages. It's been assumed that Neanderthals originated and thrived on the European continent well before the arrival of modern humans. However, recent evidence suggests a genetic contribution from a yet unknown non-European group, indicating a long and dynamic history of interaction between Eurasian and African hominin populations. Here, Israel Hershkovitz, Yossi Zaidner and colleagues present fossil, artifact, and radiometric evidence from the Levant region of the Middle East that illustrates this complexity. According to Hershkovitz et al., the newly discovered Nesher Ramla Homo exhibits anatomical features that are more archaic than contemporaneous Eurasian Neanderthals and the modern humans who also lived in the Levant. The findings indicate that this archaic lineage may represent one of the last surviving populations of Middle Pleistocene Homo in southwest Asia, Africa and Europe. In the companion study, Zaidner et al. provide the archaeological context of the new fossils, reporting on the associated radiometric ages, artifact assemblages and the behavioral and environmental insights they offer. Zaidner et al. show that the Nesher Ramla Homo were well versed in technologies that were previously only known among H. sapiens and Neanderthals. Together, the findings provide archaeological support for close cultural interactions and genetic admixture between different human lineages before 120,000 years ago. This may help explain the variable expression of the dental and skeletal features of later Levantine fossils. "The interpretation of the Nesher Ramla fossils and stone tools will meet with different reactions among paleoanthropologists. Notwithstanding, the age of the Nesher Ramla material, the mismatched morphological and archaeological affinities, and the location of the site at the crossroads of Africa and Eurasia make this a major discovery," writes Marta Lahr in an accompanying Perspective.
IMAGE: .STATIC SKULL & MANDIBLE & PARIETAL ORTHOGRAPHIC. view more
CREDIT: TEL AVIV UNIVERSITY
The discovery of a new Homo group in this region, which resembles Pre-Neanderthal populations in Europe, challenges the prevailing hypothesis that Neanderthals originated from Europe, suggesting that at least some of the Neanderthals' ancestors actually came from the Levant.
The new finding suggests that two types of Homo groups lived side by side in the Levant for more than 100,000 years (200-100,000 years ago), sharing knowledge and tool technologies: the Nesher Ramla people who lived in the region from around 400,000 years ago, and the Homo sapiens who arrived later, some 200,000 years ago.
The new discovery also gives clues about a mystery in human evolution: How did genes of Homo sapiens penetrate the Neanderthal population that had presumably lived in Europe long before the arrival of Homo sapiens?
The researchers claim that at least some of the later Homo fossils found previously in Israel, like those unearthed in the Skhul and Qafzeh caves, do not belong to archaic (early) Homo sapiens, but rather to groups of mixed Homo sapiens and Nesher Ramla lineage.
Nesher Ramla Homo type - a prehistoric human previously unknown to science: Researchers from Tel Aviv University and the Hebrew University of Jerusalem have identified a new type of early human at the Nesher Ramla site, dated to 140,000 to 120,000 years ago. According to the researchers, the morphology of the Nesher Ramla humans shares features with both Neanderthals (especially the teeth and jaws) and archaic Homo (specifically the skull). At the same time, this type of Homo is very unlike modern humans - displaying a completely different skull structure, no chin, and very large teeth. Following the study's findings, researchers believe that the Nesher Ramla Homo type is the 'source' population from which most humans of the Middle Pleistocene developed. In addition, they suggest that this group is the so-called 'missing' population that mated with Homo sapiens who arrived in the region around 200,000 years ago - about whom we know from a recent study on fossils found in the Misliya cave.
Two teams of researchers took part in the dramatic discovery, published in the prestigious Science journal: an anthropology team from Tel Aviv University headed by Prof. Israel Hershkovitz, Dr. Hila May and Dr. Rachel Sarig from the Sackler Faculty of Medicine and the Dan David Center for Human Evolution and Biohistory Research and the Shmunis Family Anthropology Institute, situated in the Steinhardt Museum at Tel Aviv University; and an archaeological team headed by Dr. Yossi Zaidner from the Institute of Archaeology at the Hebrew University of Jerusalem.
Timeline: The Nesher Ramla Homo type was an ancestor of both the Neanderthals in Europe and the archaic Homo populations of Asia.
Prof.Israel Hershkovitz: "The discovery of a new type of Homo" is of great scientific importance. It enables us to make new sense of previously found human fossils, add another piece to the puzzle of human evolution, and understand the migrations of humans in the old world. Even though they lived so long ago, in the late middle Pleistocene (474,000-130,000 years ago), the Nesher Ramla people can tell us a fascinating tale, revealing a great deal about their descendants' evolution and way of life."
The important human fossil was found by Dr. Zaidner of the Hebrew University during salvage excavations at the Nesher Ramla prehistoric site, in the mining area of the Nesher cement plant (owned by Len Blavatnik) near the city of Ramla. Digging down about 8 meters, the excavators found large quantities of animal bones, including horses, fallow deer and aurochs, as well as stone tools and human bones. An international team led by the researchers from Tel Aviv and Jerusalem identified the morphology of the bones as belonging to a new type of Homo, previously unknown to science. This is the first type of Homo to be defined in Israel, and according to common practice, it was named after the site where it was discovered - the Nesher Ramla Homo type.
Dr. Yossi Zaidner: "This is an extraordinary discovery. We had never imagined that alongside Homo sapiens, archaic Homo roamed the area so late in human history. The archaeological finds associated with human fossils show that "Nesher Ramla Homo" possessed advanced stone-tool production technologies and most likely interacted with the local Homo sapiens". The culture, way of life, and behavior of the Nesher Ramla Homo are discussed in a companion paper also published in Science journal today.
Prof. Hershkovitz adds that the discovery of the Nesher Ramla Homo type challenges the prevailing hypothesis that the Neanderthals originated in Europe. "Before these new findings," he says, "most researchers believed the Neanderthals to be a 'European story', in which small groups of Neanderthals were forced to migrate southwards to escape the spreading glaciers, with some arriving in the Land of Israel about 70,000 years ago. The Nesher Ramla fossils make us question this theory, suggesting that the ancestors of European Neanderthals lived in the Levant as early as 400,000 years ago, repeatedly migrating westward to Europe and eastward to Asia. In fact, our findings imply that the famous Neanderthals of Western Europe are only the remnants of a much larger population that lived here in the Levant - and not the other way around."
According to Dr. Hila May, despite the absence of DNA in these fossils, the findings from Nesher Ramla offer a solution to a great mystery in the evolution of Homo: How did genes of Homo sapiens penetrate the Neanderthal population that presumably lived in Europe long before the arrival of Homo sapiens? Geneticists who studied the DNA of European Neanderthals have previously suggested the existence of a Neanderthal-like population which they called the 'missing population' or the 'X population' that had mated with Homo sapiensmore than 200,000 years ago. In the anthropological paper now published in Science, the researchers suggest that the Nesher Ramla Homo type might represent this population, heretofore missing from the record of human fossils. Moreover, the researchers propose that the humans from Nesher Ramla are not the only ones of their kind discovered in the region, and that some human fossils found previously in Israel, which have baffled anthropologists for years - like the fossils from the Tabun cave (160,000 years ago), Zuttiyeh cave (250,000), and Qesem cave (400,000) - belong to the same new human group now called the Nesher Ramla Homo type.
"People think in paradigms," says Dr. Rachel Sarig. "That's why efforts have been made to ascribe these fossils to known human groups like Homo sapiens, Homo erectus, Homo heidelbergensis or the Neanderthals. But now we say: No. This is a group in itself, with distinct features and characteristics. At a later stage small groups of the Nesher Ramla Homo type migrated to Europe - where they evolved into the 'classic' Neanderthals that we are familiar with, and also to Asia, where they became archaic populations with Neanderthal-like features. As a crossroads between Africa, Europe and Asia, the Land of Israel served as a melting pot where different human populations mixed with one another, to later spread throughout the Old World. The discovery from the Nesher Ramla site writes a new and fascinating chapter in the story of humankind."
Prof. Gerhard Weber, an associate from Vienna University, argues that the story of Neanderthal evolution will be told differently after this discovery: "Europe was not the exclusive refugium of Neanderthals from where they occasionally diffused into West Asia. We think that there was much more lateral exchange in Eurasia, and that the Levant is geographically a crucial starting point, or at a least bridgehead, for this process."
IMAGE: GEOGRAPHICAL AND TEMPORAL DISTRIBUTION OF NEWLY SAMPLED INDIVIDUALSview more
CREDIT: IVPP
A joint research team led by Prof. FU Qiaomei from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences sequenced the ancient genomes of 31 individuals from southern East Asia, thus unveiling a missing piece of human prehistory.
The study was published in Cell on June 24.
Prof. FU's team used DNA capture techniques to retrieve ancient DNA from Guangxi and Fujian, two provincial-level regions in southern China. They sequenced genome-wide DNA from 31 individuals dating back 11,747 to 194 years ago. Of these, two date back to more than 10,000 years ago, making them the oldest genomes sampled from southern East Asia and Southeast Asia to date.
Previous ancient DNA studies showed that ~8,000-4,000-year-old Southeast Asian Hòabìnhian hunter-gatherers possessed deeply divergent Asian ancestry, whereas the first Southeast Asian farmers beginning ~4,000 years ago show a mixture of ancestry associated with Hòabìnhian hunter-gatherers and present-day southern Chinese populations. In coastal southern China, ~9,000-4,000-year-old individuals from Fujian province show ancestry not as deeply divergent as the Hòabìnhian.
In Guangxi, FU and her team's sampling showed that the ancestry present was unlike that sampled previously in Fujian and Southeast Asia. Instead, they found a unique East Asian ancestral population (represented by the 11,000-year-old Longlin individual from Guangxi). Their findings highlight that 11,000 years ago, at least three genetically distinct ancestries composed the human landscape in southern East Asia and Southeast Asia: Fujian ancestry, Hòabìnhian ancestry, and Guangxi ancestry.
In addition to sharing Longlin ancestry, the Dushan and Baojianshan individuals in Guangxi also show strong evidence for admixture in southern China ~9,000 to 6,000 years ago. Dushan and Baojianshan were a mixture of local Guangxi ancestry, southern ancestry previously sampled in Fujian, and Deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers.
Previously, it was shown that southern Chinese populations expanded to Southeast Asia, mixing with and eventually replacing Hòabìnhians in Southeast Asia. FU's team showed that the dynamics were more complex, since populations carrying Hòabìnhian ancestry either co-existed with populations carrying Guangxi ancestry in southern China or gene flow upwards from Southeast Asia to southern China also occurred as early as ~8,000-6,000 years ago.
The study fills a research gap in the region connecting East and Southeast Asia, revealing a new genetic ancestry different from that found in coastal areas of southern China and in Southeast Asia.
Furthermore, it shows the impact of migration and admixture of populations at the crossroads of East and Southeast Asia in the last 11,000 years, revealing a long history of intermingling between these two regions.
"While we now have a better understanding of the population history in the last 11,000 years at the crossroads of East and Southeast Asia, future sampling in regions near the Yangtze River and southwest China are needed for a comprehensive understanding of the genetic history of humans in southern China," said Prof. FU.
Genetic samples from ancient humans in these regions will likely further clarify the remarkably diverse genetic prehistory of humans in southeastern Asia, and inform the genetic shifts that occurred between 6,000 and 1,500 years ago and contributed to the genetic composition observed today in southern China.
IMAGE: SHAFTHOLE AXE TYPE FÅRDRUP. THIS AXE IS OF NORDIC CRAFTSMANSHIP AND HIDES INFORMATION ON THE FIRST ATTEMPT TO ESTABLISH TRADING NETWORKS WITH SOCIETIES ACROSS THE ALPS. A SMALL GROUP OF... view more
CREDIT: PHOTO: HEIDE W. NØRGAARD, BY PERMISSION OF THE NATIONAL MUSEUM, COPENHAGEN.
New research presents over 300 new analyses of bronze objects, raising the total number to 550 in 'the archaeological fingerprint project'. This is roughly two thirds of the entire metal inventory of the early Bronze Age in southern Scandinavia. For the first time, it was possible to map the trade networks for metals and to identify changes in the supply routes, coinciding with other socio-economic changes detectable in the rich metal-dependent societies of Bronze Age southern Scandinavia.
The magnificent Bronze Age in southern Scandinavia rose from copper traded from the British Isles and Slovakia 4000 years ago. 500 years later these established trade networks collapsed and fresh copper was then traded from the southern Alps, the so-called Italian Alps. This large-scale study could show that during the first 700 years of the Nordic Bronze Age the metal supplying networks and trade routes changed several times. These 700 years of establishment and change led to a highly specialised metalwork culture boasting beautiful artwork such as the Trundholm Sun wagon and spiral decorated belt plates branding high-ranking women; even depicted on today's Danish banknotes.
The study by H. Nørgaard, Moesgaard Museum and her colleagues H. Vandkilde from Aarhus University and E. Pernicka from the Curt-Engelhorn Centre in Mannheim built on the so far largest dataset of chemical and isotope data of ancient bronze artefacts. In total 550 objects were used to model the changes that took place: These changes correlate with major shifts in social organisation, settlements, housing, burial rites and long distance mobility.
"Now, this multi-disciplinary approach - based jointly on conventional archaeological methods and novel scientific methodologies processing large data quantities - allows us to detect these correlating changes and identify contemporaneity with societal changes recognised by colleague researchers", says Heide Nørgaard the project´s PI.
"It is highly likely that both people and technologies arrived to Scandinavia and that Scandinavians travelled abroad to acquire copper by means of the Nordic amber, highly valued by European trading partners".
Thousands of years ago, archaic humans such as Neanderthals and Denisovans went extinct. But before that, they interbred with the ancestors of present-day humans, who still to this day carry genetic mutations from the extinct species.
Over 40 percent of the Neanderthal genome is thought to have survived in different present-day humans of non-African descent, but spread out so that any individual genome is only composed of up to two percent Neanderthal material. Some human populations also carry genetic material from Denisovans - a mysterious group of archaic humans that may have lived in Eastern Eurasia and Oceania thousands of years ago.
The introduction of beneficial genetic material into our gene pool, a process known as adaptive introgression, often happened because it was advantageous to humans after they expanded across the globe. To name a few examples, scientists believe some of the mutations affected skin development and metabolism. But many mutations are yet still undiscovered.
Now, researchers from GLOBE Institute at the University of Copenhagen have developed a new method using deep learning techniques to search the human genome for undiscovered mutations.
"We developed a deep learning method called 'genomatnn' that jointly models introgression, which is the transfer of genetic information between species, and natural selection. The model was developed in order to identify regions in the human genome where this introgression could have happened," says Associate Professor Fernando Racimo, GLOBE Institute, corresponding author of the new study.
"Our method is highly accurate and outcompetes previous approaches in power. We applied it to various human genomic datasets and found several candidate beneficial gene variants that were introduced into the human gene pool," he says.
The new method is based on a so-called convolutional neural network (CNN), which is a type of deep learning framework commonly used in image and video recognition.
Using hundreds of thousands of simulations, the researchers at the University of Copenhagen trained the CNN to identify patterns in images of the genome that would be produced by adaptive introgression with archaic humans.
Besides confirming already suggested genetic mutations from adaptive introgression, the researchers also discovered possible mutations that were not known to be introgressed.
"We recovered previously identified candidates for adaptive introgression in modern humans, as well as several candidates which have not previously been described," says postdoc Graham Gower, first author of the new study.
Some of the previously undescribed mutations are involved in core pathways in human metabolism and immunity.
"In European genomes, we found two strong candidates for adaptive introgression from Neanderthals in regions of the genome that affect phenotypes related to blood, including blood cell counts. In Melanesian genomes, we found candidate variants introgressed from Denisovans that potentially affected a wide range of traits, such as blood-related diseases, tumor suppression, skin development, metabolism, and various neurological diseases. It's not clear how such traits are affected in present-day carriers of the archaic variants, e.g. neutrally, positively or negatively, although historically the introgressed genetic material is assumed to have had a positive effect on those individuals carrying them," he explains.
The next stage for the research team is to adapt the method to more complex demographic and selection scenarios to understand the overall fate of Neanderthal genetic material. Graham Gower points out that the team aims to follow up on the function of the candidate variants in the genome that they found in this study.
Looking forward, it remains a challenge to search the human genome for genetic material from as yet unsampled populations, so-called ghost populations. However, the researchers are hopeful that they can further train the neural network to recognize mutations from these unsampled populations.
"Future work could also involve developing a CNN that can detect adaptive introgression from a ghost population, for cases in which genomic data from the source is unavailable," says Graham Gower.
