Have we found all the major Maya cities? Not even close, new research suggests

 

Using laser-guided imaging to peer through dense jungle forests, Tulane University researchers have uncovered vast unexplored Maya settlements in Mexico and a better understanding of the ancient civilization's extent and complexity.

The new research, published in the journal Antiquity, was led by Tulane University anthropology doctoral student Luke Auld-Thomas and his advisor, Professor Marcello A. Canuto.

The team used lidar, a laser-based detection system, to survey 50 square miles of land in Campeche, Mexico, an area largely overlooked by archaeologists. Their findings included evidence of more than 6,500 pre-Hispanic structures, including a previously unknown large city complete with iconic stone pyramids.

“Our analysis not only revealed a picture of a region that was dense with settlements, but it also revealed a lot of variability,” said Auld-Thomas, a doctoral student in Tulane’s Anthropology Department and instructor at Northern Arizona University. “We didn’t just find rural areas and smaller settlements. We also found a large city with pyramids right next to the area’s only highway, near a town where people have been actively farming among the ruins for years. The government never knew about it; the scientific community never knew about it. That really puts an exclamation point behind the statement that, no, we have not found everything, and yes, there’s a lot more to be discovered.”

The Middle American Research Institute (MARI) at Tulane University has been pioneering the use of lidar technology in archaeological research. Over the past decade, the MARI has built a state-of-the art Geographic Information Systems (GIS) lab, managed by Francisco Estrada-Belli, to analyze remote sensing data, such as lidar.

Lidar technology uses laser pulses to measure distances and create three-dimensional models of specific areas. It has allowed scientists to scan large swaths of land from the comfort of a computer lab, uncovering anomalies in the landscape that often prove to be pyramids, family houses and other examples Maya infrastructure.

“Thanks to generous funding from the Hitz Foundation, MARI has been at the forefront of the use of lidar technology in archaeological research over the past decade,” said Canuto, director of the MARI. “Now our efforts are expanding from data analysis to data collection and acquisition. The work conducted on these data from Campeche represent how MARI’s ‘lidar footprint’ is expanding.”

This research may also help resolve ongoing debates about the true extent of Maya settlements.

"Because lidar allows us to map large areas very quickly, and at really high precision and levels of detail, that made us react, 'Oh wow, there are so many buildings out there we didn't know about, the population must have been huge,’” Auld-Thomas said. “The counterargument was that lidar surveys were still too tethered to known, large sites, such as Tikal, and therefore had developed a distorted image of the Maya lowlands. What if the rest of the Maya area was far more rural and what we had mapped so far was the exception instead of the rule?"

The study highlights the transformative power of lidar technology in unveiling the secrets of ancient civilizations. It also provides compelling evidence of a more complex and varied Maya landscape than previously thought.

"Lidar is teaching us that, like many other ancient civilizations, the lowland Maya built a diverse tapestry of towns and communities over their tropical landscape,” Canuto said. “While some areas are replete with vast agricultural patches and dense populations, others have only small communities. Nonetheless, we can now see how much the ancient Maya changed their environment to support a long-lived complex society."

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Journal

Antiquity

DOI

10.15184/aqy.2024.148 

Ancient gene influences immunity of First Nations Peoples of Oceania

 

CU Anschutz scientists say findings could explain why the people are more susceptible to some infectious diseases

Peer-Reviewed Publication

University of Colorado Anschutz Medical Campus

 An ancient gene mutation among First Nations inhabitants of Oceania may make them more susceptible to infectious diseases like influenza, according to a new study by scientists at the University of Colorado Anschutz Medical Campus.

“We found quite a diverse set of genes in this population but there was one allele that really stood out in terms of genetic composition,” said the study’s lead author Paul Norman, PhD, professor of biomedical informatics at the University of Colorado School of Medicine. “We did some investigating, and we suspect this allele to be of archaic human origin.”

The study was published today in the journal Cell in collaboration with researchers from Australia, Papua New Guinea, Mexico and the United Kingdom.

The researchers traced the allele, a variant of a gene that arises from a mutation, to the `archaic people’ or Denisovans who diverged from modern humans before eventually going extinct. Scientists believe the First Nations inhabitants of Australia, New Guinea, American Samoa, New Caledonia, the Solomon Islands and other parts of Oceania encountered and interbred with Denisovans after leaving Africa and traveling through Europe and Eurasia. That’s where researchers believe they picked up the allele.

It’s known as KIR3DLI*114 and the study said it is widespread and unique to Oceania as an allele derived from these archaic people. They suspect it may affect the body’s immune response to infection, among factors accounting for the severity and poor outcomes of infectious diseases among First Nations peoples across Oceania.

“Likely following emigration out of Africa, present day First Nations Oceanians diverged from Eurasians,” the study said. “Subsequent admixture with archaic humans introduced new genetic material, having major impact on genes of the immune system.”

The scientists studied the immunogenic composition of this group and identified `a unique and divergent form of KIR3DL1’ with characteristics of archaic human genetic sequences. Then they investigated the origin, distribution and functions of the allele to determine if it impacted the course of natural killer (NK) cell-driven immunity across Oceania.

Norman said the allele likely offered immuno-protection at some point but now may make First Nations peoples more susceptible to certain infectious diseases and other ailments.

“It must have had a protective quality once and we want to see what that is,” he said.

The study found up to 30% of First Nations individuals in Oceania carry this allele or about five million people.

The implications are wide-ranging for innate and adaptive immunity, autoimmunity, cancer, immunotherapy and neurological disease. The study shows the direct impact of archaic genetics on First Nations peoples of Oceania.

“This is the first real demonstration of a really clear function of one of these archaic genes,” Norman said. “The bigger picture is that we are using these methods to study these populations with the goal of addressing health disparities today and treating diseases across the populations.”

Norman noted that this real-world study represents “our comprehensive collaboration with immunologists and infectious disease experts from the University of Melbourne Australia and Oxford, UK, structural biologists from Monash University, and indigenous health researchers from Charles Darwin and Queensland Universities in Australia. We are very grateful to all the participants for their contribution to this unique study.”

“Well-man” thrown from castle identified from 800-year-old Norse saga

Peer-Reviewed Publication

Cell Press

 

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Well-man skeleton

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Credit: Åge Hojem NTNU Vitenskapsmuseet

A passage in the Norse Sverris Saga, the 800-year-old story of King Sverre Sigurdsson, describes a military raid that occurred in AD 1197, during which a body was thrown into a well at Sverresborg Castle, outside Trondheim in central Norway, likely as an attempt to poison the main water source for the local inhabitants. A new study published in the Cell Press journal iScience on October 25 describes how researchers used ancient DNA to corroborate the events of the saga and discover details about the “Well-man,” blending history and archaeology with science and setting a precedent for future research on historical figures.

“This is the first time that a person described in these historical texts has actually been found,” says Professor Michael D. Martin of the Norwegian University of Science and Technology’s University Museum in Trondheim, Norway. “There are a lot of these medieval and ancient remains all around Europe, and they’re increasingly being studied using genomic methods.”

In 1938, bones were found in the well at Sverresborg Castle, but researchers at the time lacked the tools to do much aside from visual analysis. Now, radiocarbon dating and advanced gene-sequencing technology have allowed researchers to craft a more intricate picture of who the Well-man was. Radiocarbon dating confirmed that the body is approximately 900 years old, and studies conducted in 2014 and 2016 confirmed that the body belonged to a male who was between 30 and 40 years old at the time of death.

“The text is not absolutely correct—what we have seen is that the reality is much more complex than the text,” says archaeologist Anna Petersén of the Norwegian Institute of Cultural Heritage Research in Oslo, Norway.

“We can corroborate what actually happened in a more neutral way,” says Dr. Martin Rene Ellegaard of the Norwegian University of Science and Technology. As part of his work toward a doctoral degree, Ellegaard used samples of a tooth obtained from the Well-man’s skeleton to sequence his genome. Using this information, the team was able to ascertain that he most likely had blue eyes and blond or light-brown hair, and his ancestors likely hailed from the southernmost Norwegian county of present-day Vest-Agder.

The researchers were able to draw conclusions about the Well-man’s ancestry thanks to a large amount of reference data from the genomes of modern-day Norwegians made available through a collaboration with Professor Agnar Helgason at deCODE Genetics in Iceland. “Most of the work that we do is reliant on having reference data,” says Ellegaard. “So the more ancient genomes that we sequence and the more modern individuals that we sequence, the better the analysis will be in the future.”

“Those reference data are literally thousands of genomes of modern Norwegians and many thousands of other European genomes,” says Martin.

However, this technology has its limitations, as sampling the Well-man’s genome required removing the outer surface from his tooth—to avoid contamination from those who had handled it in non-sterile environments, such as during excavation—and grinding the tooth into a powder. This means that the sample can no longer be used for further tests, and researchers were not able to get data on any pathogens the Well-man may have been carrying at his time of death.

 “It was a compromise between removing surface contamination of the people who have touched the tooth and then removing some of the possible pathogens … there are lots of ethical considerations,” says Ellegaard. “We need to consider what kind of tests we’re doing now because it will limit what we can do in the future.”

The researchers say that they would like to test samples from other historical figures. “The important Norwegian Saint Olaf is thought to be buried somewhere in Trondheim Cathedral,” says Martin, “so I think that if eventually his remains are uncovered, there could be some effort to describe him physically and trace his ancestry using genetic sequencing.”

Speaking to this new technique of blending of history and science, Petersén concludes, “It’s a fantastic result on what Ellegaard and Martin’s method can bring to archaeology in such a strange or rare context like this is.” 

High-res lidar exposes large, high-elevation medieval cities along Asia’s Silk Roads

Peer-Reviewed Publication

Washington University in St. Louis

 

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A drone captured images of Tugunbulak in 2018. (Credit: M. Frachetti)

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Credit: Michael Frachetti

The first-ever use of cutting-edge drone-based lidar in Central Asia allowed archaeologists to capture stunning details of two newly documented trade cities high in the mountains of Uzbekistan.

A team of researchers led by Michael Frachetti, professor of archaeology in Arts & Sciences at Washington University in St. Louis, and Farhod Maksudov, director of the National Center of Archaeology in Uzbekistan, used drone-based lidar to map the archaeological scale and layout of two recently discovered high-elevation sites in Uzbekistan.  The medieval cities are among the largest ever documented in the mountainous parts of the Silk Road, the vast network of ancient trade routes that connected Europe and Eastern Asia. 

Images and details of the discovery were recently published in Nature. Co-authors include Jack Berner, a graduate student in the Department of Anthropology at WashU; Edward Henry, an assistant professor of anthropology and geography at Colorado State University and WashU alum (PhD ’18);  Tao Ju, a professor of computer science and engineering in the McKelvey School of Engineering at WashU; and Xiaoyi Liu, an undergraduate student in the McKelvey School of Engineering at WashU. The expedition was supported by the National Geographic Society.

The drone-lidar scans provided remarkably detailed views of the plazas, fortifications, roads, and habitations that shaped the lives and economies of highland communities, traders, and travelers from the sixth through 11th centuries in Central Asia. The two cities are located in rugged terrain 2,000 to 2,200 meters above sea level (roughly comparable to Machu Picchu in Peru), making them unusual examples of thriving mountain urbanism.

The smaller city, today called Tashbulak, covered about 12 hectares, while the larger city of Tugunbulak reached 120 hectares, “making it one of the largest regional cities of its time,” Frachetti said.

“These would have been important urban hubs in central Asia, especially as you moved out of lowland oases and into more challenging high-altitude settings,” he said. “While typically seen as barriers to Silk Road trade and movement, the mountains actually were host to major centers for interaction. Animals, ores, and other precious resources likely drove their prosperity.”

“This site had an elaborate urban structure with specific material culture that greatly varied from the lowland sedentary culture,” Maksudov said. “It’s clear that the people inhabiting Tugunbulak for more than a thousand years ago were nomadic pastoralists who maintained their own distinct, independent culture and political economy.”

Lidar technology is commonly used to map archaeological landscapes blocked by dense vegetation, but it has additional value where vegetation is sparse, such as the mountains of Uzbekistan. “Drone operation is strictly regulated in Uzbekistan, so this discovery is also thanks to the political support and permissions we received through local partners and government,” Frachetti said.

The centimeter-level scans allowed for advanced computer analysis of the ancient archaeological surfaces, providing an unprecedented view of the cities’ architecture and organization. “These are some of the highest-resolution lidar images of archeological sites ever published,” Frachetti said. “They were made possible, in part, because of the unique erosion dynamics in this mountain setting.”

Frachetti, Maksudov, and their team first discovered the highland cities using predictive computer models and old-fashioned foot surveys between 2011 and 2015, tracing presumed routes of the Silk Road in southeastern Uzbekistan. The project took years to materialize. The extra time ultimately proved to be a blessing, allowing the researchers to make the most of the latest advances in drone-based lidar. “The final high-res maps were a composite of more than 17 drone flights over three weeks,” Frachetti said. “It would have taken us a decade to map such large sites manually.” 

A drone captured images of Tugunbulak in 2018. (Credit: M. Frachetti)

Frachetti and graduate students in his Spatial Analysis, Interpretation, and Exploration (SAIE) Lab compiled the drone-lidar data into 3D models, which were passed to Liu and Ju, who applied computational algorithms to analyze the archaeological surfaces and auto-trace millions of lines to predict likely architectural alignments. The final step was to match the digital output with comparable architectural cases, revealing a huge ancient city otherwise invisible to the naked eye. “The project reflects a truly interdisciplinary effort,” Ju said. “The analysis techniques have potential applications in many domains that utilize lidar scans.”

Both cities warrant much closer inspection, Frachetti said. Preliminary digging at one of the fortified structures at Tugunbulak suggests that the fortress — a building protected by three-meter-thick rammed earth walls — might have been a factory where local metalsmiths turned rich deposits of iron ore into steel. Such industry would have been a key feature of the city and its economy.

It’s already clear that Tashbulak and Tugunbulak weren’t just remote outposts or rest stops. “The Silk Road wasn’t just about the endpoints of China and the West,” Frachetti said. “Major political forces were at play in Central Asia. The complex heart of the network was also a driver of innovation.”

Frachetti hopes to use the same combination of on-the-ground detective work and drone-based lidar to get pictures of other high-altitude settlements along the Silk Road and beyond. “We could really change the map of urban development in medieval Asia,” he said.

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Journal

Nature

DOI

10.1038/s41586-024-08086-5 

Earliest known instance of butchery in India

 

Peer-Reviewed Publication

Florida Museum of Natural History

 

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Scientists studied stone tools, bone flakes and rare elephant remains at a middle Pleistocene site. Their findings shed light on the evolution of giant elephants and humans alike.

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Credit: Illustration by Chen Yu

During the late middle Pleistocene, between 300 and 400 thousand years ago, at least three ancient elephant relatives died near a river in the Kashmir Valley of South Asia. Not long after, they were covered in sediment and preserved along with 87 stone tools made by the ancestors of modern humans.

The remains of these elephants were first discovered in 2000 near the town of Pampore, but the identity of the fossils, cause of death and evidence of human intervention remained unknown until now.

A team of researchers including Advait Jukar, a curator of vertebrate paleontology at the Florida Museum of Natural History, published two new papers on fossils from the Pampore site. In one, researchers describe their discovery of elephant bone flakes which suggests that early humans struck the bones to extract marrow, an energy-dense fatty tissue. The findings are the earliest evidence of animal butchery in India.

The fossils themselves are also rare. In a second study the researchers described the bones, which belong to an extinct genus of elephants called Palaeoloxodon, whose members were more than twice the weight of today’s African elephants. Only one set of Palaeoloxodon bones for this species had been discovered previously, and the fossils from this study are by far the most complete.

To date, only one fossil hominin — the Narmada human — has ever been found on the Indian subcontinent. Its mix of features from older and more recent hominin species indicate the Indian subcontinent must have played an important role in early human dispersal. Prior to the fossil’s discovery in 1982, paleontologists only had stone tool artifacts to give a rough sketch of our ancestors’ presence on the subcontinent.

“So, the question is, who are these hominins? What are they doing on the landscape and are they going after big game or not?” Jukar asked. “Now we know for sure, at least in the Kashmir Valley, these hominins are eating elephants.”

The stone tools likely used for marrow extraction at the Pampore site were made with basalt, a type of rock not found in the local area. Paleontologists believe the raw materials were brought from elsewhere before being fully knapped, or shaped, at the site. Based on the method of construction, they concluded that the site and the tools were 300,000 to 400,000 years old.

Previously, the earliest evidence of butchery in India dated back less than ten thousand years.

“It might just be that people haven’t looked closely enough or are sampling in the wrong place,” Jukar said. “But up until now, there hasn’t been any direct evidence of humans feeding on large animals in India.”

Most of the Pampore site’s elephant remains came from one mature male Palaeoloxodon. The inside of its skull showed abnormal bone growth that likely resulted from a chronic sinus infection.

While it was clear that early humans exploited the carcass, there was no direct evidence of hunting, such as spear points lodged in the bones. The hominins could have killed the elephant or simply found the carcass after it died of natural causes — weakened by its chronic sinus infection, the elephant could possibly have gotten stuck in the soft sediments near the Jhelum River, where paleontologists eventually found it.

The Palaeoloxodon skull is the most complete specimen of its genus found on the Indian subcontinent. Researchers identified it as belonging to the extinct elephant Palaeoloxodon turkmenicus, fossils of which have only been found on one other occasion, in 1955. This earliest fossil was of a partial skull fragment from Turkmenistan. While it looked different from other members of the genus Palaeoloxodon, there wasn’t enough material to determine with certainty whether it was, in fact, a separate species.

“The problem with Palaeoloxodon is that their teeth are largely indistinguishable between species. So, if you find an isolated tooth, you really can’t tell what species of Palaeoloxodon it belongs to,” Jukar said. “You have to look at their skulls.”

Fortunately, the Pampore specimen’s hyoids — bones at the back of the throat that attach to the tongue — were still intact. Hyoids are fragile but distinctive between species, providing a special tool for taxonomizing.

Palaeoloxodon originated in Africa about a million years ago before dispersing into Eurasia. Many species in the genus are known for having an unusually large forehead unlike that of any living elephant species, with a crest that that bulges out over their nostrils. Earlier species of Palaeoloxodon from Africa, however, do not have the bulge. Meanwhile, P. turkmenicus is somewhere in between, with an expanded forehead with no crest.

“It shows this kind of intermediate stage in Palaeoloxodon evolution,” Jukar said. “The specimen could help paleontologists fill in the story of how the genus migrated and evolved.”

Given that hominins have been eating meat for millions of years, Jukar suspects that a lot more evidence of butchery is simply waiting to be found.

“The thing I’ve come to realize after many years is that you just need a lot more effort to go and find the sites, and you need to essentially survey and collect everything,” he said. “Back in the day when people collected fossils, they only collected the good skulls or limb bones. They didn’t collect all the shattered bone, which might be more indicative of flakes or breakage made by people.”

The stone tool and elephant butchery study was published in Quaternary Science Reviews.

The taxonomy study was published in the Journal of Vertebrate Paleontology.

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Journal

Quaternary Science Reviews

DOI

10.1016/j.quascirev.2024.108894

Violence if you’re a woman in ancient Andes populations

The extent to which “civilization” heightens or lessens the likelihood of violent conflict throughout human history has remained one of the most enduring questions among anthropologists. But a new collaborative study of archaeological groups from the Andes region of South America suggests that being part of a centrally organized state society is only part of the equation.

“Our findings suggest that being in a ‘civilization’ may reduce violence, but only for women, and only slightly then,” said Thomas J. Snyder, a doctoral candidate in the Evolutionary Wing of the University of California, Davis, Anthropology Department and lead author of the study. “The effect for women is most pronounced for lethal violence, which can be more plausibly linked to warfare than nonlethal violence.”

The article, “Political organization and gender predict violence in the Andean archaeological record,” was published today in the Proceedings of the National Academy of Sciences. The research is a collaboration of UC Davis and the University of Pittsburgh. 

Researchers investigated the type and frequency of violence experienced by adults in the pre-Hispanic Andean region in large organized centrally organized states (also referred to as “civilizations”), as well as more politically autonomous communities. They looked at existing data on 8,607 adults over a period of 3,000 years from 169 published articles representing 155 sites. The sites were in Peru, Ecuador, Chile and Bolivia.

In autonomous communities, the odds of potentially lethal violent encounters are equivalent between the sexes. In states, they are consistent for males, but decrease for females, researchers found. 

While violence can occur in subtle ways, such as unequal access to necessary resources, this study focused on direct, intentional, interpersonal violence, which can occur in wars or battles, or in households. Notably, women may not be shielded from wartime violence, whether by being taken prisoner — or in some cases, fighting defensively in smaller communities, researchers said.

This study has important implications for how future scholars engage with concepts of violence, gender and sociopolitical change, Snyder said.

“An individual’s sex was as important or more important than the kind of society they inhabited in affecting the risk of trauma,” he said. “Gender, rather than just sociopolitical organization, has a critically important impact on the experience of interpersonal conflict.” 

Why do we love carbs? The origins predate agriculture and maybe even our split from Neanderthals

 

 — If you’ve ever struggled to reduce your carb intake, ancient DNA might be to blame.

 It has long been known that humans carry multiple copies of a gene that allows us to begin breaking down complex carbohydrate starch in the mouth, providing the first step in metabolizing starchy foods like bread and pasta. However, it has been notoriously difficult for researchers to determine how and when the number of these genes expanded.

Now, a new study led by the University at Buffalo and the Jackson Laboratory (JAX), reveals how the duplication of this gene — known as the salivary amylase gene (AMY1) —may not only have helped shape human adaptation to starchy foods, but may have occurred as far back as more than 800,000 years ago, long before the advent of farming.

Reported today in the Oct. 17 advanced online issue of Science, the study ultimately showcases how early duplications of this gene set the stage for the wide genetic variation that still exists today, influencing how effectively humans digest starchy foods.

“The idea is that the more amylase genes you have, the more amylase you can produce and the more starch you can digest effectively,” says the study's corresponding author, Omer Gokcumen, PhD, professor in the Department of Biological Sciences, within the UB College of Arts and Sciences. 

Amylase, the researchers explain, is an enzyme that not only breaks down starch into glucose, but also gives bread its taste.

 Gokcumen and his colleagues, including co-senior author, Charles Lee, professor and Robert Alvine Family Endowed Chair at JAX, used optical genome mapping and long-read sequencing, a methodological breakthrough crucial to mapping the AMY1 gene region in extraordinary detail. Traditional short-read sequencing methods struggle to accurately distinguish between gene copies in this region due to their near-identical sequence. However, long-read sequencing allowed Gokcumen and Lee to overcome this challenge in present-day humans, providing a clearer picture of how AMY1 duplications evolved.

Ancient hunter-gatherers and even Neanderthals already had multiple AMY1 copies

Analyzing the genomes of 68 ancient humans, including a 45,000-year-old sample from Siberia, the research team found that pre-agricultural hunter-gatherers already had an average of four to eight AMY1 copies per diploid cell, suggesting that humans were already walking around Eurasia with a wide variety of high AMY1 copy numbers well before they started domesticating plants and eating excess amounts of starch.

The study also found that AMY1 gene duplications occurred in Neanderthals and Denisovans. 

“This suggests that the AMY1 gene may have first duplicated more than 800,000 years ago, well before humans split from Neanderthals and much further back than previously thought,” says Kwondo Kim, one of the lead authors on this study from the Lee Lab at JAX.

“The initial duplications in our genomes laid the groundwork for significant variation in the amylase region, allowing humans to adapt to shifting diets as starch consumption rose dramatically with the advent of new technologies and lifestyles,” Gokcumen adds.

The seeds of genetic variation

The initial duplication of AMY1 was like the first ripple in a pond, creating a genetic opportunity that later shaped our species. As humans spread across different environments, the flexibility in the number of AMY1 copies provided an advantage for adapting to new diets, particularly those rich in starch.

“Following the initial duplication, leading to three AMY1 copies in a cell, the amylase locus became unstable and began creating new variations," says Charikleia Karageorgiou, one of the lead authors of the study at UB. “From three AMY1 copies, you can get all the way up to nine copies, or even go back to one copy per haploid cell.”

The complicated legacy of farming

The research also highlights how agriculture impacted AMY1 variation. While early hunter-gatherers had multiple gene copies, European farmers saw a surge in the average number of AMY1 copies over the past 4,000 years, likely due to their starch-rich diets. Gokcumen’s previous research showed that domesticated animals living alongside humans, such as dogs and pigs, also have higher amylase gene copy numbers compared to animals not reliant on starch-heavy diets.

“Individuals with higher AMY1 copy numbers were likely digesting starch more efficiently and having more offspring,” Gokcumen says. “Their lineages ultimately fared better over a long evolutionary timeframe than those with lower copy numbers, propagating the number of the AMY1 copies.”

The findings track with a University of California, Berkeley-led study published last month in Nature, which found that humans in Europe expanded their average number of AMY1 copies from four to seven over the last 12,000 years.

“Given the key role of AMY1 copy number variation in human evolution, this genetic variation presents an exciting opportunity to explore its impact on metabolic health and uncover the mechanisms involved in starch digestion and glucose metabolism,” says Feyza Yilmaz, an associate computational scientist at JAX and a lead author of the study. “Future research could reveal its precise effects and timing of selection, providing critical insights into genetics, nutrition, and health.”

Traces of ancient immigration patterns to Japan found in 2000-year-old genome

Genetic analysis of an individual from the Yayoi period reveals immigration patterns from the Korean Peninsula

Peer-Reviewed Publication

School of Science, The University of Tokyo

 

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Human remains from the Yayoi period, approximately 2,300 years ago, from which DNA was extracted.

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Credit: Kim et al 2024

A joint research group led by Jonghyun Kim and Jun Ohashi of the University of Tokyo has demonstrated that the majority of immigration to the Japanese Archipelago in the Yayoi and Kofun periods (between 3000 BCE and 538 CE) came from the Korean Peninsula. The researchers analyzed the complete genome of a “Yayoi” individual and found that, among the non-Japanese populations, the results bore the most similarity to Korean populations. Although it is widely accepted that modern Japanese populations have a dual ancestry, the discovery provides insight into the details of immigration patterns to the archipelago that have eluded scientists thus far. The findings were published in the Journal of Human Genetics.

Today, Japan is an international hub for both business and pleasure. However, this was not always the case. The Japanese Archipelago was relatively isolated during the Jomon period until around 3000 BCE. Then, during the Yayoi and Kofun periods, immigration to the islands from continental Asia began.

“East Asian-related and Northeast Asian-related ancestries account for over 80% of nuclear genomes of the modern Japanese population,” explains Ohashi, the principal investigator of the study. “However, how the Japanese population acquired these genetic ancestries—that is, the origins of the immigration—is not fully understood.”

Various theories have been proposed to explain the genetic variety in the modern population. Currently, the two contenders are the two-way and three-way admixture models. According to the two-way model, the main source of immigration was the same during the Yayoi and Kofun periods, while the three-way model assumes two different sources. To investigate which model was the better fit, the researchers analyzed the complete nuclear genome of an individual from the Doigahama Site, the archeological site of a Yayoi period cemetery in Yamaguchi prefecture, Japan.

The researchers compared the genome of this Yayoi-period individual with the genome of ancient and modern populations in East Asia and Northeast Asia. The comparison showed close similarity to Kofun period individuals with distinct Jomon-related, East Asian-related, and Northeast Asian-related ancestries. However, a comparison with modern genomes also revealed that the Yayoi individual, except for modern Japanese populations, was the closest to modern Korean populations, which also have both East Asian-related and Northeast Asian-related ancestries.

“Our results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula,” says Ohashi. “The results also mean the three-way admixture model, which posits that a Northeast Asian group migrated to the Japanese Archipelago during the Yayoi period and an East Asian group during the Kofun period, is incorrect.”

Despite the significance of these findings, Ohashi is already looking ahead.

“Since our study has identified the primary origins of the immigrants, our next goal is to examine the genomes of more Yayoi individuals to clarify why more than 80% of the genomic components of the modern Japanese population are derived from immigration and how the admixture between continental Asian and indigenous Jomon people progressed within the Japanese Archipelago.”

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Journal

Journal of Human Genetics

DOI

10.1038/s10038-024-01295-w 

Landscape effects of hunter-gatherer practices reshape idea of agriculture

 

Indigenous hunter-gatherer practices play key role in plant dispersal, genetic diversity and conservation, according to new research led by Penn State anthropologists

Peer-Reviewed Publication

Penn State

 

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Solanum diversiflorum (bush tomato) fruit.

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Credit: Rebecca Bliege Bird

UNIVERSITY PARK, Pa. — Some of the wild plants that grow across the Australian landscape may not be so wild, according to new research led by Penn State scientists.

The researchers studied four wild Australian plants ­— three test species and one control group — and how the hunting-gathering practices of the Martu Aboriginal people affect where these non-domesticated plants grow on the landscape. They found that the three test species, especially the wild bush tomato, rely on human activity for seed dispersal. The findings, published in Nature Communications, challenge the conventional notion of agriculture and suggest that humans impacted plants’ genetic diversity long before the advent of farming.

“This research is one of the first to show that peoples who are not already engaged in agriculture are still having long-term effects on plant populations,” said Rebecca Bliege Bird, first author of the study and professor of anthropology at Penn State. “In Australia, we’re talking about 50,000 years of Aboriginal involvement with these plants.”

The Martu Aboriginal people have lived in Australia for thousands of years and largely maintained their hunter-gatherer lifestyle to the current day, eschewing the permanency of farming specific crops for their nomadic customs, the researchers explained. Many avoided contact with European settlers and their descendants until the 1960s, when the government removed them from their ancestral lands prior to conducting inter-ballistic missile tests. They began returning to their lands in the 1980s, according to the researchers.

To see how Martu customs and practices affect plant distribution across the landscape, the researchers focused on three edible plants important for sustenance and cultural identity ­— the bush raisin, the bush tomato and love grass, which the Martu winnow and turn into flour. The researchers also looked at the distribution of the fanflower, which is not actively foraged.

The researchers accompanied Martu harvesters on foraging expeditions over a 10-year period and surveyed plants at active and archaeological dinner camp locations where Martu peoples processed and consumed these and other foods. They also used satellite data and ecological surveys to understand the landscape impacts of fires intentionally set by Martu hunters to drive out game. Then they entered the data — like site type, nearest water permanence and fire frequency — into statistical models to see which variables most likely contributed to the presence or absence of the four plants on the landscape.

They found that the three edible plants, especially the bush tomato and love grass, highly depend on both the dispersion of seed and the use of landscape fire for propagation across the landscape. For instance, Martu foragers may taste bush tomatoes while picking the fruit to make sure it’s sweet, discarding the bitter seeds in the bush tomato patch. Or after foraging and transporting the fruit nearer to the community, they may discard the seeds while processing the fruit in bulk around a campfire, explained Bliege Bird. The bush raisin only persists in landscapes where people are actively burning landscape fires for hunting small animals.

“The findings call into question our whole notions of what agriculture is,” said Douglas Bird, study co-author and professor of anthropology at Penn State. “Rather than thinking about the difference between agricultural societies and hunter-gatherer societies as a matter of kind, we’d be better off thinking about it as a matter of degree — that people influence plants long before they engage in what we think of as farming.”

The findings have implications for global conservation efforts of plant and animal species and emphasizes the importance of indigenous involvement in those efforts, according to the researchers.

“In Australia, the importance of an anthropogenic — or human-influenced — landscape for certain species was just critical in the 20th century,” Bliege Bird said. “In addition to promoting the persistence of edible plants, many small native mammals in Australia, especially those in the desert, relied on the anthropogenic fire mosaic. When Aboriginal fire activity was removed, a lot of those small animals went extinct locally or even on a continental scale. Recognizing indigenous involvement in landscapes and ecosystems not only helps us design better conservation policy but contributes to supporting indigenous rights to access land and traditional resources.”

Underwater caves yield new clues about Sicily’s first residents

Findings may help explain early expansion of Homo sapiens into the Mediterranean islands

Peer-Reviewed Publication

Washington University in St. Louis

 

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WashU archaeologists are investigating coastal and underwater caves in southeastern Sicily, tracing early human dispersal onto the island. (Photo: Ilaria Patania)

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Credit: Ilaria Patania

Archaeological surveys led by scientists at Washington University in St. Louis suggest that coastal and underwater cave sites in southern Sicily contain important new clues about the path and fate of early human migrants to the island.

A new study in PLOS ONE reports and assesses the contents of 25 caves and rock shelters, most of them first identified between 1870 and the 1990s but essentially lost to science over time. Study authors also conducted new land and underwater surveys in previously unexplored coastal areas and uncovered three new sites that contain potentially important archaeological sediments.

“What we are looking for is not just the first person who arrived, but the first community,” said Ilaria Patania, an assistant professor of archaeology in Arts & Sciences. “Understanding the timing of the initial colonization of Sicily provides key data for the pattern and mode of the early expansion of Homo sapiens into the Mediterranean.”

Sicily is considered by many scholars to be the earliest island in the region to be permanently occupied by human ancestors, but when and how the early migrants accomplished this feat remains unknown. Sicily is less than two miles from mainland Italy, but the water crossing would have been extremely difficult for early humans.

Other studies have primarily focused on possible entry points on the island’s northern side.

“This research shows that new ways of thinking and looking can reveal patterns that weren’t visible before,” said T.R. Kidder, the Edward S. and Tedi Macias Professor of anthropology in Arts & Sciences at WashU, a co-author of the new study.

“Previous scholars assumed that sites on the southern coast of Sicily would be eroded or too damaged to yield useful information,” Kidder said. “But finding underwater sites opens up a whole new terrain to study. It allows us to reconsider routes of migration of these earliest modern human ancestors.”

Dangerous water crossing

Sicily, the largest Mediterranean island, is located just off the “toe” of Italy’s boot.

In the ancient Greek poem the “Odyssey,” Homer describes how Odysseus sailed his ship past the mythical sea monsters Scylla and Charybdis as he crossed the Sicily strait. The strait was well known to sailors of the past; they attributed the deadly forces of its waves and whirlpools to powerful monsters.

In modern times, thousands of migrants from North Africa attempt to cross the strait each year. Many don’t make it, some capsizing just a few hundred meters from landing.

Patania, a native of the island of Sicily, has a deep respect for the power of the sea. Her grandfather was a fisherman who worked on the same shores she now studies.

“Very early on, I was taught that the sea can be a great resource,” she said. “At the same time, you never turn your back on the sea. The sea can be very dangerous.”

This idea plays out in her research. “I’m very interested in how humans occupy marginal environments,” Patania said. “These are environments where if everything goes well, we are in perfect harmony with nature. But if something changes — and this could be something like global climate change, or something smaller, like the arrival of a new animal — it could be a catastrophe.”

Scholars of the region agree that humans had made it to Sicily by 16,000 years after the last glacial maximum. But that established date is puzzlingly late, given that humans are known to have dispersed by land into Siberia about 30,000 years earlier. The discrepancy has led some to wonder if humans actually arrived on Sicily much before the currently accepted dates.

Also, no one yet knows whether humans arrived on Sicily by seafaring, or by foot over a land bridge — or even what direction they came from.

“A challenge for understanding the spread of early modern human ancestors is that we don’t fully understand how they spread and colonized the world at a very early stage,” Kidder said. “As Ilaria says, this is a very marginal environment. Did folks come down from Italy and cross the Straits of Messina, or did they come from the south along the African coast? Or, is it possible that they were island hopping across the Mediterranean? Locating sites on the south coast helps us consider pathways and thus modes of behavior.”

Eyes on the sea

Patania leads a long-term research project focused on the early occupation of Sicily. “In southeast Sicily, very few Upper Paleolithic sites have been excavated and analyzed using scientific methods,” she said.

“Our project is still in its early stages, but already we have identified and assessed over 40 sites of interest, of which about 17 are sites that have been relocated with greater precision based on older identifications,” Patania said.

She and her team prepared for their recent cave explorations by poring through the archives of local town libraries in Sicily, reading historical bulletins and news articles as far back as the 19th century.

The researchers identified potential sites and reviewed records and photographs of materials recovered by local avocational archaeologists. When possible, they interviewed workers that had been involved in earlier excavations, and they also talked with local recreational divers and fishermen.

For example, one of the co-authors on the new study is a retired tugboat captain. He has no formal scientific training, but he spent decades working on the decks of boats in and around the Port of Augusta.

“The moment I said that I was looking for paleosols, and that paleosols look like clay dirt that could be red or gray underwater, he said, ‘I know exactly what you are looking for,’” Patania said.

Patania also partnered with the superintendent of cultural and natural heritage of Siracusa and Ragusa (two provinces of Sicily) and the superintendent of the sea of Sicily to locate and recruit other local experts and stakeholders.

As the research has progressed, Patania also has spoken with officers in the Italian navy about training members of their specialized dive team to help identify underwater archaeological features. These divers spend a lot of time in local waters completing their regular tasks related to clearing ordnance and other debris from World War II.

“We’ve started with the area close to the coast, and we’re slowly going to move further out in the years to come,” Patania said.

Excavations continue

Two of the new sites in the PLOS ONE study may contain Upper Paleolithic human occupation traces, including fossil fauna, study authors said.

Corruggi is located at the southernmost tip of Sicily. The site was originally identified by other researchers in the 1940s.

“This site is where a second land bridge would have connected this island with the island of Malta,” Patania said.

“When we inspected this site, we found teeth from a European wild ass and stone tools,” she said. “Analyzing the remains from this site might give us insight on the very last leg of the human journey south into the southernmost coast of Sicily and off toward Malta.”

During summer 2024, project team members worked on excavating the second site, a cave called Campolato.

“Here we have discovered evidence for sea-level changes caused by the last glaciation and a localized earthquake that we are still investigating,” Patania said.

“We hope to reconstruct not only the timing of human occupation, but also the environment these people lived in and how they negotiated with natural events like earthquakes, climatic and environmental changes and maybe even volcanic eruptions,” she said.