It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
New insights into the Denisovans – the new hominin group that interbred with modern day humans
Trinity College Dublin
Scientists believe individuals of the most recently discovered “hominin” group (the Denisovans) that interbred with modern day humans passed on some of their genes via multiple, distinct interbreeding events that helped shape early human history.
In 2010, the first draft of the Neanderthal genome was published, and comparisons with modern human genomes revealed that Neanderthal and modern humans had interbred in the past. A few months later, analysis of a genome sequenced from a finger bone excavated in the Denisova cave in the Altai mountains in Siberia revealed that this bone fragment was from a newly discovered hominin group that we now call Denisovans, who also interbred with modern humans.
“This was one of the most exciting discoveries in human evolution in the last decade,” said Dr Linda Ongaro, Postdoctoral Research in Trinity College Dublin’s School of Genetics and Microbiology, and first author of a fascinating new review article published in leading international journal Nature Genetics.
“It’s a common misconception that humans evolved suddenly and neatly from one common ancestor, but the more we learn the more we realise interbreeding with different hominins occurred and helped to shape the people we are today.
“Unlike Neanderthal remains, the Denisovan fossil record consists of only that finger bone, a jawbone, teeth, and skull fragments. But by leveraging the surviving Denisovan segments in Modern Human genomes scientists have uncovered evidence of at least three past events whereby genes from distinct Denisovan populations made their way into the genetic signatures of modern humans.”
Each of these presents different levels of relatedness to the sequenced Altai Denisovan, indicating a complex relationship between these sister lineages.
In the review article, Dr Ongaro and Prof. Emilia Huerta-Sanchez outline evidence suggesting that several Denisovan populations, who likely had an extensive geographical range from Siberia to Southeast Asia and from Oceania to South America, were adapted to distinct environments.
They further outline a number of genes of Denisovan origin that gave modern day humans advantages in their different environments.
Dr Ongaro added: “Among these is a genetic locus that confers a tolerance to hypoxia, or low oxygen conditions, which makes a lot of sense as it is seen in Tibetan populations; multiple genes that confer heightened immunity; and one that impacts lipid metabolism, providing heat when stimulated by cold, which confers an advantage to Inuit populations in the Arctic.
“There are numerous future directions for research that will help us tell a more complete story of how the Denisovans impacted modern day humans, including more detailed genetic analyses in understudied populations, which could reveal currently hidden traces of Denisovan ancestry. Additionally, integrating more genetic data with archaeological information – if we can find more Denisovan fossils – would certainly fill in a few more gaps.”
Hebrew University and National Academy of Sciences of Tajikistan uncover multi-layered site in Tajikistan's Zeravshan Valley, offering new insights into human expansion
[Hebrew University] In an important discovery, archaeologists from the Hebrew University of Jerusalem and the National Academy of Sciences of Tajikistan have uncovered a multi-layered archaeological site in the Zeravshan Valley, central Tajikistan, shedding rare light on early human settlement in the region. The findings from the site, known as Soii Havzak, provide crucial evidence that Central Asia played a vital role in early human migration and development.
Led by Prof. Yossi Zaidner of the Institute of Archaeology at Hebrew University and Dr. Sharof Kurbanov from the National Academy of Sciences of Tajikistan, the research, published in Antiquity, revealed a rich array of stone tools, animal bones, and ancient vegetation that date back to various periods between 20,000 and 150,000 years ago.
"It turns out that the Zeravshan Valley, known primarily as a Silk Road route in the Middle Ages, was a key route for human expansion long before that—between 20,000 and 150,000 years ago," explained Prof. Zaidner. "This region may have served as a migration route for several human species, such as modern Homo sapiens, Neanderthals, or Denisovans, which may have coexisted in this area, and our research aims to uncover who were the humans that inhabited these parts of the Central Asia and the nature of their interactions."
The archaeological team excavated three areas at Soii Havzak, unearthing layers of human activity. The well-preserved remains offer valuable clues to the ancient climate and environment, as well as the potential for discovering human remains that could identify which human species inhabited the region.
"The preservation of organic materials, such as burnt wood remains, as well as bones, is remarkable. This allows us to reconstruct the region's ancient climate and provides hope that further excavations might reveal clues about human biology in the region," said Prof. Zaidner. "This is crucial for understanding the development of human populations and behavior in Central Asia."
The research has broader implications for the study of human evolution and migration, particularly in understanding how ancient human groups may have interacted with each other. The team believes that Soii Havzak location in the mountainous corridor of Central Asia may have served as a significant transition point for human populations, enabling the spread of early humans across vast regions.
"We hope that ongoing research at this site will reveal new insights into how different human groups—like modern humans, Neanderthals and Denisovans—may have interacted in this region," said Prof. Zaidner. "This discovery is a significant step toward understanding ancient human history in Central Asia and marks an important collaboration between international scientific teams."
The excavation at Soii Havzak will continue over the coming years, with further digs planned to explore deeper layers and conduct more in-depth analyses of the findings. The research is expected to deepen our understanding of human development in Central Asia, potentially transforming the historical narrative of human migration and interaction in this critical region.
Bones and stone artifacts discovered during the excavations at Soii Havzak
Soii Havzak: a new Palaeolithic sequence in Zeravshan Valley, central Tajikistan
Article Publication Date
4-Nov-2024
Tuesday, October 22, 2024
Evolution in action: How ethnic Tibetan women thrive in thin oxygen at high altitudes
New study from Case Western Reserve University reveals link between oxygen delivery and reproductive success among women living on the high Tibetan Plateau
Breathing thin air at extreme altitudes presents a significant challenge—there’s simply less oxygen with every lungful. Yet, for more than 10,000 years, Tibetan women living on the high Tibetan Plateau have not only survived but thrived in that environment.
A new study led by Cynthia Beall, Distinguished University Professor Emerita at Case Western Reserve University, answers some of those questions. The new research, recently published in the journal Proceedings of the National Academy of Sciences of the United States of America(PNAS), reveals how the Tibetan women’s physiological traits enhance their ability to reproduce in such an oxygen-scarce environment.
The findings, Beall said, not only underscore the remarkable resilience of Tibetan women but also provide valuable insights into the ways humans can adapt in extreme environments. Such research also offers clues about human development, how we might respond to future environmental challenges, and the pathobiology of people with illnesses associated with hypoxia at all altitudes.
“Understanding how populations like these adapt,” Beall said, “gives us a better grasp of the processes of human evolution.”
The study
Beall and her team research studied 417 Tibetan women age 46 to 86 who live between 12,000 and 14,000 feet above sea level in location in Upper Mustang, Nepal on the southern edge of the Tibetan Plateau.
They collected data on the women’s reproductive histories, physiological measurements, DNA samples and social factors. They wanted to understand how oxygen delivery traits in the face of high-altitude hypoxia (low levels of oxygen in the air and the blood) influence the number of live births—a key measure of evolutionary fitness.
Adaptation into thin air
They discovered that the women who had the most children had a unique set of blood and heart traits that helped their bodies deliver oxygen. Women reporting the most live births, had levels of hemoglobin, the molecule that carries oxygen, near the sample’s average, but their oxygen saturation was higher, allowing more efficient oxygen delivery to cells without increasing blood viscosity; the thicker the blood, the more strain on the heart.
“This is a case of ongoing natural selection,” said Beall, also the university’s Sarah Idell Pyle Professor of Anthropology. “Tibetan women have evolved in a way that balances the body’s oxygen needs without overworking the heart."
A window into human evolution
Beall’s interdisciplinary research team, which included longtime collaborators Brian Hoit and Kingman Strohl, from the Case Western Reserve School of Medicine, and other U.S. and international researchers, conducted fieldwork in 2019. The team worked closely with local communities in the Nepal Himalayas, hiring local women as research assistants and collaborating with community leaders.
One genetic trait they studied likely originated from the Denisovans who lived In Siberia about 50,000 years ago; their descendants later migrated onto the Tibetan Plateau. The trait is a variant of the EPAS1 gene that is unique to populations indigenous to the Tibetan Plateau and regulates hemoglobin concentration. Other traits, such as increased blood-flow to the lungs and wider heart ventricles, further enhanced oxygen delivery. These traits contributed to greater reproductive success, offering insight into how humans adapt to lifelong levels of low oxygen in the air and their bodies.
Higher oxygen content and transport characterize high-altitude ethnic Tibetan women with the highest lifetime reproductive success
Article Publication Date
21-Oct-2024
Monday, October 21, 2024
Why do we love carbs? The origins predate agriculture and maybe even our split from Neanderthals
Study co-led by UB finds the gene for starch-digesting saliva may have first duplicated more than 800,000 years ago, seeding the genetic variation that shapes our modern diet
University at Buffalo
image:
The lab of Omer Gokcumen helped analyze the genomes of 68 ancient humans for answers about our ability to begin breaking down starch in the mouth.
Credit: Meredith Forrest Kulwicki/University at Buffalo
BUFFALO, N.Y. —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.”
Other UB authors on the study include PhD students Petar Pajic and Kendra Scheer.
The research was a collaboration with the University of Connecticut Health Center and was supported by the National Science Foundation and the National Human Genome Research Institute, National Institutes of Health.
Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation
Article Publication Date
17-Oct-2024
Why do we love carbs? The origins predate agriculture and maybe even our split from Neanderthals
Study from The University of Buffalo and The Jackson Laboratory for Genomic Medicine finds the gene for starch-digesting saliva may have first duplicated more than 800,000 years ago, seeding the genetic variation that shapes our modern diet
Jackson Laboratory
image:
A graphiical representation of the amylase gene locus and how it evolved to influence how humans digest complex carbohydrates like bread and pasta.
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 of Buffalo (UB) and The Jackson Laboratory (JAX) 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 study's findings, reported in the Oct. 17 advanced online issue of Science, reveal that 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.
"The idea is that the more amylase genes you have, the more amylase you can produce and the more starch you can digest effectively,” said 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 explained, 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,” said 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,” said Gokcumen.
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," said 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 AMY1 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 said. “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,” said Feyza Yilmaz, an associate computational scientist at JAX and a lead author of the study. “Future research could reveal its precise effects and timing selection, providing critical insights into genetics, nutrition, and health.”
The research was a collaboration with the University of Connecticut Health Center and was supported by the National Science Foundation and the National Institutes of Health – National Human Genome Research Institute.
Journal
Science
Method of Research
Experimental study
Subject of Research
People
Article Title
Reconstruction of the human amylase locus reveals ancient duplications seeding modern- 2 day variation
Researchers reveal that Denisovans, ancient humans, lived on the Tibetan Plateau. Credit: Dongju Zhang / Wikipedia / CC BY-SA 4.0
Denisovans lived on the high Tibetan plateau for over 100,000 years, as revealed by a recent study. This sheds light on these ancient humans, first discovered in 2010.
Researchers studied many animal bones found at Baishiya Karst Cave, 3,280 meters high near Xiahe County in China’s Gansu province. This cave is one of just three places where these extinct humans lived.
The study found that Denisovans could hunt, cut up, and cook various large and small animals such as woolly rhinos, blue sheep, wild yaks, marmots, and birds
Archaeologists at the cave found a rib bone fragment in sediment dating back to 48,000 to 32,000 years ago. This discovery suggests Denisovans were alive more recently than scientists had thought.
Lived and thrived on the Tibetan plateau
With limited fossil evidence, understanding how our ancient human ancestors, the Denisovans, lived has been challenging. However, the latest study reveals remarkable resilience among those who inhabited Baishiya Karst Cave.
They thrived in one of Earth’s toughest environments through both warm and cold periods, making the most of the diverse animals in the grasslands.
Dongju Zhang, an archaeologist and professor at Lanzhou University in China, co-authored the study published in Nature. Reflecting on the findings, Zhang emphasized the longstanding presence of Denisovans on the Tibetan plateau and posed questions about their lifestyle and environmental adaptation.
“They used all these animals available to them, so that means their behavior is flexible,” Zhang added.
Frido Welker, an associate professor at the Biomolecular Paleoanthropology Group at the University of Copenhagen’s Globe Institute, noted that the rib likely belonged to a Denisovan who lived during a period when modern humans were still spreading throughout Eurasia. He suggested that future research in the area could reveal whether these two groups interacted there.
“It does put this fossil and the (sediment) layer in a context where we know in the wider region humans were likely to be present, and that’s interesting,” he said.
Fossils found in Denisova Cave in the Altai Mountains of Siberia
Denisovans were initially recognized just over a decade ago through DNA analysis of a small piece of finger bone. Since then, fewer than a dozen Denisovan fossils have been unearthed worldwide.
Most of these fossils were discovered in Denisova Cave, nestled in Siberia’s Altai Mountains, which gave the group its name. Genetic studies later revealed that Denisovans, much like Neanderthals, had interbred with early modern humans.
Traces of Denisovan DNA found in present-day populations suggest these ancient people likely once inhabited large parts of Asia.
Notably, it wasn’t until 2019 that researchers identified the first Denisovan fossil outside of Denisova Cave, as reported by CNN.
Wednesday, July 03, 2024
Extinct humans survived on the Tibetan plateau for 160,000 years
UNIVERSITY OF READING
Bone remains found in a Tibetan cave 3,280 m above sea level indicate an ancient group of humans survived here for many millennia, according to a new study published in Nature.
The Denisovans are an extinct species of ancient human that lived at the same time and in the same places as Neanderthals and Homo sapiens. Only a handful Denisovan remains have ever been discovered by archaeologists. Little is known about the group, including when they became extinct, but evidence exists to suggest they interbred with both Neanderthals and Homo sapiens.
A research team led by Lanzhou University, China, the University of Copenhagen, Denmark, the Institute of Tibetan Plateau Research, CAS, China, and involving the University of Reading studied more than 2,500 bones from the Baishiya Karst Cave on the high-altitude Tibetan Plateau, one of the only two places where Denisovans are known to have lived.
Their new analysis, published today (Wednesday, 3 July) in Nature, has identified a new Denisovan fossil and shed light on the species’ ability to survive in fluctuating climatic conditions — including the ice age — on the Tibetan plateau from around 200,000 to 40,000 years ago.
Dr Geoff Smith, a zooarchaeologist at the University of Reading, is a co-author of the study. He said: “We were able to identify that Denisovans hunted, butchered and ate a range of animal species. Our study reveals new information about the behaviour and adaptation of Denisovans both to high altitude conditions and shifting climates. We are only just beginning to understand the behaviour of this extraordinary human species.”
Dietary diversity
Bone remains from Baishya Karst Cave were broken into numerous fragments preventing identification. The team used a novel scientific method that exploits differences in bone collagen between animals to determine which species the bone remains came from.
Dr Huan Xia, of Lanzhou University, said: “Zooarchaeology by Mass Spectrometry (ZooMS) allows us to extract valuable information from often overlooked bone fragments, providing deeper insight into human activities.”
The research team determined that most of the bones were from blue sheep, known as the bharal, as well as wild yaks, equids, the extinct woolly rhino, and the spotted hyena. The researchers also identified bone fragments from small mammals, such as marmots, and birds.
Dr Jian Wang, of Lanzhou University, said: “Current evidence suggests that it was Denisovans, not any other human groups, who occupied the cave and made efficient use of all the animal resources available to them throughout their occupation.”
Detailed analysis of the fragmented bone surfaces shows the Denisovans removed meat and bone marrow from the bones, but also indicate the humans used them as raw material to produce tools.
A new Denisovan fossil
The scientists also identified one rib bone as belonging to a new Denisovan individual. The layer where the rib was found was dated to between 48,000 and 32,000 years ago, implying that this Denisovan individual lived at a time when modern humans were dispersing across the Eurasian continent. The results indicate that Denisovans lived through two cold periods, but also during a warmer interglacial period between the Middle and Late Pleistocene eras.
Dr Frido Welker, of the University of Copenhagen, said: “Together, the fossil and molecular evidence indicates that Ganjia Basin, where Baishiya Karst Cave is located, provided a relatively stable environment for Denisovans, despite its high-altitude.
"The question now arises when and why these Denisovans on the Tibetan Plateau went extinct.”
