How Prehistoric Humans Simplified the World’s Food Webs

Illustration depicting all mammal species that would inhabit Southern California today if not for human-linked extinction. Extinct species appear in black and white.
Credit: Oscar Sanisidro/University of Alcalá

Research conducted with the help of a University at Albany anthropologist has revealed the cascading effects that humans have had on mammal declines and their food webs over the last 130,000 years, a new study in the journal Science shows.

The study, which was carried out by researchers in the United States, United Kingdom, Denmark and Spain, set out to determine the magnitude of food web loss among mammals since the Late Pleistocene, following the arrival and expansion of human populations around the world.

“We’ve known for a long time that as humans spread out of Africa, everywhere they went, waves of animal extinctions followed their arrival,” said John Rowan, an assistant professor of anthropology at UAlbany who co-authored the study. “When humans got to North America, there were saber-toothed cats, dire wolves, mammoths, mastodons and giant bears. But all these animals start to disappear soon after our species show up.”

While scientists were aware of the human link to mammal extinctions, little was understood regarding how those losses reverberated throughout food webs, which characterize how species interact with one another in an ecosystem. Extinction alone can impact the links in a food web, but so can reductions and shifts in geographic range due to human impacts, such as habitat destruction.

Study of Ancient Skulls Sheds Light on Human Interbreeding With Neandertals

Homo neanderthalensis adult male. Reconstruction based on Shanidar 1 by John Gurche for the Human Origins Program, NMNH.
Photo Credit: Chip Clark.

Research has established that there are traces of Neandertal DNA in the genome of modern humans. Now an exploratory study that assessed the facial structure of prehistoric skulls is offering new insights, and supports the hypothesis that much of this interbreeding took place in the Near East – the region ranging from North Africa to Iraq.

“Ancient DNA caused a revolution in how we think about human evolution,” says Steven Churchill, co-author of the study and a professor of evolutionary anthropology at Duke University. “We often think of evolution as branches on a tree, and researchers have spent a lot of time trying to trace back the path that led to us, Homo sapiens. But we’re now beginning to understand that it isn’t a tree – it’s more like a series of streams that converge and diverge at multiple points.”

“Our work here gives us a deeper understanding of where those streams came together,” says Ann Ross, corresponding author of the study and a professor of biological sciences at North Carolina State University.

“The picture is really complicated,” Churchill says. “We know there was interbreeding. Modern Asian populations seem to have more Neandertal DNA than modern European populations, which is weird – because Neandertals lived in what is now Europe. That has suggested that Neandertals interbred with what are now modern humans as our prehistoric ancestors left Africa, but before spreading to Asia. Our goal with this study was to see what additional light we could shed on this by assessing the facial structure of prehistoric humans and Neandertals.”

The brains of Neanderthals developed differently from those of modern humans

Fewer chromosome segregation errors in modern human than Neanderthal neural stem cells. Left side: microscopy image of the chromosomes (in cyan) of a modern human neural stem cell of the neocortex during cell division. Right side: same type of image, but of a cell where three amino acids in the two proteins KIF18a and KNL1, involved in chromosome separation, have been changed from the modern human to the Neanderthal variants. These “neanderthalized” cells show twice as many chromosomes separation errors (red arrow). 
Credit: Felipe Mora-Bermúdez / MPI-CBG

Neanderthals are the closest relatives to modern humans. The neocortex, the largest part of the outer layer of the brain, is unique to mammals and crucial for many cognitive capacities. Researchers from the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden and the Max Planck Institute for Evolutionary Anthropology in Leipzig have now discovered that neural stem cells – the cells from which neurons in the developing neocortex derive – spend more time preparing their chromosomes for division in modern humans than in Neanderthals. This results in fewer errors when chromosomes are distributed to the daughter cells in modern humans than in Neanderthals or chimpanzees, and could have consequences for how the brain develops and functions.

After the ancestors of modern humans split from those of Neanderthals and Denisovans, their Asian relatives, about one hundred amino acids, the building blocks of proteins in cells and tissues, changed in modern humans and spread to almost all modern humans. The biological significance of these changes is largely unknown. However, six of those amino acid changes occurred in three proteins that play key roles in the distribution of chromosomes, the carriers of genetic information, to the two daughter cells during cell division.

1.700-year-old Korean genomes show genetic heterogeneity in Three Kingdoms period Gaya

Facial reconstruction of four Ancient Korean individuals based on Ancient DNA data
Full Size Original
Credit: Current Biology

An international team led by The University of Vienna and the Ulsan National Institute of Science and Technology in collaboration with the National Museum of Korea has successfully sequenced and studied the whole genome of eight 1.700-year-old individuals dated to the Three Kingdoms period of Korea (approx. 57 BC-668 AD). The first published genomes from this period in Korea and bring key information for the understanding of Korean population history. The Team has been led by Pere Gelabert and Prof. Ron Pinhasi of the University of Vienna together with Prof. Jong Bhak and Asta Blazyte from the UNIST and Prof. Kidong Bae from the National Museum of Korea.

The study, published in Current Biology, showed that ancient Koreans from Gaya confederacy were more diverse than the present-day Korean population. The eight ancient skeletal remains used for DNA extraction and bioinformatic analyses came from the Daesung-dong tumuli, the iconic funerary complex of the Gaya confederacy, and from Yuha-ri shell mound; both archeological sites located in Gimhae, South Korea. 

Great white sharks may have contributed to megalodon extinction

Tooth size comparison between the extinct Early Pliocene Otodus megalodon tooth and a modern great white shark. 
Credit: MPI for Evolutionary Anthropology

The diet of fossil extinct animals can hold clues to their lifestyle, behavior, evolution and ultimately extinction. However, studying an animal’s diet after millions of years is difficult due to the poor preservation of chemical dietary indicators in organic material on these timescales. An international team of scientists led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, applied a new method to investigate the diet of the largest shark to have ever existed, the iconic Otodus megalodon. This new method investigates the zinc isotope composition of the highly mineralized part of teeth and proves to be particularly helpful to decipher the diet of these extinct animals.

Megatooth sharks like Otodus megalodon, more commonly known as megalodon, lived between 23 and 3.6 million years ago in oceans around the globe and possibly reached as large as 20 meters in length. For comparison, the largest great white sharks today reach a total length of only six meters. Many factors have been discussed to explain the gigantism and extinction of megalodon, with its diet and dietary competition often being thought of as key factors.

Researchers aim X-rays at century-old plant secretions for insight into Aboriginal Australian cultural heritage

Century-old plants exudate samples in amber jars. Researchers mapped the chemistry of these samples using high-energy photons. Scientists can analyze other historical artifact chemistries by applying this technique in the future.
Credit: Flinders University, South Australia, Kaurna Country

By revealing the chemistry of plant secretions, or exudates, these studies build a basis for better understanding and conserving art and tools made with plant materials.

For tens of thousands of years, Aboriginal Australians have created some of the world’s most striking artworks. Today their work continues long lines of ancestral traditions, stories of the past and connections to current cultural landscapes, which is why researchers are keen on better understanding and preserving the cultural heritage within.

In particular, knowing the chemical composition of pigments and binders that Aboriginal Australian artists employ could allow archaeological scientists and art conservators to identify these materials in important cultural heritage objects. Now, researchers are turning to X-ray science to help reveal the composition of the materials used in Aboriginal Australian cultural heritage – starting with the analysis of century-old samples of plant secretions, or exudates.

Aboriginal Australians continue to use plant exudates, such as resins and gums, to create rock and bark paintings and for practical applications, such as hafting stone points to handles. But just what these plant materials are made of is not well known.

Tooth unlocks mystery of Denisovans in Asia

Views of the TNH2-1 specimen
Credit: Flinders University

What links a finger bone and some fossil teeth found in a cave in the remote Altai Mountains of Siberia to a single tooth found in a cave in the limestone landscapes of tropical Laos?

The answer to this question has been established by an international team of researchers from Laos, Europe, the US and Australia.

The human tooth was chanced upon during an archaeological survey in a remote area of Laos. The scientists have shown it originated from the same ancient human population first recognized in Denisova Cave (dubbed the Denisovans), in the Altai Mountains of Siberia (Russia).

The research team made the significant discovery during their 2018 excavation campaign in northern Laos. The new cave Tam Ngu Hao 2, also known as Cobra Cave, is located near to the famous Tam Pà Ling Cave where another important 70,000-year-old human (Homo sapiens) fossils had been previously found.

The international researchers are confident the two ancient sites are linked to Denisovans occupations despite being thousands of kilometers apart.

Ancient grains

Laura Motta, University of Michigan paleoethnobotanist, shows peas excavated from the Karanis site in Egypt.
Image credit: Eric Bronson, Michigan Photography

For a long time, researchers believed the diets of ancient people were nutritionally poor.

Everyday ancient Mediterranean civilizations relied on a diet of grains and pulses (chickpeas, lentils and other members of the bean family). Researchers thought this food lacked micronutrients such as zinc and iron, while also containing components that inhibit the uptake of what nutrients the food did have.

But a University of Michigan pilot study on crops grown in Egypt during Roman times suggests that ancient grains were more nutrient dense than grains grown in the same region today. Now, building on that study, U-M is part of a five-university consortium to receive a €3.7 million grant (about $3.85 million), called the AGROS project, awarded by the Belgian program Excellence of Science.

The researchers will use cutting-edge technologies to examine the nutritional profile of the food and how its nutrients changed based on the historical methods of food preparation.

The genetic origins of the world's first farmers clarified

Ancient DNA extraction in Mainz’s lab. Work done in sterile conditions to avoid contamination from modern DNA.
Credit: Joachim Burger / JGU

The genetic origins of the first agriculturalists in the Neolithic period long seemed to lie in the Near East. A new study published in the journal Cell shows that the first farmers actually represented a mixture of Ice Age hunter-gatherer groups, spread from the Near East all the way to south-eastern Europe. Researchers from the University of Bern and the SIB Swiss Institute of Bioinformatics as well as from the Johannes Gutenberg University Mainz and the University of Fribourg were involved in the study. The method they developed could help reveal other human evolution patterns with unmatched resolution. 

The first signs of agriculture and a sedentary lifestyle are found in the so-called 'Fertile Crescent', a region in the Near East where people began to settle down and domesticate animals and plants about 11,000 years ago. The question of the origin of agriculture and sedentism has occupied researchers for over 100 years: did farming spread from the Near East through cultural diffusion or through migration? Genetic analyses of prehistoric skeletons so far supported the idea that Europe's first farmers were descended from hunter-gatherer populations in Anatolia. While that may well be the case, this new study shows that the Neolithic genetic origins cannot clearly be attributed to a single region. Unexpected and complex population dynamics occurred at the end of the Ice Age, and led to the ancestral genetic makeup of the populations who invented agriculture and a sedentary lifestyle i.e. the first Neolithic farmers. 

The first farmers emerged from a mixing process starting 14,000 years ago 

Previous analyses had suggested that the first Neolithic people were genetically different from other human groups from that time. Little was known about their origins. Nina Marchi, one of the study's first authors from the Institute of Ecology and Evolution at the University of Bern and SIB says: "We now find that the first farmers of Anatolia and Europe emerged from a population admixed between hunter-gatherers from Europe and the Near East." According to the authors, the mixing process started around 14,000 years ago, which was followed by a period of extreme genetic differentiation lasting several thousand years. 

A novel approach to model population history from prehistoric skeletons 

The Klein7 individual from the Kleinhadersdorf site in the Lower Austrian Weinviertel, whose genome was analyzed in the paper.
Credit: BDA / Christine Neugebauer-Maresch

This research was made possible by combining two techniques: the production of high-quality ancient genomes from prehistoric skeletons, coupled with demographic modeling on the resulting data. The research team coined the term "demo genomic modeling" for this purpose. "It is necessary to have genome data of the best possible quality so that the latest statistical genomic methods can reconstruct the subtle demographic processes of the last 30 thousand years at high resolution", says Laurent Excoffier, one of the senior authors of the study. Laurent Excoffier is a professor at the Institute of Ecology and Evolution at the University of Bern and group leader at SIB. He initiated the project together with Joachim Burger of the Johannes Gutenberg University in Mainz and Daniel Wegmann of the University of Fribourg. Nina Marchi adds: "Simply comparing the similarity of different ancient genomes is not enough to understand how they evolved. We had to reconstruct the actual histories of the populations studied as accurately as possible. This is only possible with complex population genetic statistics." 

Interdisciplinary key to solve such ancient puzzles 

Joachim Burger of the University of Mainz and second senior author emphasizes the necessity of interdisciplinarity: "It took close to ten years to gather and analyze the skeletons suitable for such a study. This was only possible by collaborating with numerous archaeologists and anthropologists, who helped us to anchor our models historically". The historical contextualization was coordinated by Maxime Brami, who works with Burger at Johannes Gutenberg University. The young prehistorian was surprised by some of the study's findings: "Europe's first farmers seem to be descended from hunter-gatherer populations that lived all the way from the Near East to the Balkans. This was not foreseeable archaeologically". 

Towards a general model of human population evolution 

Genetic data from fossils (skeletons) are badly damaged and must be processed accordingly using bioinformatics, as Daniel Wegmann from the University of Fribourg and group leader at SIB explains: "The high-resolution reconstruction of the prehistory of the Europeans was only possible thanks to methods that we specifically developed to analyze
ancient fossil genomes." Joachim Burger adds: "With these approaches, we have not only elucidated the origins of the world's first Neolithic populations, but we have established a general model of the evolution of human populations in Southwest Asia and Europe." 

"Of course, spatial and temporal gaps remain, and this does not imply the end of studies on the evolution of humans in this area", concludes Laurent Excoffier. Thus, the team's research plan is already set; they want to supplement their demographic model with genomes from the later phases of the Neolithic and Bronze Ages to provide an increasingly detailed picture of human evolution. 

Source/Credit: University of Bern

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Researchers unravel mummy bird mystery

Carol Anne Barsody scans the mummy bird for a 3D model that will be included in a multisensory exhibition she is planning to hold in October.
Credit: Ryan Young/Cornell University

Over the last several months, a certain bird – believed to be a sacred ibis – has been drawing a lot of attention, and covering a lot of ground, from the College of Arts and Sciences to the College of Veterinary Medicine, College of Engineering and, later, the Lab of Ornithology.

Not bad for an animal that has been dead and mummified for more than 1,500 years.

The so-called “mummy bird” has had help getting around. Carol Anne Barsody, a master’s student in archaeology, has been trying to learn everything she can about the artifact, which is part of the Anthropology Collections in the College of Arts and Sciences, by consulting an array of researchers from across the university.

“One of the things I love about this project is that it incorporates expertise from across Cornell, all working together on a common goal,” Barsody said. “Where else but Cornell can you speak with a curator of vertebrates about a skeleton, and then call the vet school and have it X-rayed? There are so many different resources that students can utilize. And interdisciplinary projects make for stronger research.”

What began as a passion project, and grew into an independent study and then a proposed master’s thesis, has become a cross-campus fascination that encompasses everything from ancient burial rituals to the lost history of donated artifacts, the totemic power of animals, the ways museums can better engage the public, and even Egyptian beer.

Study ties present-day Native American tribe to ancestors in San Francisco Bay Area

U. of I. anthropology professor Ripan Malhi and his colleagues found genomic evidence linking present-day members of the Muwekma Ohlone Tribe in the San Francisco Bay Area with individuals who lived in the region several hundred to 2,000 years ago. 
Credit/Photo by L. Brian Stauffer

A genomic study of Native peoples in the San Francisco Bay Area finds that eight present-day members of the Muwekma Ohlone Tribe share ancestry with 12 individuals who lived in the region several hundred to 2,000 years ago.

Reported in the Proceedings of the National Academy of Sciences, the study challenges the notion that the Ohlone migrated to the area between A.D. 500-1,000, said Ripan Malhi, a professor of anthropology at the University of Illinois Urbana-Champaign, who led the research with Stanford University population genetics and society professor Noah Rosenberg in collaboration with a team of other scientists and members of the Muwekma Ohlone Tribe. The Muwekma Ohlone Tribal Council requested, contributed to and oversaw the study.

Previous studies of artifacts and language patterns suggested that the Ohlone were relative newcomers to the region. But the genomic research found a deep signal of continuity between the ancient population and the new one, the team reported.