Thursday, June 26, 2014

Study provides first direct evidence of plants in the Neanderthal diet

The popular conception of the Neanderthal as a club-wielding carnivore is, well, rather primitive, according to a new study conducted at MIT. Instead, our prehistoric cousin may have had a more varied diet that, while heavy on meat, also included plant tissues, such as tubers and nuts.

Scientists from MIT and the University of La Laguna in Spain have identified human fecal remains from El Salt, a known site of Neanderthal occupation in southern Spain that dates back 50,000 years. The researchers analyzed each sample for metabolized versions of animal-derived cholesterol, as well as phytosterol, a cholesterol-like compound found in plants. While all samples contained signs of meat consumption, two samples showed traces of plants — the first direct evidence that Neanderthals may have enjoyed an omnivorous diet.

"We have passed through different phases in our interpretation of Neanderthals," says Ainara Sistiaga, a graduate student at the University of La Laguna who led the analysis as a visiting student at MIT. She and her colleagues have published their study in the journal PLoS ONE.

"It's important to understand all aspects of why humanity has come to dominate the planet the way it does," adds co-author Roger Summons, a professor of geobiology in MIT's Department of Earth, Atmospheric and Planetary Sciences. "A lot of that has to do with improved nutrition over time."

Unearthing a prehistoric meal

While scientists have attempted to reconstruct the Neanderthal diet, much of the evidence has been inconclusive. For example, researchers have analyzed bone fragments for carbon and nitrogen isotopes — signs that Neanderthals may have consumed certain prey, such as pigs versus cows. But such isotopic data only differentiate between protein sources — underestimating plant intake, and thereby depicting the Neanderthal as exclusively carnivorous.

Other researchers recently identified plant microfossils trapped in Neanderthal teeth — a finding that suggests the species may have led a more complex lifestyle, harvesting and cooking a variety of plants in addition to hunting prey. But Sistiaga says it is also possible that Neanderthals didn't eat plants directly, but consumed them through the stomach contents of their prey, leaving traces of plants in their teeth.

Equally likely, she says, is another scenario: "Sometimes in prehistoric societies, they used their teeth as tools, biting plants, among other things. We can't assume they were actually eating the plants based on finding microfossils in their teeth."

Signs in the soil

For a more direct approach, Sistiaga looked for fecal remains in El Salt, an excavation site in Alicante, Spain, where remnants of multiple Neanderthal occupations have been unearthed. Sistiaga and her colleagues dug out small samples of soil from different layers, and then worked with Summons to analyze the samples at MIT.

In the lab, Sistiaga ground the soil into a powder, then used multiple solvents to extract any organic matter from the sediment. Next, she looked for certain biomarkers in the organic residue that would signal whether the fecal remains were of human origin.

Specifically, Sistiaga looked for signs of coprostanol, a lipid formed when the gut metabolizes cholesterol. As humans are able to break down more cholesterol than any other mammal, Sistiaga looked for a certain peak level of coprostanol that would indicate the sample came from a human.

She and Summons then used the same geochemical techniques to determine the proportions of coprostanol — an animal-derived compound — to 5B-stigmastanol, a substance derived from the breakdown of phytosterol derived from plants.

Each sample contained mostly coprostanol — evidence of a largely meat-based diet. However, two samples also held biomarkers of plants, which Sistiaga says may indicate a rather significant plant intake. As she explains it, gram for gram, there is more cholesterol in meat than there is phytosterol in plants — so it would take a significant plant intake to produce even a small amount of metabolized phytosterol.

In other words, while Neanderthals had a mostly meat-based diet, they may have also consumed a fairly regular portion of plants, such as tubers, berries, and nuts.

"We believe Neanderthals probably ate what was available in different situations, seasons, and climates," Sistiaga says.

Sistiaga, Summons, and their colleagues plan to use similar geochemical biomarker techniques, coupled with micromorphological analysis, to analyze soil samples in Olduvai Gorge, Tanzania — a 1.8-million-year-old site where some of the earliest evidence of human ancestry have been discovered.

"We're working in a micro context," Sistiaga says. "Until now, people have carried out residue analysis on pots, tools, and other objects, but 90 percent of archaeology is sediment. We're opening a new window to the information that is enclosed in Paleolithic soil and sediment."

Friday, June 20, 2014

First proof of early human technology exacerbating disease burden

The discovery of a schistosomiasis parasite egg in a 6200-year-old grave at a prehistoric town by the Euphrates river in Syria may be the first evidence that agricultural irrigation systems in the Middle East contributed to disease burden, according to new Correspondence published in The Lancet Infectious Diseases.

Schistosomiasis is a disease caused by several species of flatworm parasites that live in the blood vessels of the bladder and intestines. Infection can result in anaemia, kidney failure, and bladder cancer. This research shows it may have been spread by the introduction of crop irrigation in ancient Mesopotamia, the region along the Tigris-Euphrates river system that covers parts of modern-day Iraq, Iran, Kuwait, Syria, and Turkey.

According to one of the authors Dr Piers Mitchell, at the University of Cambridge, UK, the discovery might be among the oldest evidence of man-made technology inadvertently causing disease outbreaks.

"The individual who contracted the parasite might have done so through the use of irrigation systems that were starting to be introduced in Mesopotamia around 7500 years ago. The parasite spends part of its life cycle in snails that live in warm fresh water, before leaving the snail to burrow through the skin of people wading or swimming in the water. These irrigation systems distributed water to crops and may have triggered the beginning of the enormous disease burden that schistosomiasis has caused over the past 6000 years."

The discovery at Tell Zeidan in Syria was made by an international team of archaeologists and biological anthropologists working at Cambridge (UK), The Cyprus Institute (Cyprus), and the University of Chicago's Oriental Institute (USA). It shows that the parasite infected humans there at least a thousand years earlier than has been found in Egypt. The oldest Schistosomiasis egg found previously was in Egyptian mummies from 5200 years ago.

The egg was found in the pelvic area of the burial where the intestines and bladder would have been during life. Control soil samples from the head and foot areas of the grave contained no parasitic eggs, suggesting that the gravesite was not contaminated with the parasite more recently.

"Schistosomiasis has become progressively more common over time so that it causes a huge burden across the world today, with over 200 million people infected. It causes anaemia which significantly decreases physical productivity in infected people, and may also cause bladder cancer. We would expect these consequences in ancient peoples to have had a significant impact upon early civilizations in the region"*, says Dr Mitchell.

Humans have been changing Chinese environment for 3,000 years

Ancient levee system set stage for massive, dynasty-toppling floods

Known as the “cradle of Chinese civilization,” the Yellow River was the birthplace of the prosperous northern Chinese civilizations in early Chinese history. However, the Yellow River is also referred to as “China’s Sorrow” because of its frequent and devastating flooding. Research maps and images courtesy of the Journal of Archaeological and Anthropological Sciences.

For thousands of years, Mother Nature has taken the blame for tremendous human suffering caused by massive flooding along the Yellow River, long known in China as the “River of Sorrow” and “Scourge of the Sons of Han.”
Now, new research from Washington University in St. Louis links the river’s increasingly deadly floods to a widespread pattern of human-caused environmental degradation and related flood-mitigation efforts that began changing the river’s natural flow nearly 3,000 years ago.
WUSTL archaeologist T.R. Kidder excavates at Sanyangzhuang, an ancient, flood-buried community known as China’s Pompeii.
“Human intervention in the Chinese environment is relatively massive, remarkably early and nowhere more keenly witnessed than in attempts to harness the Yellow River,” said T.R. Kidder, PhD, lead author of the study and an archaeologist at Washington University. “In some ways, these findings offer a new benchmark for the beginning of the Anthropocene, the epoch in which humans became the most dominant global force in nature.”
Forthcoming in the Journal of Archaeological and Anthropological Sciences, the study offers the earliest known archaeological evidence for human construction of large-scale levees and other flood-control systems in China.
A catastrophic flood
It also suggests that the Chinese government’s long-running efforts to tame the Yellow River with levees, dikes and drainage ditches actually made periodic flooding much worse, setting the stage for a catastrophic flood circa A.D. 14-17, which likely killed millions and triggered the collapse of the Western Han Dynasty.
“New evidence from China and elsewhere show us that past societies changed environments far more than we’ve ever suspected,” said Kidder, the Edward S. and Tedi Macias Professor in Arts & Sciences and chair of anthropology at WUSTL. “By 2,000 years ago, people were controlling the Yellow River, or at least thought they were controlling it, and that’s the problem.”
Kidder’s research, co-authored with Liu Haiwang, senior researcher at China’s Henan Provincial Institute of Cultural Relics and Archaeology, relies on a sophisticated analysis of sedimentary soils deposited along the Yellow River over thousands of years.
Locator Map: The Yellow River Vallley of China, with Box A identifying the flood plain regions researched in this study.The star in Box B is the location of the Anshang and Sanyangzhuang sites. The approximate extent of the Loess Plateau is indicated by shading. VIEW LARGER>
It includes data from the team’s ongoing excavations at the sites of two ancient communities in the lower Yellow River flood plain of China’s Henan province.
The Sanyangzhuang site, known today as “China’s Pompeii,” was slowly buried beneath five meters of sediment during a massive flood circa A.D. 14–17, leading to exceptional preservation of its buildings, fields, roads and wells.
The Anshang site, discovered in 2012, includes the remains of a human-constructed levee and three irrigation/drainage ditches dating to the Zhou Dynasty (c. 1046–256 BC).
Researchers examined about 50 vertical feet of exposed soil layers at the Anshang site, carefully cleaning sections of a quarry wall to reveal patterns of sedimentary deposits dating back about 10,000 years. Nearly a third of this 10,000-year cross-section has been deposited in the last 2,000 years, indicating that the rate of deposit has steadily increased at a pace that mirrors the expansion of human activity in the region.
The southwest corner of the brick quarry dig site at Anshang shows remnants of the bank/levee in the sedimentary record. VIEW LARGER>
While ancient levees may be difficult to spot with an untrained eye, geoarchaeologists employ an array of precise analytic tools to confirm a site’s sedimentary history. Soil layers are identified by coloration and tested for physical and chemical alterations linked to human activity. Timeframes are identified through radiocarbon dating of freshwater snail shells and other organic soil matter.
“Thin microscopic sections of dirt samples show organization of soil grains, revealing whether an earthen structure was human-built or laid down as part of a natural sedimentation process,” Kidder said. “Our analysis clearly shows that these levees are not naturally formed berms, but are indeed artificially created through the work of humans.”
Kidder’s research suggests the Chinese began building drainage/irrigation canals and bank/levee systems along the lower reaches of the Yellow River about 2,900–2,700 years ago. By the beginning of the first millennium A.D., the levee system had been extended much farther up river, lining the banks for several hundred miles, he estimated.
The levees were built in part because of increasing erosion upstream, which was caused by more intensive agriculture and the expansion of the growing Chinese civilization. The sedimentary record shows a vicious cycle of primitive levees built larger and larger as erosion increased and periodic floods grew more widespread and destructive.
Boxed section of Image A shows the first stage of a bank/levee exposed in the excavation at Anshang. Image B offers a closer view of the boxed section showing mixed and loaded/rammed sediments near the base of the bank/levee. VIEW LARGER>
“Our evidence suggests that the first levees were built to be about 6-7 feet high, but within a decade the one at Anshang was doubled in height and width,” Kidder said. “It’s easy to see the trap they fell into: building levees causes sediments to accumulate in the river bed, raising the river higher, and making it more vulnerable to flooding, which requires you to build the levee higher, which causes the sediments to accumulate, and the process repeats itself. The Yellow River has been an engineered river — entirely unnatural — for quite a long time.”
Help for understanding climate change’s effects
Kidder, an authority on river basin geoarchaeology, has gathered data from the Yellow River excavation sites over the last five summers. He also conducts similar geoarchaeology research along the Mississippi River at a Native American site called Poverty Point in Louisiana.
He argues that geoarchaeology — a relatively new science that combines aspects of geology and archaeology — offers the potential to make dramatic contributions to our understanding of how climate change and other large-scale environmental forces are shaping human history.
While there are many theories behind the fall of the Western Han Dynasty, Kidder’s research suggests human interaction with the environment played a central role in its demise. In this study, he offers a big-picture explanation for how a complex mix of well-intentioned government policies and technological innovations gradually led the dynasty down a disastrous path of its own making.
The Yellow River, he argues, had existed for eons as a relatively calm and stable waterway until large numbers of Chinese farmers began disturbing the fragile environment of the upper river’s Loess Plateau. Built up over the ages by wind-blown sands from the nearby Gobi Desert and Qaidam Basin, the plateau has long boasted some of the world’s most erosion-prone soils.
As early as 700 B.C., Chinese authorities were encouraging peasant farmers to move into remote regions of the plateau, citing the need to feed a large and growing population while establishing a buffer of human settlement against the threat of nomadic invaders along its northern border. Construction of The Great Wall swelled populations still further.
Meanwhile, new iron-making technologies vastly increased the effectiveness of plows and other farm tools while spurring rapid deforestation of timber used in iron refining. Widespread erosion in the river’s upper regions caused it to carry incredibly heavy loads of sediment downstream where deposits gradually raised the river bed above levees and surrounding fields.
Implications for modern river management
Slowly, over thousands of years, human intervention began to have a dramatic impact on the river’s character. Periodic breaches of the levee system led to devastating floods, with some shifting the river’s main channel hundreds of miles from its initial course.
Map showing historically identified courses of the Yellow River and its historic mega-deltas. The 1938–1947 course evolved after the dykes were destroyed to (unsuccessfully) prevent Japanese forces from advancing across the Central Plains. VIEW LARGER>
A census taken by China in A.D. 2 suggests the area struck by the massive A.D. 14-17 flood was very heavily populated, with an average of 122 people per square kilometer, or approximately 9.5 million people living directly in the flood’s path.
“The misery and suffering must have been unimaginable,” Kidder said.
Historical accounts indicate that communities hit by the flood were soon in complete disarray, with reports of people resorting to banditry to obtain food and stay alive. By A.D. 20-21, the flood-torn region had become the epicenter of a popular rebellion, one that soon would spell the end of the Western Han Dynasty’s five-century reign of power.
“The big issue here is that human beings clearly changed the environment, and that these changes had real consequences for human history,” Kidder said. “It happened in the past and can happen again.”
While the research offers new insight into Chinese history, it also has interesting implications for modern river management policies around the globe, such as those causing similar flooding problems along the Missouri and Mississippi rivers in the United States.
“To think that we can avoid similar catastrophe today due to better technology is a dangerous notion,” he said. “When in doubt, bet on Mother Nature because physics will win every time.”
“Human-caused environmental change is nothing new,” Kidder said. “We’ve been doing this for a very long time, and the magnitude of change is increasing. Unlike ancient China, where human mistakes devastated a single river valley, we now have the technology to make mistakes that can cause devastation on a truly global scale.”

Skulls with mix of Neandertal and primitive traits illuminate human evolution

Researchers studying a collection of skulls in a Spanish cave identified both Neandertal-derived features and features associated with more primitive humans in these bones. This "mosaic pattern" supports a theory of Neandertal evolution that suggests Neandertals developed their defining features separately, and at different times – not all at once. Having this new data from the Sima de los Huesos site, as the Spanish cave is called, has allowed scientists to better understand hominin evolution during the Middle Pleistocene, a period in which the path of hominin evolution has been controversial.

"The Middle Pleistocene was a long period of about half a million years during which hominin evolution didn't proceed through a slow process of change with just one kind of hominin quietly evolving towards the classic Neandertal," said lead author Juan-Luis Arsuaga, Professor of Paleontology at the Complutense University of Madrid.

"With the skulls we found," co-author Ignacio Martínez, Professor of Paleontology at the University of Alcalá, added, "it was possible to characterize the cranial morphology of a human population of the European Middle Pleistocene for the first time."

About 400 to 500 thousand years ago, in the heart of the Pleistocene, archaic humans split off from other groups of that period living in Africa and East Asia, ultimately settling in Eurasia, where they evolved characteristics that would come to define the Neandertal lineage. Several hundred thousand years after that, modern humans—who had evolved in Africa—settled in Eurasia, too. They interbred with Neandertals, but even then showed signs of reproductive incompatibility. Because of this, modern humans eventually replaced Neandertals.

The degree of divergence between Neandertals and modern humans over such a short period of time has surprised scientists. Why did Neandertals differentiate so quickly from other early hominins? What pattern of changes did Neandertals undergo?

To answer these questions, scientists have needed an accurate picture of European populations around 400,000 years ago, the early stages of the Neandertal lineage. This has been challenging, however, because the European fossil record—an important tool for answering these questions—is isolated and dispersed, consisting of remains from disparate timelines. Samples at the Sima de los Huesos site in Atapuerca, Spain, however, are different.

"What makes the Sima de los Huesos site unique," Arsuaga said, "is the extraordinary and unprecedented accumulation of hominin fossils there; nothing quite so big has ever been discovered for any extinct hominin species—including Neanderthals."

"This site has been excavated continuously since 1984," Martínez added. "After thirty years, we have recovered nearly 7,000 human fossils corresponding to all skeletal regions of at least 28 individuals. This extraordinary collection includes 17 fragmentary skulls, many of which are very complete."

The 17 skulls belong to a single population of a fossil hominin species. Some of have been studied before, but seven are presented anew here, and six are more complete than ever before. With these intact samples at their fingertips, the researchers made progress characterizing defining features.

Their work has helped address hypotheses about Neandertal evolution, specifically the accretion model hypothesis, which suggests that Neandertals evolved their defining features at different times, not in a single linear sweep.

"For decades the nature of the evolutionary process that gave rise to Neanderthals has been discussed," explained Martínez. "An important question in these debates was whether the 'neandertalization process' involved all regions of the skull from the beginning, or if, on the contrary, there were various stages in this process that affected different parts of the skull at different times."

The researchers' skull samples showed Neandertal features present in the face and teeth, but not elsewhere; the nearby braincase, for example, still showed features associated with more primitive hominins.

"We think based on the morphology that the Sima people were part of the Neanderthal clade," Arsuaga said, "although not necessarily direct ancestors to the classic Neanderthals." They were part of an early European lineage that includes Neanderthals, but is more primitive than the later Pleistocene variety.

Critically, many of the Neandertal-derived features the researchers observed were related to mastication, or chewing. "It seems these modifications had to do with an intensive use of the frontal teeth," Arsuaga said. "The incisors show a great wear as if they had been used as a 'third hand," typical of Neanderthals."

The work of Arsuaga et al. suggests that facial modification was the first step in Neandertal evolution. This mosaic pattern fits the prediction of the accretion model.

"One thing that surprised me about the skulls we analyzed," Arsuaga said, "is how similar the different individuals were. The other fossils of the same geological period are different and don´t fit in the Sima pattern. This means that there was a lot of diversity among different populations in the Middle Pleistocene."

Indeed, other European Middle Pleistocene Homo sapiens do not exhibit the suite of Neandertal-derived features seen in this fossil group. Thus, more than one evolutionary lineage appears to have coexisted during the European Middle Pleistocene, with that represented by the Sima sample being closer to the Neandertals.

Arsuaga and his team were delighted to work on this effort. "Finding a single tooth is a great success in any other site of comparable age, so imagine what it is like to painstakingly reconstruct 17 skulls," he said. "It's like finding a treasure."

Friday, June 6, 2014

Mitochondrial DNA of first Near Eastern farmers is sequenced for the first time

The mitochondrial DNA of the first Near Eastern farmers has been sequenced for the first time. In the research, published in the journal PLOS Genetics, experts analysed samples from three sites located in the birthplace of Neolithic agricultural practices: the Middle Euphrates basin and the oasis of Damascus, located in today’s Syria and date at about 8,000 BC.

The paper is signed by Daniel Turbón and Alejandro Pérez Pérez, from the Department of Animal Biology of the University of Barcelona (UB); Eva Fernández, from Liverpool John Moores University; Cristina Gamba, Eduardo Arroyo Pardo and Pedro Cuesta, from Complutense University of Madrid; Eva Prats, from the Spanish National Research Council, and Josep Anfruns and Miquel Molist, from the Universitat Autònoma de Barcelona (UAB). The study is focused on the analysis of mitochondrial DNA —a type of non-Mendelian maternally inherited DNA— from the first Neolithic farmers, by means of samples obtained by the UAB research group which were first processed by the UB research group.

The Neolithic: a profound revolution in human societies

Agricultural and husbandry practices originated around 12,000 years ago in a region of the Near East known as the Fertile Crescent. This phenomenon, known as “Neolithic”, meant a profound social, cultural and economic transformation of human populations (agricultural production, sedentary farming lifestyle, origin of the first cities and modern societies, etc.).

Eva Fernández, first author of the article who got her PhD from UB, explains that “the Neolithic Revolution rapidly expanded from these territories into Europe, where the hunter-gatherer subsistence economy —prevailing till then— was replaced by an agropastoral producing system”. To know the nature of the diffusion of the Neolithic —in other words, to know if it was a population migration process or a cultural adoption— has been widely debated for the last fifty years. Different research fields, for instance archaeology, physical anthropology, linguistics and, more recently, human paleogenetics, have made contributions to the discussion.

The unknown genetics of first Near Eastern farmers

The genetic composition of first Neolithic populations was one of the mysteries of science till today, although some advances in European Neolithic populations’ genetics were made during the last decade. Professor Daniel Turbón points out that the results revealed by the study published in PLOS Genetics “are the first ones regarding first Near Eastern farmers; in other words, the genetic stock of original Neolithic”. However, it is important to remember that other data have been published about European first farmers, to be exact in Catalonia (by Cristina Gamba et al., 2012), the Basque Country (by Hervella et al.) and Germany (by Wolfgang Haak et al., 2010, and Brandt et al., 2013).

“Conclusions of previous studies —explains Turbón— are based on the comparison with current Near East populations, as first agricultural societies’ genetics have remained unknown until now”.

From the Near East to Europe

The study published in PLOS Genetics provides a new framework to interpret the results of other studies about European Neolithic populations, stress the authors. According to conclusions, genetic affinities have been observed between the mitochondrial DNA of first Neolithic populations and the DNA of first Catalan and German farmers. This suggests that probably Neolithic expansion took place through pioneer migrations of small groups of population. Moreover, the two main migration routes ―Mediterranean and European― might have been genetically linked.

“The most significant conclusion —highlights Eva Fernández— is that the degree of genetic similarity between the populations of the Fertile Crescent and the ones of Cyprus an Crete supports the hypothesis that Neolithic spread in Europe took place through pioneer seafaring colonization, not through a land-mediated expansion through Anatolia, as it was thought until now”.

How did the Neolithic Revolution spread?

Other scientific studies had already provided signs of an alternative scenario of Neolithic spread in Europe different from the one through Anatolia. According to Turbón, “recent archaeological finds have proved that the Neolithic arrived to Cyprus around 10,600 years ago, some years after the first documentation of agricultural practices in the Near East”. Architecture and burial models found in Cyprus’ sites are similar to the ones found in the Middle Euphrates basin, “that indicates a direct colonisation of these territories”, highlights the author. “Besides, spatial interpolation of radiocarbon dates from different Neolithic sites in the Near East and Europe also suggests a first seafaring expansion through Cyprus”, he concludes.

In order to support these conclusions, the scientific team aims at analysing a greater number of human Neolithic samples from other regions of the Fertile Crescent, and at increasing the number of genetic markers analysed in the samples.