Monday, March 10, 2014
Ancient DNA from archaeological skeletons shows that European’s had darker skin, hair, and eye pigmentation 5,000 years ago
There has been much research into the factors that have influenced the human genome since the end of the last Ice Age. Anthropologists at Johannes Gutenberg University Mainz (JGU) and geneticists at University College London (UCL), working in collaboration with archaeologists from Berlin and Kiev, have analyzed ancient DNA from skeletons and found that selection has had a significant effect on the human genome even in the past 5,000 years, resulting in sustained changes to the appearance of people.
The results of this current research project have been published this week in an article entitled "Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 years" in the journal Proceedings of the National Academy of Sciences (PNAS).
For a number of years population geneticists have been able to detect echoes of natural selection in the genomes of living humans, but those techniques are typically not very accurate about when that natural selection took place. The researchers in Mainz and London now decided to take a new approach. This involved analyzing DNA from archaeological skeletons and then comparing the prehistoric data with that of contemporary Europeans using computer simulations. Where the genetic changes could not be explained by the randomness of inheritance, the researchers were able to infer that positive selection played a role, i.e., that frequency of a certain mutation increased significantly in a given population.
While investigating numerous genetic markers in archaeological and living individuals, Sandra Wilde of the Palaeogenetics Group at the JGU Institute of Anthropology noticed striking differences in genes associated with hair, skin, and eye pigmentation. "Prehistoric Europeans in the region we studied would have been consistently darker than their descendants today," says Wilde, first author of the PNAS article. "This is particularly interesting as the darker phenotype seems to have been preferred by evolution over hundreds of thousands of years. All our early ancestors were more darkly pigmented." However, things must have changed in the last 50,000 years as humans began to migrate to northern latitudes.
"In Europe we find a particularly wide range of genetic variation in terms of pigmentation," adds co-author Dr. Karola Kirsanow, who is also a member of the Palaeogenetics Group at Mainz University. "However, we did not expect to find that natural selection had been favoring lighter pigmentation over the past few thousand years."
The signals of selection that the Mainz palaeogeneticists and their colleagues at University College London have identified are comparable to those for malaria resistance and lactase persistence, meaning that they are among the most pronounced that have been discovered to date in the human genome. The authors see several possible explanations.
"Perhaps the most obvious is that this is the result of adaptation to the reduced level of sunlight in northern latitudes," says Professor Mark Thomas of UCL, corresponding author of the study. "Most people of the world make most of their vitamin D in their skin as a result UV exposure. But at northern latitudes and with dark skin, this would have been less efficient. If people weren’t getting much vitamin D in their diet, then having lighter skin may have been the best option."
"But this vitamin D explanation seems less convincing when it comes to hair and eye color," Wilde continues. "Instead, it may be that lighter hair and eye color functioned as a signal indicating group affiliation, which in turn played a role in the selection of a partner." Sexual selection of this kind is common in animals and may also have been one of the driving forces behind human evolution over the past few millennia.
"We were expecting to find that changes in the human genome were the result of population dynamics, such as migration. In general we expect genetic changes due to natural selection to be the exception rather than the rule. At the same time, it cannot be denied that lactase persistence, i.e., the ability to digest the main sugar in milk as an adult, and pigmentation genes have been favored by natural selection to a surprising degree over the last 10,000 years or so," adds Professor Joachim Burger, senior author of the study. "But it should be kept in mind that our findings do not necessarily mean that everything selected for in the past is still beneficial today. The characteristics handed down as a result of sexual selection can be more often explained as the result of preference on the part of individuals or groups rather than adaptation to the environment."
Thursday, March 6, 2014
Photos: Archaeological Exploration of Sardis/Harvard University
By any measure, the ancient city of Sardis — home of the fabled King Croesus, a name synonymous with gold and vast wealth, and the city where coinage was invented — is an archaeological wonder.
The ruins of Sardis, in what is now Turkey, have been a rich source of knowledge about classical antiquity from the 7th century B.C., when the city was the capital of Lydia, through later Greek and Roman occupations.
Scholars digging at Sardis, the capital of ancient Lydia later occupied by Greeks and Romans. Sardis, in modern Turkey, was the fabled home of King Croesus, the richest man of his day, according to lore.
Now, however, Sardis has given up another treasure in the form of two enigmatic ritual deposits, which are proving more difficult to fathom than the coins for which the city was famous.
“The two deposits each consist of a small pot with a lid, a coin, a group of sharp metal implements and an egg, one of which is intact except for a hole carefully punched in it in antiquity,” explains Will Bruce, a classics graduate student a the University of Wisconsin-Madison who has been digging at Sardis for the past six years. Bruce made the finds last summer.
The dig at Sardis is overseen by Nicholas Cahill, a UW-Madison professor of art history. Cahill has directed field research at Sardis for decades. Both ritual deposits, says Cahill, date from the Roman era of Sardis, about A.D. 70 or 80.
An inverted bowl, covering another bowl with a ritual deposit, emerges from the earth. The bowls contained a ritual deposit of a coin, small metal implements and an egg.
Bruce and his team were excavating below the floor of a first century room, built over the ruins of an earlier building, which had probably been destroyed in a massive earthquake in A.D. 17.
Digging beneath the floor, Bruce and his colleagues first uncovered a thin-walled, nearly intact jug and, nearby, an assemblage of mostly unbroken pottery. “It looked like we were reaching a more intact deposit instead of fill,” says Bruce.
Within that assemblage, Bruce began to carefully uncover an inverted bowl, which turned out to be sitting on top of another bowl. The bowls, still filled with dirt, were carefully removed and immediately turned over to conservators who cleaned and dissembled them to find a set of small pointed instruments, a coin with a lion and portrait of Nero, and the intact egg.
Graduate student Will Bruce excavates a coin horde at Sardis, which was the home of King Croesus, a name synonymous in myth and history with gold and wealth.
“The ritual offerings were dug into pits in the floor, after the room was constructed,” says Cahill. “We know they were renovating the room periodically, because in another part of the space there was a dump of painted wall plaster buried under the floor, presumably in a renovation.”
“The meaning of these deposits is still quite open to interpretation,” notes Cahill, “but burying votive deposits below ground or in a wall was a fairly common practice,” perhaps as a ritual offering to protect the house. Roman literary sources suggest eggs were used in particular rituals.
For the archaeologists, part of the intrigue is that similar groups of bowls, needles, coins and eggs were discovered at Sardis more than 100 years ago when the temple of Artemis was excavated by Princeton University archaeologists. “It is an exact parallel to what they found in the early 20th century,” according to Cahill.
A gold coin found at Sardis. Another coin, bearing the likeness of Emporer Nero, was also found.
The coin was also unique. Sardis is famous as the place where coinage was invented in the Western world, first using electrum, an alloy of silver and gold, and later of pure gold and silver. Nearby sources of gold made ancient Lydia, and King Croesus, fabulously wealthy. While these Lydian coins are very rare, coins and coin hoards from later Greek and Roman occupiers of Sardis are routinely found.
But the coin found with the egg, says Cahill, seems to be special.
“The coin has a portrait of Nero on the front. The original reverse was hammered flat, and the image of a lion engraved in its place, which is very odd.” Expert numismatists have never seen anything like it. “The image of the lion is important because it is emblematic of the Lydian kings and of their native mother goddess Cybele,” Cahill says.
The discovery is unusual, Cahill notes, because finding ritualistic objects intact and in place after thousands of years is no everyday discovery, even in a rich archaeological context such as Sardis. “Ancient ritual was important to people. It is most unusual to find such fragile things so perfectly preserved.”
Monday, March 3, 2014
We humans like to think of ourselves as unique for many reasons, not least of which being our ability to communicate with words. But ground-breaking research by an expert from the University of New England shows that our 'misunderstood cousins,' the Neanderthals, may well have spoken in languages not dissimilar to the ones we use today.
Pinpointing the origin and evolution of speech and human language is one of the longest running and most hotly debated topics in the scientific world. It has long been believed that other beings, including the Neanderthals with whom our ancestors shared Earth for thousands of years, simply lacked the necessary cognitive capacity and vocal hardware for speech.
Associate Professor Stephen Wroe, a zoologist and palaeontologist from UNE, along with an international team of scientists and the use of 3D x-ray imaging technology, made the revolutionary discovery challenging this notion based on a 60,000 year-old Neanderthal hyoid bone discovered in Israel in 1989.
"To many, the Neanderthal hyoid discovered was surprising because its shape was very different to that of our closest living relatives, the chimpanzee and the bonobo. However, it was virtually indistinguishable from that of our own species. This led to some people arguing that this Neanderthal could speak," A/Professor Wroe said.
"The obvious counterargument to this assertion was that the fact that hyoids of Neanderthals were the same shape as modern humans doesn't necessarily mean that they were used in the same way. With the technology of the time, it was hard to verify the argument one way or the other."
However advances in 3D imaging and computer modelling allowed A/Professor Wroe's team to revisit the question.
"By analysing the mechanical behaviour of the fossilised bone with micro x-ray imaging, we were able to build models of the hyoid that included the intricate internal structure of the bone. We then compared them to models of modern humans. Our comparisons showed that in terms of mechanical behaviour, the Neanderthal hyoid was basically indistinguishable from our own, strongly suggesting that this key part of the vocal tract was used in the same way.
"From this research, we can conclude that it's likely that the origins of speech and language are far, far older than once thought."
Thursday, February 27, 2014
Academics at Royal Holloway, University of London, and the Universities of Colorado and Utah have analysed fossils which revealed that the ancestors of Native Americans may have set up home in a region between Siberia and Alaska which contained woody plants that they could use to make fires. The discovery breaks new ground as until now no-one had any idea of where the native Americans spent the next 10,000 years before they appeared in Alaska and the rest of the North America.
Professor Scott Elias, from the Department of Geography at Royal Holloway said: "This work fills in a 10,000-year missing link in the story of the peopling of the New World. "
The findings, which are published in the journal Science, reveal that the ancestors of Native Americans may have lived on the Bering Land Bridge, which is now under the waters of the Bering and Chukchi Seas. The land bridge and some adjacent regions were not as dry as the rest of Beringia, and this central part of Beringia was covered in shrub tundra - the dominant vegetation in modern Arctic Alaska. It is dominated by dwarf willow and birch shrubs, mosses and lichens.
Professor Elias explained: "We believe that these ancestors survived on the shrub tundra of the Bering Land Bridge because this was the only region of the Arctic where any woody plants were growing. They needed the wood for fuel to make camp fires in this bitterly cold region of the world. They would have used dwarf shrub wood to get a small fire going, then placed large mammal bones on top of the fire, to ignite the fats inside the bones. Once burning, large leg bones of ice-age mammals would have burned for hours, keeping people alive through Arctic winter nights."
The academics made the discovery after analysing insect and plant fossils extracted from sediment cores taken from the ancient land bridge surface, which lies on the sea floor 50-60 metres below the water's surface.
Wednesday, February 26, 2014
Scientists from the University of Cambridge have demonstrated that an abrupt weakening of the summer monsoon affected northwest India 4,100 years ago. The resulting drought coincided with the beginning of the decline of the metropolis-building Indus Civilisation, which spanned present-day Pakistan and India, suggesting that climate change could be why many of the major cities of the civilisation were abandoned.
The research, reported online on 25 February, 2014, in the journal Geology, involved the collection of snail shells preserved in the sediments of an ancient lake bed. By analysing the oxygen isotopes in the shells, the scientists were able to tell how much rain fell in the lake where the snails lived thousands of years ago.
The results shed light on a mystery surrounding why the major cities of the Indus Civilisation (also known as the Harappan Civilisation, after Harappa, one of the five cities) were abandoned. Climate change had been suggested as a possible reason for this transformation before but, until now, there has been no direct evidence for climate change in the region where Indus settlements were located.
Moreover, the finding now links the decline of the Indus cities to a documented global scale climate event and its impact on the Old Kingdom in Egypt, the Early Bronze Age civilisations of Greece and Crete, and the Akkadian Empire in Mesopotamia, whose decline has previously been linked to abrupt climate change.
"We think that we now have a really strong indication that a major climate event occurred in the area where a large number of Indus settlements were situated," said Professor David Hodell, from Cambridge's Department of Earth Sciences. "Taken together with other evidence from Meghalaya in northeast India, Oman and the Arabian Sea, our results provide strong evidence for a widespread weakening of the Indian summer monsoon across large parts of India 4,100 years ago."
Hodell together with University of Cambridge archaeologist Dr Cameron Petrie and Gates scholar Dr Yama Dixit collected Melanoides tuberculata snail shells from the sediments of the ancient lake Kotla Dahar in Haryana, India. "As today, the major source of water into the lake throughout the Holocene is likely to have been the summer monsoon," said Dixit. "But we have observed that there was an abrupt change, when the amount of evaporation from the lake exceeded the rainfall – indicative of a drought."
At this time large parts of modern Pakistan and much of western India was home to South Asia's great Bronze Age urban society. As Petrie explained: "The major cities of the Indus civilisation flourished in the mid-late 3rd and early 2nd millennium BC. Large proportions of the population lived in villages, but many people also lived in 'megacities' that were 80 hectares or more in size – roughly the size of 100 football pitches. They engaged in elaborate crafts, extensive local trade and long-ranging trade with regions as far away as the modern-day Middle East. But, by the mid 2nd millennium BC, all of the great urban centres had dramatically reduced in size or been abandoned."
Many possible causes have been suggested, including the claim that major glacier-fed rivers changed their course, dramatically affecting the water supply and the reliant agriculture. It has also been suggested that an increasing population level caused problems, there was invasion and conflict, or that climate change caused a drought that large cities could not withstand long-term.
"We know that there was a clear shift away from large populations living in megacities," said Petrie. "But precisely what happened to the Indus Civilisation has remained a mystery. It is unlikely that there was a single cause, but a climate change event would have induced a whole host of knock-on effects.
"We have lacked well-dated local climate data, as well as dates for when perennial water flowed and stopped in a number of now abandoned river channels, and an understanding of the spatial and temporal relationships between settlements and their environmental contexts. A lot of the archaeological debate has really been well-argued speculation."
The new data, collected with funding from the Natural Environment Research Council, show a decreased summer monsoon rainfall at the same time that archaeological records and radiocarbon dates suggest the beginning of the Indus de-urbanisation. From 6,500 to 5,800 years ago, a deep fresh-water lake existed at Kotla Dahar. The deep lake transformed to a shallow lake after 5,800 years ago, indicating a weakening of the Indian summer monsoon. But an abrupt monsoon weakening occurred 4,100 years ago for 200 years and the lake became ephemeral after this time.
Until now, the suggestion that climate change might have had an impact on the Indus Civilisation was based on data showing a lessening of the monsoon in Oman and the Arabian Sea, which are both located at a considerable distance from Indus Civilisation settlements and at least partly affected by different weather systems.
Hodell and Dixit used isotope geochemical analysis of shells as a proxy for tracing the climate history of the region. Oxygen exists in two forms – the lighter 16O and a heavier 18O variant. When water evaporates from a closed lake (one that is fed by rainfall and rivers but has no outflow), molecules containing the lighter isotope evaporate at a faster rate than those containing the heavier isotopes; at times of drought, when the evaporation exceeds rainfall, there is a net increase in the ratio of 18O to 16O of the water. Organisms living in the lake record this ratio when they incorporate oxygen into the calcium carbonate (CaCO3) of their shells, and can therefore be used, in conjunction with radiocarbon dating, to reconstruct the climate of the region thousands of years ago.
Speculating on the effect lessening rainfall would have had on the Indus Civilisation, Petrie said: "Archaeological records suggest they were masters of many trades. They used elaborate techniques to produce a range of extremely impressive craft products using materials like steatite, carnelian and gold, and this material was widely distributed within South Asia, but also internationally. Each city had substantial fortification walls, civic amenities, craft workshops and possibly also palaces. Houses were arranged on wide main streets and narrow alleyways, and many had their own wells and drainage systems. Water was clearly an integral part of urban planning, and was also essential for supporting the agricultural base.
At around the time we see the evidence for climatic change, archaeologists have found evidence of previously maintained streets start to fill with rubbish, over time there is a reduced sophistication in the crafts they used, the script that had been used for several centuries disappears and there were changes in the location of settlements, suggesting some degree of demographic shift."
"We estimate that the climate event lasted about 200 years before recovering to the previous conditions, which we still see today, and we believe that the civilisation somehow had to cope with this prolonged period of drought," said Hodell.
The new research is part of a wider joint project led by the University of Cambridge and Banaras Hindu University in India, which has been funded by the British Council UK-India Education and Research Initiative to investigate the archaeology, river systems and climate of north-west India using a combination of archaeology and geoscience. The multidisciplinary project hopes to provide new understanding of the relationships between humans and their environment, and also involves researchers at Imperial College London, the University of Oxford, the Indian Institute of Technology Kanpur and the Uttar Pradesh State Archaeology Department.
"It is essential to understand the link between human settlement, water resources and landscape in antiquity, and this research is an important step in that direction," explained Petrie. "We hope that this will hold lessons for us as we seek to find means of dealing with climate change in our own and future generations."
Wednesday, February 19, 2014
Aerial photographs. Photo credit: Skyview, courtesy of the Israel Antiquities Authority
The remnants of a rural settlement that was occupied for approximately two centuries during the Second Temple Period were uncovered in August 2013 – January 2014 near the 'Burma Road' (not far from Mitzpe Harel). The find was made during an Israel Antiquities Authority archaeological salvage excavation, before the start of work on a natural gas pipeline to Jerusalem as part of a national project directed by Israel Natural Gas Lines (INGL).
In June 2013, Israel Natural Gas Lines began construction of the 35km-long project, which runs from the coastal plain to the outskirts of Jerusalem. In light of the finds, the Israel Antiquities Authority and the INGL have agreed that engineering plans for the gas line are to be revised, bypassing the site and preserving it as an accessible archaeological site beside the Burma Road.
The excavations, which covered about 750 square meters, revealed a small rural settlement with a few stone houses and a network of narrow alleys. Each building, which probably housed a single nuclear family, consisted of several rooms and an open courtyard. According to Irina Zilberbod, excavation director on behalf of the Antiquities Authority, "The rooms generally served as residential and storage rooms, while domestic tasks were carried out in the courtyards".
The site, whose name has not survived, is nestled at the top of a spur 280 meters above sea level, with commanding views of the surrounding countryside. These large tracts of land were used as they are today to cultivate orchards and vineyards, which were the economic mainstay of the region’s early settlers.
The excavations have shown that the site reached the height of its development in the Hellenistic period (during the third century BCE), when Judea was ruled by the Seleucid monarchy following Alexander the Great, and that it was abandoned at the end of the Hasmonean dynasty.
It is not known why the site was abandoned, but it is probably related to economic problems and not to a violent incident. As Jerusalem Regional Archaeologist Dr. Yuval Baruch explains, "The phenomenon of villages and farms being abandoned at the end of the Hasmonean dynasty or the beginning of Herod the Great's succeeding rule is one that we are familiar with from many rural sites in Judea, and it may be related to Herod's massive building projects in Jerusalem, particularly the construction of the Temple Mount, and the mass migration of villagers to the capital to work on these projects."
The excavations yielded numerous and varied finds from all occupation periods, including basalt and limestone grinding and milling tools for domestic use, pottery cooking pots, jars for storing liquids (oil and wine,) pottery oil lamps for domestic use, and over sixty coins, including coins from the reigns of the Seleucid King Antiochus III and the Hasmonean King Alexander Jannaeus.
Coin from the reign of King Antiochus III. Photo: Clara Amit, courtesy of the Israel Antiquities Authority
Saturday, February 15, 2014
Extraordinary find of 800,000 year old footprints In England makes a direct connection to the earliest humans in northern Europe
A team of scientists led by the British Museum, Natural History Museum and Queen Mary University of London have discovered a series of footprints left by early humans in ancient estuary muds over 800,000 years ago at Happisburgh in Norfolk, The footprints are direct evidence of the earliest known humans in northern Europe. The new evidence, published today in the science journal PLOS ONE reveals how the footprints were discovered and recorded on the foreshore at Happisburgh during May 2013.
The footprint surface was exposed at low tide as heavy seas removed the beach sands to reveal a series of elongated hollows cut into compacted silts. "At first we weren’t sure what we were seeing," explains Dr Nick Ashton of the British Museum "but as we removed any remaining beach sand and sponged off the seawater, it was clear that the hollows resembled prints, perhaps human footprints, and that we needed to record the surface as quickly as possible before the sea eroded it away." Over the next two weeks the surface was recorded using photogrammetry, a technique that can stitch together digital photographs to create a permanent record and 3D images of the surface. It was the analysis of these images that confirmed that the elongated hollows were indeed ancient human footprints, perhaps of five individuals. Ashton concludes "this is an extraordinarily rare discovery. The Happisburgh site continues to re-write our understanding of the early human occupation of Britain and indeed of Europe".
The analyses showed that the prints were from a range of adult and juvenile foot sizes and that in some cases the heel, arch and even toes could be identified, equating to modern shoes of up to UK size 8. Dr Isabelle De Groote from Liverpool John Moores University studied the prints in more detail. "In some cases we could accurately measure the length and width of the footprints and estimate the height of the individuals who made them. In most populations today and in the past foot length is approximately 15% of height. We can therefore estimate that the heights varied from about 0.9 m to over 1.7 m. This height range suggests a mix of adults and children with the largest print possibly being a male." The orientation of the footprints suggests that they were heading in a southerly direction.
Over the last ten years the sediments at Happisburgh have revealed a series of sites with stone tools and fossil bones, dating back to over 800,000 years. This latest discovery is from the same deposits. "Although we knew that the sediments were old, we had to be certain that the hollows were also ancient and hadn’t been created recently." Say Dr Simon Lewis, a geoarchaeologist at Queen Mary University of London. "There are no known erosional processes that create that pattern. In addition, the sediments are too compacted for the hollows to have been made recently."
The age of the site is based on its geological position beneath the glacial deposits that form the cliffs, but also the association with extinct animals. Simon Parfitt of the Natural History Museum and University College London has studied the mammalian fossils from Happisburgh. "These include an extinct type of mammoth, extinct horse and early forms of vole. Together they support an age of over 800,000 years." The site also preserves plant remains and pollen, together with beetles and shells, which allows a detailed reconstruction of the landscape. At this time Britain was linked by land to continental Europe and the site at Happisburgh would have been on the banks of a wide estuary several miles from the coast. There would have been muddy freshwater pools on the floodplain with salt marsh and coast nearby. Deer, bison, mammoth, hippo and rhino grazed the river valley, surrounded by more dense coniferous forest. The estuary provided a rich array of resources for the early humans with edible plant tubers, seaweed and shellfish nearby, while the grazing herds would have provided meat through hunting or scavenging.
So who were these humans? Fossil remains of our forebears are still proving elusive. However, as Professor Chris Stringer of the Natural History Museum explains "The humans who made the Happisburgh footprints may well have been related to the people of similar antiquity from Atapuerca in Spain, assigned to the species Homo antecessor ('Pioneer Man'). These people were of a similar height to ourselves and were fully bipedal. They seem to have become extinct in Europe by 600,000 years ago and were perhaps replaced by the species Homo heidelbergensis. Neanderthals followed from about 400,000 years ago, and eventually modern humans some 40,000 years ago."
The importance of the Happisburgh footprints is highlighted by the rarity of footprints surviving elsewhere. Only those at Laetoli in Tanzania at about 3.5 million years and at Ileret and Koobi Fora in Kenya at about 1.5 million years are more ancient. As Nick Ashton concludes "these footprints provide a very tangible link to our forebears and deep past." The work at Happisburgh continues, but as the cliffs erode, new sites are being discovered, but also destroyed by the encroaching sea. The footprints were unfortunately rapidly eroded away, but it is hoped that new footprints will be revealed in the future.
The work at Happisburgh forms part of a new major exhibition at the Natural History Museum Britain: One Million Years of the Human Story opening on 13 February 2014.