Thursday, October 20, 2016

Neanderthals responsible for weakerimmune systems of people with European ancestry

It's long been clear that people from different parts of the world differ in their susceptibility to developing infections as well as chronic inflammatory and autoimmune diseases. Now, two studies reported in Cell on October 20 show that those differences in disease susceptibility can be traced in large part to differences at the genetic level directing the way the immune systems of people with European and African ancestry are put together.

The researchers also found that differences between populations have been selected for over time because they conferred advantages to people facing distinct health challenges in the places where they lived. As a result, according to the new evidence, people of African ancestry generally show stronger immune responses than Europeans do.

The discovery suggests that European populations have been selected to display reduced immune responses since our ancestors first made their way out of Africa. Intriguingly, the immune systems of Europeans were partly shaped by the introduction of new genetic variants through interbreeding between some of our early European ancestors and Neanderthals.

"Our findings show that population differences in transcriptional responses to immune activation are widespread, and that they are mainly accounted for by genetic variants that differ in their frequencies between human populations," said Lluis Quintana-Murci of Institut Pasteur and CNRS in Paris, France, who led one of the two studies.

"I was expecting to see ancestry-associated differences in immune response but not such a clear trend towards an overall stronger response to infection among individuals of African descent," added Luis Barreiro of the University of Montreal and the CHU Sainte-Justine in Canada, senior author of the other study.

Quintana-Murci and colleagues used RNA-sequencing to characterize the way that immune cells, known as primary monocytes, derived from 200 people of self-reported African or European ancestry would respond to attack by a bacteria or a virus. The researchers detected many differences in the activity of particular genes in those immune cells both within and between populations. They also discovered that changes in a single gene encoding an important immune receptor lead to decreased inflammation only in Europeans.

The researchers found strong evidence of selection on genes that control the immune response. Their evidence also shows that Europeans "borrowed" some key regulatory variants from Neanderthals, which in particular affect the way their immune systems respond to viral challenges.

Barreiro and colleagues took a similar approach to test for the effects of African versus European ancestry on changes in the activity of immune cells. His group focused on another type of immune cell known as primary macrophages and their response to live bacterial pathogens.

The researchers infected macrophages derived from 80 African and 95 European individuals with either Listeria monocytogenes or Salmonella typhimurium to look for differences in response and related them to ancestry. Their studies identified thousands of genes showing population differences in transcriptional response to infection. They also found that African ancestry is associated with a stronger inflammatory response, which limited the growth of bacteria.

In many cases, the activity of particular genes was tied to a single genetic variant, with strong differences in frequency between European and African populations. The researchers also observed the signature of past selection on those genes and additional evidence for an important role of genetic variants passed on to modern humans from Neanderthals. "This strongly suggests that a diminished inflammatory response has conferred a selective advantage to European populations,"Quintana-Murci said.

"The genetic and molecular basis of ancestry-related differences in disease susceptibility has been a mystery," Barreiro said. "These results provide a first description of differences in immune response and associated genetic basis that might explain differences in susceptibility to disease between people of African and European ancestry. More generally, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection."

The researchers noted that the two studies made strikingly similar findings despite the fact that they focused on different types of immune cells. They say that more work is now needed to better understand the role of environmental and other factors, including epigenetic changes, in the differences they've observed.

Modern humans, Neanderthals and Denisovans: more interbreeding than previously thought

Relationships between the ancestors of modern humans and other archaic populations such as Neanderthals and Denisovans were likely more complex than previously thought, involving interbreeding within and outside Africa, according to a new estimator developed by geneticists. Findings were reported at the American Society of Human Genetics (ASHG) 2016 Annual Meeting in Vancouver, B.C.

In recent years, genetics has led to the revision of many assumptions about archaic populations, explained Ryan J. Bohlender, PhD, a postdoctoral researcher at the University of Texas MD Anderson Cancer Center and first author on the research. For example, the 2010 release of the Neanderthal genome led to the discovery that Neanderthals and the ancestors of modern Europeans interbred. A few years later, scientists discovered the existence of Denisovans, a population known of only through genetics, through a fossilized sample of DNA.

"My colleagues and I set out to find out what we might share with these ancient populations and how our histories interacted," Dr. Bohlender said. They developed an estimation tool to model these interactions based on parameters such as current estimates of population size and dates when populations separated - how long ago they stopped interbreeding - and look for inconsistencies with information known from genetic studies about the overlap between the modern human genome and those of ancient populations. Compared to previous estimators, this one made increased use of genetic data to cut down on statistical bias. The researchers then allowed estimates of population size and separation dates to vary in a series of simulations, in order to find out if adjusting these parameters better fit the genetic data.

"Using this process, we found that the population in Africa was likely about 50 percent larger than previously thought. We also found that an archaic-modern human separation date of 440,000 years ago was the best fit, suggesting that Neanderthals diverged from our lineage 100,000 years more recently than we thought," Dr. Bohlender said. "We got the same separation date using data from multiple modern human populations, which is a good sign."

In addition, their results suggest that throughout Eurasia, ancient populations interbred less than previously believed, and that - contrary to previous findings - the level of mixing with Neanderthals did not differ significantly between Europe and East Asia.

The findings bring up many new questions, including to what extent the new estimator can be trusted, why it produces results that differ from prevailing estimates, and how to reconcile these differences.

"Overall, our findings confirm the human family tree is more complicated than we think it is," Dr. Bohlender said. "For example, other archaic populations are likely to have existed, like the Denisovans, who we didn't know about except through genetics." They plan to try out simulations with multiple other populations, to see if this adds some clarity to the results.

Dr. Bohlender also believes that more detailed studies of African populations may shed some light. "Africans have been underrepresented in genetics research - they're not as well studied as European and Asian populations, yet they are more diverse genetically than any other group," he said.

From Here the Romans Breached Jerusalem’s City Wall 2,000 Years Ago

Fascinating evidence of breaking through Jerusalem’s Third Wall at the end of the Second Temple period was discovered in an excavation the Israel Antiquities Authority is conducting in the city center.

Impressive and fascinating evidence of the battlefield and the breaching of the Third Wall that surrounded Jerusalem at the end of the Second Temple period was exposed in recent months in the Russian Compound in the city center. The finds were discovered in an archaeological excavation the Israel Antiquities Authority conducted in the location where the new campus of the Bezalel Academy of Arts and Design is slated to be constructed.  During the course of the excavation archaeologists discovered the remains of a tower jutting from the city wall. Opposite the tower’s western facade were scores of ballista and sling stones that the Romans had fired from catapults towards the Jewish guards defending the wall, who were stationed at the top of the tower.

According to Dr. Rina Avner and Kfir Arbib, excavation directors on behalf of the Israel Antiquities Authority, “This is a fascinating testimony of the intensive bombardment by the Roman army, led by Titus, on their way to conquering the city and destroying the Second Temple. The bombardment was intended to attack the sentries guarding the wall and provide cover for the Roman forces so they could approach the wall with battering rams and thereby breach the city’s defenses”.

The historian Josephus, an eye witness to the war, provided many details about this wall. According to him, the wall was designed to protect the new quarter of the city that had developed outside its boundaries, north of the two existing city walls. This quarter was named Beit Zeita. The building of the Third Wall was begun by Agrippa I; however, he suspended its construction so as not to incur the wrath of Emperor Claudius and to dispel any doubts regarding his loyalty. The construction of the Third Wall was resumed some two decades later by the defenders of Jerusalem, as part of fortifying the city and the Jewish rebels’ preparations for the Great Revolt against Rome.

Josephus described in detail the route of the wall that began at Hippicus Tower, which is now identified with David’s Citadel. From there the wall continued north to the enormous Psephinus Tower, which defended the northwestern corner of the city wall. At that point the wall turned east and descended toward the Tomb of Queen Helena, which is identified with the place known as the Tombs of the Kings.

An unresolved debate among researchers has been going from the early twentieth century up until the current excavation as to the identity of the Third Wall and the question concerning Jerusalem’s boundaries on the eve of the Roman onslaught led by Titus. It seems that the new discovery in the Russian Compound is proof of the wall’s existence in this area.
The excavation findings will be presented in a conference entitled "“New Studies in the archaeology of Jerusalem and its Region” conference ", to be held on Thursday, October 27, 2016, at the Mount Scopus campus of the Hebrew University of Jerusalem.

Monday, October 17, 2016

Neanderthals gave us HPV16 responsible for most cervical and oral cancers

With recent studies proving that almost everyone has a little bit of Neanderthal DNA in them----up to 5 percent of the human genome--- it's become clear our ancestors not only had some serious hominid interspecies sex going on, but with it, a potential downside: the spread of sexually transmitted infections, or STIs.

For wherever life goes, germs are soon to follow.

In the case of the most common STI, human papillomaviruses (HPVs), almost everyone hosts a number of infections, with strain HPV16 responsible for most cervical and oral cancers.

By reconstructing the ancestry and timing of the family tree of HPV16 in greater detail than ever before, and by comparing the evolutionary histories of viruses and humans, a new pattern has emerged. Now, researchers have generated compelling evidence that HPV16 co-diverged with archaic and modern humans---only to be repopulated at a much later date through their contact by Neanderthals, challenging the assumption that HPV16 co-evolved with modern humans. The study, by Ville Pimenoff at the Catalan Institute of Oncology and Ignacio Bravo at the French National Center for Scientific Research was published in the advanced online edition of Molecular Biology and Evolution (DOI: 10.1093/molbev/msw214).

During the evolution of HPV16, variants A and B/C/D co-diverged with archaic and modern humans, respectively. When populations of modern humans left Africa and had sexual intercourse with Neanderthals and Denisovans, they were infected by the viral variant that had evolved with archaic humans, and this virus thrived and expanded among modern humans

This scenario finally explains unsolved questions: why human diversity is largest in Africa, while HPV16 diversity is largest in East-Asia, and why the HPV16A variant is virtually absent in Sub-Saharan Africa while it is by far the most common one in the rest world.

"Oncogenic viruses are very ancient," said Ignacio Bravo. "The history of humans is also the history of the viruses we carry and we inherit. Our work suggests that some aggressive oncogenic viruses were transmitted by sexual contact from archaic to modern humans."

They propose that interactions between the host and viral genomes may explain why most humans are exposed to HPVs and cure the infection, while in a few unfortunate cases the infection persists and can lead to cancer. The different degree of archaic ancestry in our genomes could be partly responsible for differential susceptibility to cancer. Since HPVs do not infect bones, current Neanderthal and Denisovan genomes do not contain HPVs. As a next step, the authors hope to trace HPVs sequences in ancient human skin remains as a more direct test of their hypothesis.

Monday, October 3, 2016

New insights on the origins of Greek civilization

When University of Cincinnati researchers uncovered the tomb of a Bronze Age warrior -- left untouched for more than 3,500 years and packed with a spectacular array of precious jewelry, weapons and riches -- the discovery was hailed by experts as "the find of a lifetime."

Now, only a year after archaeologists completed the excavation, new understandings of the artifacts -- particularly the discovery of four golden rings -- and the insights they provide to the origins of Greek civilization may prove to be the team's next big discovery.

Shari Stocker, a senior research associate in UC's Department of Classics, and Jack Davis, the university's Carl W. Blegen chair in Greek archaeology, will reveal the UC-based team's findings from the so-called "Griffin Warrior" grave Thursday, Oct. 6, at The American School of Classical Studies at Athens, Greece.

The husband-and-wife team's highly anticipated lecture is generating worldwide attention, including a feature in the New York Times.

The 'find of a lifetime'

Stocker and Davis, along with other UC staff specialists and students, stumbled upon the remarkably undisturbed and intact tomb last May while excavating near the city of Pylos, an ancient city on the southwest coast of Greece.

Inside they discovered the well-preserved remains of what is believed to have been a powerful Mycenaean warrior or priest in his early- to mid-30s who was buried around 1500 B.C. near the archeological excavation of the Palace of Nestor.

Immortalized in Homer's "Odyssey," the large administrative center was destroyed by fire sometime around 1180 B.C., but remains the best-preserved Bronze Age palace on the Greek mainland. UC archaeologist Carl Blegen first discovered the Mycenaean ruins in 1939, where he unearthed a number of clay tablets written in Linear B script, the earliest known written form of Greek.

The warrior's tomb, hailed by the Greek Culture Ministry as the "most important to have been discovered [in continental Greece] in 65 years," revealed more than 2,000 objects arrayed on and around the body, including four solid gold rings, silver cups, precious stone beads, fine-toothed ivory combs and an intricately built sword, among other weapons.

The skeleton was dubbed the "Griffin Warrior" for the discovery of an ivory plaque adorned with a griffin -- a mythical beast with the body of a lion and the head and wings of an eagle -- buried with him.

The UC excavation is remarkable not just for the unparalleled riches discovered in the warrior-priest's tomb -- to find an unlooted, intact grave is, in itself, a rare and historic feat -- but for what the grave and its bounty reveals about the dawn of the Mycenaean civilization, a transformative period in the Bronze Age.

Unlocking an ancient mystery

A significant number of the artifacts found in the warrior's grave were made by Minoans, a culturally dominant civilization to the Mycenaeans that arose on the large island of Crete, southeast of Pylos. How then, the researchers puzzled, did a man from the Greek mainland accumulate such a large cache of Minoan-made riches?

One longstanding theory is that the Greeks of the Griffin Warrior's era -- dubbed Mycenaean after their principal city, Mycenae -- are thought to have imported or robbed the riches from the affluent non-Greek Minoan civilization on Crete.

"The grave was right around the time the Mycenaeans were conquering the Minoans," explained Stocker. "We know that there were extensive raids and shortly after the date of our grave, Minoan-Crete fell to the Mycenaeans."

But Stocker and Davis say that the artifacts found in the warrior's grave suggest a far greater cultural sharing between the ancient civilizations than just mere plunder. Instead, they insist, the carefully selected and hand-placed items reveal much about the heart of the relationship of the burgeoning mainland Greek culture to the more refined culture of Crete.

History revealed through remarkable rings

The discovery of four gold signet rings bearing highly detailed Minoan iconography offers one of the best examples of this Mycenaean-Minoan cultural transfer and paints a more vivid picture of early Greek society, the researchers say.

The rings -- three of which the researchers are unveiling for the first time on Oct. 6 -- are crafted from multiple sheets of gold and feature iconographical references seen elsewhere in Minoan art and religious culture.

The first ring, revealed after the excavation's completion last fall, shows a scene of a bull leaping -- reminiscent of contests in which toreadors would literally leap over bulls in a show of sport and athletic prowess -- a common motif seen in Minoan imagery.The second ring, the second largest gold signet ring known in the Aegean world, shows five elaborately dressed female figures gathered by a seaside shrine.A third ring depicts a female figure, thought to be a goddess, holding a staff and flanked by two birds atop a mountain glen.The final ring shows a woman presenting a bull's horn offering to a goddess holding a mirror and seated on a high-backed throne atop of which is perched a bird.

Cultural meanings aside, the rings themselves are a remarkable find simply for the elaborate attention to detail and artisan workmanship, say Stocker and Davis.

"They're carving these before the microscope and electric tools," marveled Stocker. "This is exquisite workmanship for something so tiny and old and really shows the skill of Minoan craftsmen."

"It shows a level of superb craftsmanship that just isn't found on these other rings," said Davis, referring to the rings of Minos and Nestor, long the subjects of intense scrutiny by experts who question their authenticities, in part, due to the high level of detail on them.

But the discovery of the Minoan-style rings in a Mycenaean warrior's grave further left the research team scratching their heads: Did the Mycenaeans understand what they were taking from the Minoans and the concepts behind the iconography?

After a year of careful examination of the grave's artifacts, Davis and Stocker now say yes.

"People have suggested that the findings in the grave are treasure, like Blackbeard's treasure, that was just buried along with the dead as impressive contraband," said Davis. "We think that already in this period the people on the mainland already understood much of the religious iconography on these rings, and they were already buying into religious concepts on the island of Crete."

"This isn't just loot," he added. "It may be loot, but they're specifically selecting loot that transmits messages that are understandable to them."

"They're not just going there and robbing a jewelry store," echoed Stocker. "They're thinking about it and selecting specific items for inclusion in the burial."

The researchers point to other items in the grave that reference religious and cultural motifs seen both in the rings and Minoan imagery.

A mirror found above the Griffin Warrior's legs may relate to the fourth ring, in which a seated goddess is portrayed holding a mirror. The mirror's placement in the grave, the researchers theorize, suggest that it holds special significance to the Mycenaeans while the presence of a half-dozen combs suggest a ritual practice of hair-combing before battle.

The bull, a sacred symbol to the Minoans, can also be seen in Mycenaean imagery. In the third ring, a goddess is featured holding a horned staff while the fourth ring shows an offering to the goddess of a bull's horn. The bull is also featured in the first ring, suggesting the horns may have come from a ritualistic slaughtering following a bull-leaping event. Stocker and Davis say it is no coincidence that the Griffin Warrior was found buried with a bronze bull's head staff capped by prominent horns, which were likely a symbol of his power and authority.

A snapshot captured in time

These associations and more, which the researchers plan to further explore in upcoming publications, promise to open new doors into the understanding of the nascent Mycenaean belief system at a transitional time when Minoan works first began to gain importance on the Greek mainland, Davis and Stocker say.

"What this allows us to do gets us beyond just thinking in terms of mere borrowing of prestige items or items to show off for display," explained Davis. "This starts to get us into an understanding of actual beliefs and ideas and an ideology that existed in this time of the formation of the Mycenaean civilization, which is very difficult to get at."

That difficulty is often compounded by the Mycenaeans' practice of group burials for elite members of society. While other grave excavations in Mycenae have yielded even more remarkable riches, the presence of multiple corpses in those graves makes it difficult to determine what items were buried with each individual and why.

The Griffin Warrior's tomb contains just one skeleton, which researchers say allows them to form a better picture of who he was, why these specific items were selected to accompany him on his journey to the underworld and what those discoveries reveal about the dawn of European civilization.

"We have a snapshot here, captured in time, with the objects as they were placed around this guy," said Davis. "We can look at this not from an outside perspective, but from an insider's perspective and imagine why and how they chose to place them in the grave."

Friday, September 30, 2016

Humans occupied South America earlier than previously thought

Ancient artifacts found at an archeological site in Argentina suggest that humans occupied South America earlier than previously thought.

Approximately 13,000 years ago, a prehistoric group of hunter-gathers known as the Clovis people lived in Northern America. Previous research suggests that the Clovis culture was one of the earliest cultures in the Americas. However, more recent research from the Pampas region of Argentina supports the hypothesis that early Homo sapiens arrived in the Americas earlier than the Clovis hunters did.

The evidence for earlier human arrival in the Americas comes from a rich archaeological site in southeastern South America called Arroyo Seco 2. A group of scientists led by Gustavo Politis from CONICET and the Universidad Nacional del Centro de la Provincia de Buenos Aires present the research in a new PLOS ONE study.

At Arroyo Seco 2, the researchers excavated ancient tools, bone remains from a variety of extinct species, and broken animal bones containing fractures caused by human tools. They used radiocarbon dating to determine the age of the mammal bones and analyzed the specimens under a microscope.

The analysis revealed the presence of limb bones from extinct mammals at the site, which may indicate human activities of transporting and depositing animal carcasses for consumption at a temporary camp. The bones of some mammal species were concentrated in a specific part of the site, which could indicate designated areas for butchering activities. Microscopic examination also revealed that some bones contained fractures most likely caused by stone tools. The remains were dated between 14,064 and 13,068 years ago, and the authors hypothesize that Arroyo Seco 2 may have been occupied by humans during that time.

This timeline, along with evidence from other South American sites, indicates that humans may have arrived in southern South America prior to the Clovis people inhabiting the Americas, but after the onset of the Last Glacial Maximum, the last glacial period, which took place 19,000 to 20,000 years ago.

While the characteristics of some of these archaeological materials could be explained without human intervention, the combination of evidence strongly suggests human involvement. Humans' arrival in southern South America 14,000 years ago may represent the last step in the expansion of Homo sapiens throughout the world and the final continental colonization.

Wednesday, September 28, 2016

A Fisherman’s House was Exposed on the Beach in Ashkelon

Photo: Clara Amit

Young residents of Ashkelon and the vicinity who were employed by the Israel Antiquities Authority in an archaeological excavation in the city, recently uncovered buildings that were once used by local inhabitants that were engaged in fishing along the Mediterranean coast. The excavation was carried out for the Ashkelon municipality, at the initiative of the Ashkelon Economic Company, in an area where a new neighborhood is slated to be constructed in the northern part of city.

As part of a project being led by the Israel Antiquities Authority aimed at educating young people about their past, dozens of boys and girls were engaged in challenging and fascinating work, in revealing the coastal city’s past.

According to the excavation directors, Federico Kobrin and Haim Mamliya, “Two of the buildings that we uncovered are very curious, and it seems they were used as a fisherman’s house and a lookout tower, possibly a lighthouse, dating to the Ottoman period.  The tower was situated on a lofty hilltop, and it looks out over the beach and Mediterranean Sea. From the tower one could signal and direct ships that were sailing between the ancient ports in Ashkelon and Ashdod-Yam”.

Kobrin adds, “The fisherman’s house is divided into three rooms, and a wealth of artifacts was discovered in it that are indicative of its use: metal fishhooks, dozens of lead weights, a large bronze bell, and even a stone anchor. The building’s entrances were fixed in the north in order to prevent the high winds and sea storms from entering into it.  According to the archaeologists, "This is the first time that a building was exposed in Ashkelon that we can attribute with certainty to the fishing industry”.

Kobrin concluded that, “Working with youth was both a challenge and extremely satisfying. The young people participated in uncovering part of their city’s past; they labored diligently and conscientiously, showed their interest and curiosity regarding the finds, and it was a pleasure to work with them”.

The fisherman’s house with be preserved and incorporated in the development of the neighborhood and strip of beach for the benefit of the residents and to create a connection between them and those who lived and fished there in the past.