Friday, September 25, 2009

Ancestral populations of India

New research reveals the ancestral populations of India and their relationships to modern groups

International effort is the first genome-scale analysis of diverse Indian groups

In a study published in the September 24th issue of Nature, an international team describes how they harnessed modern genomic technology to explore the ancient history of India, the world's second most populous nation.

The new research reveals that nearly all Indians carry genomic contributions from two distinct ancestral populations. Following this ancient mixture, many groups experienced periods of genetic isolation from each other for thousands of years. The study, which has medical implications for people of Indian descent, was led by scientists at the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad, India together with US researchers at Harvard Medical School, the Harvard School of Public Health and the Broad Institute of Harvard and MIT.

"This work is an outstanding example of the power of international collaboration," said Lalji Singh, senior author of the Nature paper, who is a Bhatnagar Fellow and the former director of CCMB. "Scientists in India and the United States have together made discoveries that would have been impossible for either group working alone."

Although the genome sequences of any two unrelated people differ by just 0.1%, that tiny slice of genetic material is a rich source of information. It provides clues that can help reconstruct the historical origins of modern populations. It also points to genetic variations that heighten the risk of certain diseases. In recent years, maps of human genetic variation have opened a window onto the diversity of populations across the world, yet India has been largely unrepresented until now.

To shed light on genetic variability across the Indian subcontinent, the research team analyzed more than 500,000 genetic markers across the genomes of 132 individuals from 25 diverse groups, representing 13 states, all six language families, traditionally "upper" and "lower" castes, and tribal groups.

These genomic analyses revealed two ancestral populations. "Different Indian groups have inherited forty to eighty percent of their ancestry from a population that we call the Ancestral North Indians who are related to western Eurasians, and the rest from the Ancestral South Indians, who are not related to any group outside India," said co-author David Reich, an associate professor of genetics at Harvard Medical School and an associate member of the Broad Institute of Harvard and MIT.

The finding that nearly all Indian groups descend from mixtures of two ancestral populations applies to traditional "tribes" as well as "castes." Kumarasamy Thangaraj, a senior research scientist at CCMB in Hyderabad and a co-author said, "It is impossible to distinguish castes from tribes using the data. The genetics proves that they are not systematically different. This supports the view that castes grew directly out of tribal-like organizations during the formation of Indian society."

The one exception to the finding that all Indian groups are mixed is the indigenous people of the Andaman Islands, an archipelago in the Indian Ocean with a census of only a few hundred today. The Andamanese appear to be related exclusively to the Ancestral South Indian lineage and therefore lack Ancestral North Indian ancestry.

"The Andamanese are unique," said co-author Nick Patterson, a mathematician and researcher at the Broad Institute. "Understanding their origins provides a window onto the history of the Ancestral South Indians, and the period tens of thousands of years ago when they diverged from other Eurasians." Added Singh, "Our project to sample the disappearing tribes of the Andaman Islands has been more successful than we could have hoped, as the Andamanese are the only surviving remnant of the ancient colonizers of South Asia."

The researchers' work also has surprising and important medical implications. They discovered that many groups in modern India descend from a small number of founding individuals, and have since been genetically isolated from other groups. In scientific parlance this is called a "founder event."

"The finding that a large proportion of modern Indians descend from founder events means that India is genetically not a single large population, but instead is best described as many smaller isolated populations," said Singh. Thangaraj continued, "The widespread history of founder events helps explain why the incidence of genetic diseases among Indians is different from the rest of the world."

Founder events in other groups, such as Finns and Ashkenazi Jews, are well known to increase the incidence of recessive genetic diseases, and the new study predicts that the same will be true for many groups in India. "It is important to carry out a systematic survey of Indian groups to identify which ones descend from the strongest founder events," said Reich. "Further studies of these groups should lead to the rapid discovery of genes that cause devastating diseases, and will help in the clinical care of individuals and their families who are at risk."

"Just as important as these findings are the statistical approaches that led to them," said Alkes Price, an assistant professor of epidemiology at the Harvard School of Public Health and a co-author of the Nature study. "In studying Indian genetic variation we also developed a novel toolkit for understanding the relationships among groups and the history of mixture. We believe that these tools can drive future studies not only of Indian history but of groups worldwide."

Thursday, September 24, 2009

Not all Cohen's descended from Aaron

New genetic research indicates Jewish priesthood has multiple lineages

Recent research on the Cohen Y chromosome indicates the Jewish priesthood, the Cohanim, was established by several unrelated male lines rather than a single male lineage dating to ancient Hebrew times.

The new research builds on a decade-old study of the Jewish priesthood that traced its patrilineal dynasty and seemed to substantiate the biblical story that Aaron, the first high priest (and brother of Moses), was one of a number of common male ancestors in the Cohanim lineage who lived some 3,200 years ago in the Near East.

The current study was conducted by Michael F. Hammer, a population geneticist in the Arizona Research Laboratory's Division of Biotechnology at the University of Arizona. Hammer's collaborators in the study include Karl Skorecki of the Technion-Israel Institute of Technology and Rambum Medical Center in Haifa and colleagues and collaborating scientists from Tel Aviv University and the Russian Academy of Sciences.

The July 2009 issue of Human Genetics has published the Hammer team's newest findings in their article entitled "Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood."

Hammer and Skorecki were part of the first research group 10 years ago that found the DNA marker signature of the Cohanim, termed the Cohen Modal Haplotype. Today, Hammer and his colleagues are able to use a much larger battery of DNA markers and consequently able to develop a more fully resolved Cohen Modal Haplotype called the extended Cohen Modal Haplotype. The smaller number of markers used in the original Cohanim studies did not allow for full resolution of the history of the Jewish priesthood.

"These findings should motivate renewed interest in historical reconstructions of the Jewish priesthood as well as additional high resolution DNA marker analyses of other populations and 'lost tribes' claiming ancient Hebrew ancestry," Hammer said.

Using the new data, Hammer and his team were able to pinpoint the geographic distribution of a genetically more resolved Cohen Modal Haplotype and tease apart a multiplicity of male lines that founded the priesthood in ancient Hebrew times. The more fully resolved Cohen Modal haplotype (called the extended Cohen Modal Haplotype) accounts for almost 30 percent of Cohanim Y chromosomes from both Ashkenazi and non-Ashkenazi Jewish communities, is virtually absent in non-Jews, and likely traces to a common male ancestor that lived some 3,200 years ago in the Near East.

Additional Y chromosome lineages that are distinct from that defined by the extended Cohen Modal Haplotype, but also shared among Cohanim from different Jewish communities, reveal that the priesthood was established by several unrelated male lines.

Scandinavians come from Stone Age immigrants

Today's Scandinavians are not descended from the people who came to Scandinavia at the conclusion of the last ice age but, apparently, from a population that arrived later, concurrently with the introduction of agriculture. This is one conclusion of a new study straddling the borderline between genetics and archaeology, which involved Swedish researchers and which has now been published in the journal Current Biology.

"The hunter-gatherers who inhabited Scandinavia more than 4,000 years ago had a different gene pool than ours," explains Anders Götherström of the Department of Evolutionary Biology at Uppsala University, who headed the project together with Eske Willerslev of the Centre for GeoGenetics at the University of Copenhagen.

The study, a collaboration among research groups in Sweden, Denmark and the UK, involved using DNA from Stone Age remains to investigate whether the practices of cultivating crops and keeping livestock were spread by immigrants or represented innovations on the part of hunter-gatherers.

"Obtaining reliable results from DNA from such ancient human remains involves very complicated work," says Helena Malmström of the Department of Evolutionary Biology at Uppsala University.

She carried out the initial DNA sequencings of Stone Age material three years ago. Significant time was then required for researchers to confirm that the material really was thousands of years old.

"This is a classic issue within archaeology," says Petra Molnar at the Osteoarchaeological Research Laboratory at Stockholm University. "Our findings show that today's Scandinavians are not the direct descendants of the hunter-gatherers who lived in the region during the Stone Age. This entails the conclusion that some form of migration to Scandinavia took place, probably at the onset of the agricultural Stone Age. The extent of this migration is as of yet impossible to determine."

Monday, September 21, 2009

Pagans in Israel: Aphrodites, Herod

An ancient treasure comprising three figurines of Aphrodite, the goddess of love, which was buried underground for over 1,500 years, was uncovered during the tenth season of excavations that are carried out by researchers of the Zinman Institute of Archaeology at the University of Haifa, headed by Prof. Arthur Segal and Dr. Michael Eisenberg. "It is possible that during the fourth century A.D., when Christianity was gradually becoming the governing religion in the Roman Empire, there were still a number of inhabitants in Sussita who remained loyal to the goddess of love and therefore wished to hide and preserve these items," suggests Prof. Segal.

The hidden figurines were discovered when the researchers exposed a shop in the southeastern corner of the forum district of Sussita, which is the central area of the Roman city that was built in the second century B.C., existed through the Roman and Byzantine periods and destroyed in the great earthquake of 749 A.D. According to the researchers, it was clear that the followers had wished to hide the figurines, as they were found complete. The clay pieces are 23 cm tall and represent the common model of the goddess of love known to the experts as Venus pudica, "the modest Venus." This name was given to the form due to its upright stature and the figure's covering her private parts with the palm of her hand – perhaps another reason for concealing them from the new religion that presided over the empire.

The tenth excavation season at Sussita, which is located on the mountaintop at an altitude of 350 m. above Lake Kinneret and in the area of the Sussita National Park, yielded many spectacular findings. Besides the University of Haifa researchers, also participating in the excavations were teams from the Polish Academy of Sciences in Warsaw and from Concordia University of Minnesota, USA. The project was carried out with significant support from the Israel Nature and Natural Parks Protection Authority.

Another fascinating finding was an odeion – a small, roofed theater-like structure, the first of its kind to be exposed in Israel. According to the researchers, structures such as these were quite common in the Roman era and were intended for poetry-reading performances and musical recitals for an elect audience. While the average theater of those times had some 4,000 seats, the odeion had no more than 600 sitting places. The exposure of this structure holds within it an intriguing story. In the 1960s, when it served as a military post, this area of the city was still entirely covered with refuse three meters high as a protective military measure. When the archaeologists began digging down in 2008, all that could be seen above ground were three hewn stones. The researchers then proposed a theory that these stones hid beneath them an odeion structure, of the type that had not been found before in Israel. To their surprise, this theory proved correct. The excavation is still in its early stages, but the researchers have already been able to expose the entire perimeter of the odeion, which forms a rectangular area, at one end of which is a semi-circle. According to the researchers, the construction is of high quality and it seems that it can be dated back to the first century B.C. or A.D.

Also found in the excavations was a basilica, a roofed structure that would have been used as a substitute location for public gatherings in rainy weather. This is the second basilica to be exposed in Israel, the first being the Roman basilica of Samaria. The conservation and restoration team working alongside the archaeologists have succeeded in restoring one of the basilica's columns. "Just the look of the restored columns is enough to get an impression of the beauty and tremendousness of Roman architecture during that period," Prof. Segal exclaimed.

The American delegation exposed a living quarter, most likely dating back to the fourth century A.D., which gives a rare glimpse into the day-to-day lives of the inhabitants of Sussita during the last three centuries of the city's existence. All of the houses that were exposed surround a stone-paved courtyard. The researchers assume that this style of planning is evidence of everyday household activity taking place in the courtyard, including the cooking.

"At the close of the tenth season of excavations, we have revealed a abundance of public structures in the city, most likely associated with the reign of Herod in the first century B.C. Until now we have assumed that the wave of construction that took place during Herod's reign was primarily in Jewish cities, but the findings at Sussita are evidence of the king's influence on pagan cities under his rule too," the researchers concluded.

Thursday, September 17, 2009

A portrait of Alexander the Great at Tel Dor



Credit: No'a Raban-Gerstel, University of Haifa


A rare and surprising archaeological discovery at Tel Dor: A gemstone engraved with the portrait of Alexander the Great was uncovered during excavations by an archaeological team directed by Dr. Ayelet Gilboa of the University of Haifa and Dr. Ilan Sharon of the Hebrew University of Jerusalem. "Despite its miniature dimensions – the stone is less than a centimeter high and its width is less than half a centimeter – the engraver was able to depict the bust of Alexander on the gem without omitting any of the ruler's characteristics" notes Dr. Gilboa, Chair of the Department of Archaeology at the University of Haifa. "The emperor is portrayed as young and forceful, with a strong chin, straight nose and long curly hair held in place by a diadem."

The Tel Dor researchers have noted that it is surprising that a work of art such as this would be found in Israel, on the periphery of the Hellenistic world. "It is generally assumed that the master artists – such as the one who engraved the image of Alexander on this particular gemstone – were mainly employed by the leading Hellenistic courts in the capital cities, such as those in Alexandria in Egypt and Seleucia in Syria. This new discovery is evidence that local elites in secondary centers, such as Tel Dor, appreciated superior objects of art and could afford ownership of such items" the researchers stated.






This is an aerial view of the excavation areas in the southwestern part of Tel Dor.

Credit: Sky Balloons Inc.

The significance of the discovery at Dor is in the gemstone being uncovered in an orderly excavation, in a proper context of the Hellenistic period. The origins of most Alexander portraits, scattered across numerous museums around the world, are unknown. Some belonged to collections that existed even prior to the advent of scientific archaeology, others were acquired on the black market, and it is likely that some are even forgeries.

This tiny gem was unearthed by a volunteer during excavation of a public structure from the Hellenistic period in the south of Tel Dor, excavated by a team from the University of Washington at Seattle headed by Prof. Sarah Stroup. Dr. Jessica Nitschke, professor of classical archaeology at Georgetown University in Washington DC, identified the engraved motif as a bust of Alexander the Great. This has been confirmed by Prof. Andrew Stewart of the University of California at Berkeley, an expert on images of Alexander and author of a book on this topic.

Alexander was probably the first Greek to commission artists to depict his image – as part of a personality cult that was transformed into a propaganda tool. Rulers and dictators have implemented this form of propaganda ever since. The artists cleverly combined realistic elements of the ruler's image along with the classical ideal of beauty as determined by Hellenistic art, royal attributes (the diadem in this case), and divine elements originating in Hellenistic and Eastern art. These attributes legitimized Alexander's kingship in the eyes of his subjects in all the domains he conquered. These portraits were distributed throughout the empire, were featured on statues and mosaics in public places and were engraved on small items such as coins and seals. The image of Alexander remained a popular motif in the generations that followed his death – both as an independent theme and as a subject of emulation. The conqueror's youthful image became a symbol of masculinity, heroism and divine kingship. Later Hellenist rulers adopted these characteristics and commissioned self-portraits in the image of Alexander.

Dor was a major port city on the Mediterranean shore from the Middle Bronze Age (2000-1550 B.C.E) until the establishment of Caesarea during the Roman period. Alexander the Great passed through Dor in 332 B.C.E., following the occupation of Tyre and on his way to Egypt. It seems that the city submitted to Alexander without resistance. Dor then remained a center of Hellenization in the land of Israel until it was conquered by Alexander Janneus, Hasmonean king of Judah (c. 100 B.C.E.).

The team of archaeologists has been excavating at Tel Dor for close to thirty years and recently completed the 2009 excavation season. A number of academic institutions in Israel and abroad participate in the excavations, directed by Dr. Ayelet Gilboa of the University of Haifa and Dr. Ilan Sharon of the Hebrew University of Jerusalem. The project is supported by these two institutions along with the Israel Exploration Society, the Berman foundation for Biblical Archaeology, the Zinman Institute of Archaeology, the Wendy Goldhirsh Foundation, USA, and individual donors. The gemstone will be on public display at the Dor museum in Kibbutz Nahsholim.

Wednesday, September 9, 2009

Largest collection of Bar-Kokhba

JThe largest cache of rare coins ever found in a scientific excavation from the period of the Bar-Kokhba revolt of the Jews against the Romans has been discovered in a cave by researchers from the Hebrew University of Jerusalem and Bar-Ilan University.

The coins were discovered in three batches in a deep cavern located in a nature reserve in the Judean hills. The treasure includes gold, silver and bronze coins, as well as some pottery and weapons.

The discovery was made in the framework of a comprehensive cave research and mapping project being carried out by Boaz Langford and Prof. Amos Frumkin of the Cave Research Unit in the Department of Geography at the Hebrew University, along with Dr. Boaz Zissu and Prof. Hanan Eshel of the Martin (Szusz) Department of Land of Israel Studies and Archaeology at Bar-Ilan University, and with the support of the Israel Nature and Parks Authority.

The some 120 coins were discovered within a cave that has a "hidden wing," the slippery and dangerous approach to which is possible only via a narrow opening discovered many years ago by Dr. Gideon Mann, a physician who is one of the early cave explorers in modern Israel. The opening led to a small chamber which in turn opens into a hall that served as a hiding place for the Jewish fighters of Bar-Kokhba.

Most of the discovered coins are in excellent condition and were overstruck as rebels' coins on top of Roman coins. The new imprints show Jewish images and words (for example: the facade of the Temple in Jerusalem and the slogan "for the freedom of Jerusalem"). Other coins that were found, of gold, silver and bronze, are original Roman coins of the period minted elsewhere in the Roman Empire or in the Land of Israel.

Bar-Kokhba coins of this quality and quantity have never before been discovered in one location by researchers in the Land of Israel, although over the years antiquities looters have found and sold large numbers of coins from this period. The high value of such coins has served as an incentive for thefts in recent decades, especially in the Judean hills, where many such caves exist.

Prof. Frumkin points out the significance of this particular cave, owing to its size, its proximity to Betar, and the large collection of coins found there. Ancient Betar was the site of the "last stand" of the rebels led by Bar-Kokhba in their struggle against Roman rule in Judea from 132-35 CE.

"This discovery verifies the assumption that the refugees of the revolt fled to caves in the center of a populated area in addition to the caves found in more isolated areas of the Judean Desert," said Prof. Frumkin. He also noted that the discovery adds significantly to our knowledge of the Bar-Kokhba revolt, about which there is not a great deal of historical information.

Dr. Zissu points out that one of the fascinating aspects of the Bar-Kokhba revolt is the intensive use of the rebels and Jewish refugees of natural and man-made caves as hiding and refuge places in the face of extensive Roman search-and-destroy missions. Those who fled to the caves took with them food, weapons, drinks, coins and various documents. Sometimes they even took with them the keys to their houses that they abandoned in the hope that one day they would be able to return to them.

Apparently, the people who left behind the cache of coins that has now been found did so during the period of the revolt, following their flight from their homes or from battle with the Romans; however they were unable to return to their hiding place to recover their valuables.