Thursday, September 21, 2017

Ancient human DNA in sub-Saharan Africa

The first large-scale study of ancient human DNA from sub-Saharan Africa opens a long-awaited window into the identity of prehistoric populations in the region and how they moved around and replaced one another over the past 8,000 years.

The findings, published Sept. 21 in Cell by an international research team led by Harvard Medical School, answer several longstanding mysteries and uncover surprising details about sub-Saharan African ancestry -- including genetic adaptations for a hunter-gatherer lifestyle and the first glimpses of population distribution before farmers and animal herders swept across the continent about 3,000 years ago.

"The last few thousand years were an incredibly rich and formative period that is key to understanding how populations in Africa got to where they are today," said David Reich, professor of genetics at HMS and a senior associate member of the Broad Institute of MIT and Harvard. "Ancestry during this time period is such an unexplored landscape that everything we learned was new."

"Ancient DNA is the only tool we have for characterizing past genomic diversity. It teaches us things we don't know about history from archaeology and linguistics and can help us better understand present-day populations," said Pontus Skoglund, a postdoctoral researcher in the Reich lab and the study's first author. "We need to ensure we use it for the benefit of all populations around the world, perhaps especially Africa, which contains the greatest human genetic diversity in the world but has been underserved by the genomics community."

Long time coming

Although ancient-DNA research has revealed insights into the population histories of many areas of the world, delving into the deep ancestry of African groups wasn't possible until recently because genetic material degrades too rapidly in warm, humid climates.

Technological advances--including the discovery by Pinhasi and colleagues that DNA persists longer in small, dense ear bones--are now beginning to break the climate barrier. Last year, Reich and colleagues used the new techniques to generate the first genome-wide data from the earliest farmers in the Near East, who lived between 8,000 and 12,000 years ago.

In the new study, Skoglund and team, including colleagues from South Africa, Malawi, Tanzania and Kenya, coaxed DNA from the remains of 15 ancient sub-Saharan Africans. The individuals came from a variety of geographic regions and ranged in age from about 500 to 8,500 years old.

The researchers compared these ancient genomes--along with the only other known ancient genome from the region, previously published in 2015--against those of nearly 600 present-day people from 59 African populations and 300 people from 142 non-African groups.

With each analysis, revelations rolled in.

"We are peeling back the first layers of the agricultural transition south of the Sahara," said Skoglund. "Already we can see that there was a whole different landscape of populations just 2,000 or 3,000 years ago."

Genomic time-lapse

Almost half of the team's samples came from Malawi, providing a series of genomic snapshots from the same location across thousands of years.

The time-series divulged the existence of an ancient hunter-gatherer population the researchers hadn't expected.

When agriculture spread in Europe and East Asia, farmers and animal herders expanded into new areas and mixed with the hunter-gatherers who lived there. Present-day populations thus inherited DNA from both groups.

The new study found evidence for similar movement and mixing in other parts of Africa, but after farmers reached Malawi, hunter-gatherers seem to have disappeared without contributing any detectable ancestry to the people who live there today.

"It looks like there was a complete population replacement," said Reich. "We haven't seen clear evidence for an event like this anywhere else."

The Malawi snapshots also helped identify a population that spanned from the southern tip of Africa all the way to the equator about 1,400 years ago before fading away. That mysterious group shared ancestry with today's Khoe-San people in southern Africa and left a few DNA traces in people from a group of islands thousands of miles away, off the coast of Tanzania.

"It's amazing to see these populations in the DNA that don't exist anymore," said Reich. "It's clear that gathering additional DNA samples will teach us much more."

"The Khoe-San are such a genetically distinctive people, it was a surprise to find a closely related ancestor so far north just a couple of thousand years ago," Reich added.

The new study also found that West Africans can trace their lineage back to a human ancestor that may have split off from other African populations even earlier than the Khoe-San.

Missing links

The research similarly shed light on the origins of another unique group, the Hadza people of East Africa.

"They have a distinct appearance, language and genetics, and some people speculated that, like the Khoe-San, they might represent a very early diverging group from other African populations," said Reich. "Our study shows that instead, they're somehow in the middle of everything."

The Hadza, according to genomic comparisons, are today more closely related to non-Africans than to other Africans. The researchers hypothesize that the Hadza are direct descendants of the group that migrated out of Africa, and possibly spread within Africa as well, after about 50,000 years ago.
Another discovery lay in wait in East Africa.

Scientists had predicted the existence of an ancient population based on the observation that present-day people in southern Africa share ancestry with people in the Near East. The 3,000-year-old remains of a young girl in Tanzania provided the missing evidence.

Reich and colleagues suspect that the girl belonged to a herding population that contributed significant ancestry to present-day people from Ethiopia and Somalia down to South Africa. The ancient population was about one-third Eurasian, and the researchers were able to further pinpoint that ancestry to the Levant region.

"With this sample in hand, we can now say more about who these people were," said Skoglund.
The finding put one mystery to rest while raising another: Present-day people in the Horn of Africa have additional Near Eastern ancestry that can't be explained by the group to which the young girl belonged.

Natural selection

Finally, the study took a first step in using ancient DNA to understand genetic adaptation in African populations.

It required "squeezing water out of a stone" because the researchers were working with so few ancient samples, said Reich, but Skoglund was able to identify two regions of the genome that appear to have undergone natural selection in southern Africans.

One adaptation increased protection from ultraviolet radiation, which the researchers propose could be related to life in the Kalahari Desert. The other variant was located on genes related to taste buds, which the researchers point out can help people detect poisons in plants.

The researchers hope that their study encourages more investigation into the diverse genetic landscape of human populations in Africa, both past and present. Reich also said he hopes the work reminds people that African history didn't end 50,000 years ago when groups of humans began migrating into the Near East and beyond.

How Neanderthals grew, based on an El Sidrón child

IMAGE: Skeleton of the Neanderthal boy recovered from the El Sidrón cave (Asturias, Spain). view more 
Credit: Paleoanthropology Group MNCN-CSIC
How did Neanderthals grow? Does modern man develop in the same way as Homo neanderthalensis did? How does the size of the brain affect the development of the body? A study led by the Spanish National Research Council (CSIC) researcher, Antonio Rosas, has studied the fossil remains of a Neanderthal child's skeleton in order to establish whether there are differences between the growth of Neanderthals and that of sapiens.

According to the results of the article, which are published in Science, both species regulate their growth differently to adapt their energy consumption to their physical characteristics.

"Discerning the differences and similarities in growth patterns between Neanderthals and modern humans helps us better define our own history. Modern humans and Neanderthals emerged from a common recent ancestor, and this is manifested in a similar overall growth rate", explains CSIC researcher, Antonio Rosas, from Spain's National Natural Science Museum (MNCN).

As fellow CSIC researcher Luis Ríos highlights, "Applying paediatric growth assessment methods, this Neanderthal child is no different to a modern-day child". The pattern of vertebral maturation and brain growth, as well as energy constraints during development, may have marked the anatomical shape of Neanderthals.

Neanderthals had a greater cranial capacity than today's humans. Neanderthal adults had an intracranial volume of 1,520 cubic centimetres, while that of modern adult man is 1,195 cubic centimetres. That of the Neanderthal child in the study had reached 1,330 cubic centimetres at the time of his death, in other words, 87.5% of the total reached at eight years of age. At that age, the development of a modern-day child's cranial capacity has already been fully completed.

"Developing a large brain involves significant energy expenditure and, consequently, this hinders the growth of other parts of the body. In sapiens, the development of the brain during childhood has a high energetic cost and, as a result, the development of the rest of the body slows down," Rosas explains.

Neanderthals and sapiens
The cost, in terms of energy, of anatomical growth of the modern brain is unusually high, especially during breastfeeding and during infancy, and this seems to require a slowing down of body growth.

The growth and development of this juvenile Neanderthal matches the typical characteristics of human ontogeny, where there is a slow anatomical growth between weaning and puberty. This could compensate for the immense energy cost of developing such a large brain.

In fact, the skeleton and dentition of this Neanderthal present a physiology which is similar to that of a sapiens of the same age, except for the thorax area, which corresponds to a child between five and six years, in that it is less developed. "The growth of our Neanderthal child was not complete, probably due to energy saving", explains CSIC researcher Antonio Rosas.

The only divergent aspect in the growth of both species is the moment of maturation of the vertebral column. In all hominids, the cartilaginous joints of the middle thoracic vertebrae and the atlas are the last to fuse, but in this Neanderthal, fusion occurred about two years later than in modern humans.

"The delay of this fusion in the vertebral column may indicate that Neanderthals had a decoupling of certain aspects in the transition from infancy to the juvenile phase. Although the implications are unknown, this feature could be related to the characteristic enlarged shape of the Neanderthal torso, or slower brain growth", says Rosas.

The Neanderthal child
The protagonist of this study was 7.7 years old, weighed 26 kilos and measured 111 centimetres at the time of death. Although the genetic analyses failed to confirm the child's sex, the canine teeth and the sturdiness of the bones showed that it to be a male. 138 pieces, 30 of them teeth (including some milk teeth), and part of the skeleton- including some fragments of the skull from the individual- identified as El Sidrón J1, have recovered.

The researchers have been able to establish that our protagonist was right-handed and was already performing adult tasks, such as using his teeth as a third hand to handle skins and plant fibres. In addition, they know who his mother was, and that the child protagonist of this investigation had a younger brother in the group. Furthermore, this child was found to have suffered from enamel hypoplasia when he was two or three years old. Hypoplasia (white spots on the teeth, especially visible in the upper incisors), occurs when the teeth have less enamel than normal, the cause usually being malnutrition or disease.

Discovered in 1994, the El Sidrón cave, located in Piloña (in Asturias, northern Spain) has provided the best collection of Neanderthals that exists on the Iberian Peninsula. The team has recovered the remains of 13 individuals from the cave. The group consisted of seven adults (four women and three men), three teenagers and three younger children.

Tuesday, September 19, 2017

The Arch of Titus – from Jerusalem to Rome, and Back

A replica of one of ancient Rome’s most iconic sculptures brings ancient history and Jewish culture to life at Yeshiva University Museum this fall.

 Spoils from the Temple of Solomon. Relief in the passageway of the Arch of Titus.

 Attic inscription, Arch of Titus

The Arch of Titus – from Jerusalem to Rome, and Back allows visitors to experience the richness and ongoing influence of one of ancient Rome’s most significant monuments, as well as the ways its meaning has dramatically transformed over 2,000 years.  The exhibition will be on view in the Museum’s Popper Gallery, located at the Center for Jewish History, 15 West 16th Street, through January 14, 2018.

The exhibition explores the historical and cultural significance of the Arch from its creation as a monument celebrating the Roman triumph over the Jews in 70 CE through the medieval papacy and early modern rabbis, the Counter-Reformation, European Classicism and finally the Jewish and Israeli national re-appropriation of the Arch.
“This history, where a symbol of defeat transforms into a symbol of victory, is especially relevant in light of the recent events in Charlottesville, where symbols of a dark history have galvanized people to assert the primacy of values that are more inclusive and compassionate,” said Dr. Steven Fine, Churgin Professor of Jewish History at Yeshiva University and director of the Yeshiva University Center for Israel Studies.
The Arch of Titus – from Jerusalem to Rome, and Back was conceived and is presented by Yeshiva University Museum in partnership with the Yeshiva University Center for Israel Studies. The Museum and the Center will also co-present a special international conference on the Arch on October 29, 2017.
Built by Emperor Domitian around 82 CE to commemorate the Roman defeat of Judaea in the Jewish War of 66-74 CE, the Arch of Titus has today become an iconic representation of antiquity. The Arch preserves sculptural reliefs that depict the sacred vessels of the Jerusalem Temple being carried into Rome by celebrating Roman soldiers, including a seven-branched Menorah, which, since 1949, has been the emblem of the State of Israel.

The exhibition features a digitally carved life-size replica of the Spoils of Jerusalem relief from the interior passageway of the Arch. The replica is projected with images that reconstruct the missing sculptures and colors of the original relief, based on the original polychromy discovered in 2012 by YU’s Arch of Titus Project, working collaboratively with a team of historians, scientists, and archaeologists.
In complement to the cutting-edge visual technologies, the exhibition also features rare artifacts from collections in Italy, Israel and the United States that illuminate the monument’s vibrant history – including:
Rare prints, paintings, photographs and depictions of the Arch of Titus across the centuries;
17th- and 18th-century placards carried by the Jews of Rome at the Arch during papal processions;
A postcard written by Sigmund Freud from the Arch, in 1913, inscribed: “The Jew Survives it”;
A selection of original proposals for the Emblem of the State of Israel.
The exhibition stretches from the Roman era to the present, exploring the image and symbolism of the Arch from various vantage points as the monument transformed and was re-interpreted across history.

As a complement to the exhibition, Yeshiva University Museum is teaming with the Jewish Museum of Rome and Centro Primo Levi on The Rome Lab, an ambitious multimedia program that explores Rome's Jewish community through the centuries and today. Spearheaded by Alessandra Di Castro, director of the Jewish Museum of Rome, and Natalia Indrimi, director of Centro Primo Levi, The Rome Lab is a dreamlike space that collapses spatial and temporal coordinates around three symbolic physical places: the Jewish quarter, the Jewish Museum and the Synagogue. This historic partnership with the Jewish Museum of Rome is especially meaningful in that it comes directly after the conclusion of the exhibition on the Menorah held jointly at the Jewish Museum of Rome and the Vatican Museum.

Monday, September 18, 2017

Art and Peoples of Kharga Oasis

In 1908, The Metropolitan Museum of Art began to excavate late-antique sites in the Kharga Oasis, located in Egypt's Western Desert. The Museum's archaeologists uncovered two-story houses, painted tombs, and a church and retrieved objects that reveal the multiple cultural and religious identities of people who had lived in the region between the third and seventh centuries A.D., a time of transition between the Roman and early Byzantine periods. The finds represent a society that integrated Egyptian, Greek, and Roman culture and art. Opening October 11 at The Met, the exhibition Art and Peoples of Kharga Oasis will feature some 30 works from these excavations. 
By grouping objects according to the archaeological context in which they were discovered, the exhibition will explore the interpretation of ancient identities and artifacts and show how archaeological documentation can aid in understanding an object's original function. 
On view will be copies of frescoes with Early Christian images, ceramics, ostraca (pottery shards that were used as writing surfaces), jewelry from burials, glassware, and early 20th-century site photography. An excerpt from the 1989 documentary film Merchants and Masterpieceswill feature footage ofthe landscape and monuments of Kharga Oasis.
Students and scholars wishing to do further research may consult "Excavations of the Late Roman and Early Byzantine Sites in the Kharga Oasis," an online resource available through the Digital Collection portal of the Museum's Thomas J. Watson Library.
The exhibition is organized by Helen Evans, the Mary and Michael Jaharis Curator of Byzantine Art, Department of Medieval Art and The Cloisters, and Andrea Myers Achi. Exhibition, graphic, and lighting design is by The Met Design Department.

Thursday, September 14, 2017

Huge genetic diversity among Papuan New Guinean peoples revealed

The first large-scale genetic study of people in Papua New Guinea has shown that different groups within the country are genetically highly different from each other. Scientists at the Wellcome Trust Sanger Institute and their colleagues at the University of Oxford and the Papua New Guinea Institute of Medical Research reveal that the people there have remained genetically independent from Europe and Asia for most of the last 50,000 years, and that people from the country's isolated highlands region have been completely independent even until the present day.

Reported today (15 September) in Science, the study also gives insights into how the development of agriculture and cultural events such as the Bronze or Iron Age could affect the genetic structure of human societies.

Papua New Guinea is a country in the southwestern Pacific with some of the earliest archaeological evidence of human existence outside Africa. Largely free from Western influence and with fascinating cultural diversity, it has been of enormous interest to anthropologists and other scientists seeking to understand human cultures and evolution.

With approximately 850 domestic languages, which account for over 10 per cent of the world's total, Papua New Guinea is the most linguistically diverse country in the world. To discover if the linguistic and cultural diversity was echoed in the genetic structure of the population, researchers studied the genomes of 381 Papuan New Guinean people from 85 different language groups within the country.
The researchers looked at more than a million genetic positions in the genome of each individual, and compared them to investigate genetic similarities and differences. They found that groups of people speaking different languages were surprisingly genetically distinct from each other.

Human evolution in Europe and Asia has been greatly influenced by the development of agriculture around 10,000 years ago. When small bands of hunter-gatherers settled into villages and started farming, they expanded and over time gave rise to more genetically homogenous (similar) societies. However, despite the independent development of agriculture in Papua New Guinea at about the same time, the same process of homogenization did not occur here. This may indicate that other historical processes in Europe and Asia, such as the later Bronze and Iron Ages, were the key events that shaped the current genetic structure of those populations.

Friday, September 8, 2017

An officer and a gentlewoman from the Viking army in Birka

The drawing is a reconstruction of how the grave with the woman originally may have looked.
Credit: The illustration is made by Þórhallur Þráinsson (© Neil Price).

War was not an activity exclusive to males in the Viking world. A new study conducted by researchers at Stockholm and Uppsala Universities shows that women could be found in the higher ranks at the battlefield.

Charlotte Hedenstierna-Jonson, who led the study, explains: "What we have studied was not a Valkyrie from the sagas but a real life military leader, that happens to be a woman".

The study was conducted on one of the most iconic graves from the Viking Age. It holds the remains of a warrior surrounded by weapons, including a sword, armour-piercing arrows, and two horses.

There were also a full set of gaming pieces and a gaming board. "The gaming set indicates that she was an officer", says Charlotte, "someone who worked with tactics and strategy and could lead troops in battle". The warrior was buried in the Viking town of Birka during the mid-10th century. Isotope analyses confirm an itinerant life style, well in tune with the martial society that dominated 8th to 10th century northern Europe.

Anna Kjellström, who also participated in the study, has taken an interest in the burial previously. "The morphology of some skeletal traits strongly suggests that she was a woman, but this has been the type specimen for a Viking warrior for over a century why we needed to confirm the sex in any way we could."

And this is why the archaeologists turned to genetics, to retrieve a molecular sex identification based on X and Y chromosomes. Such analyses can be quite useful according to Maja Krezwinska: "Using ancient DNA for sex identification is useful when working with children for example, but can also help to resolve controversial cases such as this one". Maja was thus able to confirm the morphological sex identification with the presence of X chromosomes but the lack of a Y chromosome.

Jan Storå, who holds the senior position on this study, reflects over the history of the material: "This burial was excavated in the 1880ies and has served as a model of a professional Viking warrior ever since. Especially, the grave-goods cemented an interpretation for over a century". It was just assumed she was a man through all these years. "The utilization of new techniques, methods, but also renewed critical perspectives, again, shows the research potential and scientific value of our museum collections".

Tuesday, September 5, 2017

Mobile women were key to cultural exchange in Stone Age and Bronze Age Europe

At the end of the Stone Age and in the early Bronze Age, families were established in a surprising manner in the Lechtal, south of Augsburg, Germany. The majority of women came from outside the area, probably from Bohemia or Central Germany, while men usually remained in the region of their birth. This so-called patrilocal pattern combined with individual female mobility was not a temporary phenomenon, but persisted over a period of 800 years during the transition from the Neolithic to the Early Bronze Age.

The findings, published today in PNAS, result from a research collaboration headed by Philipp Stockhammer of the Institute of Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces of the Ludwig-Maximilians-Universität München. In addition to archaeological examinations, the team conducted stable isotope and ancient DNA analyses. Corina Knipper of the Curt-Engelhorn-Centre for Archaeometry, as well as Alissa Mittnik and Johannes Krause of the Max Planck Institute for the Science of Human History in Jena and the University of Tuebingen jointly directed these scientific investigations.

"Individual mobility was a major feature characterizing the lives of people in Central Europe even in the 3rd and early 2nd millennium," states Philipp Stockhammer. The researchers suspect that it played a significant role in the exchange of cultural objects and ideas, which increased considerably in the Bronze Age, in turn promoting the development of new technologies.

For this study, the researchers examined the remains of 84 individuals using genetic and isotope analyses in conjunction with archeological evaluations. The individuals were buried between 2500 and 1650 BC in cemeteries that belonged to individual homesteads, and that contained between one and several dozen burials made over a period of several generations.

"The settlements were located along a fertile loess ridge in the middle of the Lech valley. Larger villages did not exist in the Lechtal at this time," states Stockhammer.

"We see a great diversity of different female lineages, which would occur if over time many women relocated to the Lech Valley from somewhere else," remarks Alissa Mittnik on the genetic analyses and Corina Knipper explains, "Based on analysis of strontium isotope ratios in molars, which allows us to draw conclusions about the origin of people, we were able to ascertain that the majority of women did not originate from the region." The burials of the women did not differ from that of the native population, indicating that the formerly foreign women were integrated into the local community.

From an archaeological point of view, the new insights prove the importance of female mobility for cultural exchange in the Bronze Age. They also allow us to view the immense extent of early human mobility in a new light. "It appears that at least part of what was previously believed to be migration by groups is based on an institutionalized form of individual mobility," declares Stockhammer.