Saturday, January 30, 2016

1,700-year-old funerary inscriptions exposed in Zippori

 Researcher Aharoni Amitai with the inscriptions uncovered in Zippori
Copyright: Miki Peleg, courtesy Israel Antiquities Authority

Three 1,700 year old funerary inscriptions written in Aramaic and Greek were recently revealed in Moshav Zippori in the north. This occurred in the wake of information received from residents of the moshav which resulted in uncovering the inscriptions in a joint effort carried out by researchers of the Kinneret Institute for Galilean Archaeology of the Kinneret Academic College and the Israel Antiquities Authority.

Aramaic was the everyday language used by the Jews in the period of the Mishnah and Talmud, but some of them also spoke and read Greek, and thus there are also funerary inscriptions in that language. The two Aramaic inscriptions mention individuals referred to as "rabbis" who were buried in the western cemetery of Zippori; their names have not yet been deciphered.

According to Dr. Motti Aviam of the Kinneret Institute for Galilean Archaeology, the importance of the epitaphs lies in the fact that these reflect the everyday life of the Jews of Zippori and their cultural world. Researchers are uncertain as to the meaning of the term "rabbi" at the time when Rabbi Yehuda Ha-Nasi resided in Zippori together with the Tannaim and after him by the Amoraim - the large groups of sages that studied in the city’s houses of learning.

One of the surprises in the newly discovered inscriptions is that one of the deceased was called "the Tiberian". This is already the second instance of someone from Tiberias being buried in the cemetery at Zippori. It is quite possible that Jews from various parts of Galilee were brought to Zippori to be buried in the wake of the important activity carried out there by Rabbi Yehuda Ha-Nasi. Another possibility is that the man moved to Zippori and died there, but wanted to be remembered as someone who originally came from Tiberias.

In the second Aramaic epitaph the word le-olam (forever) appears for the first time in inscriptions found at Zippori. The term le-olam is known from funerary inscriptions in Bet She‘arim and elsewhere and means that the deceased’s burial place will remain his forever and that no one will take it from him. Both inscriptions end with the Hebrew blessing shalom.  

The Greek inscription mentions the name Jose, which was very common amongst Jews living in Israel and abroad.

The Greek inscription at Zippori
Copyright: Miki Peleg, courtesy Israel Antiquities Authority

So far, 17 funerary inscriptions have been documented in the Zippori study, most of them written in Aramaic, which was the everyday language of Jews in Israel at that time. Contrasting this are the funerary inscriptions found in Tiberias - the second capital of the Galilee - which were mainly written in Greek. Several of the ancient inhabitants from Zippori are mentioned in these inscriptions, which include the names of rabbis and often have the names of the professions they were engaged in.

Zippori was the first capital of the Galilee from the time of the Hasmonean dynasty until the establishment of Tiberias in the first century CE. The city continued to be central and important later on and was where Rabbi Yehuda Ha-Nasi resided and compiled the Mishnah. The Jewish life in the city was rich and diverse as indicated by the numerous ritual baths discovered in the excavation; while at the same time the influence of Roman culture was also quite evident as reflected in the design of the town with its paved streets, colonnaded main roads, theater and bathhouses. The wealth of inscriptions from the cemeteries attests to the strong Jewish presence and the city’s social elite in the Late Roman period.

The inscriptions will be studied by a team of researchers consisting of Dr. Motti Aviam, Aharoni Amitai and the historian Dr. Jacob Ashkenazi of the Kinneret Institute for Galilean Archaeology and Miki Peleg, the Lower Galilee District Archaeologist of the Israel Antiquities Authority. This joint effort is also likely to lead to new discoveries soon. Upon completion of their research the Israel Antiquities Authority and the Kinneret Academic College will present the inscriptions to the general public.

Friday, January 29, 2016

Ancient Babylonians used geometry to track Jupiter

Analysis of ancient Babylonian tablets reveals that, to calculate the position of Jupiter, the tablets' makers used geometry, a technique scientists previously believed humans had not developed until at least 1,400 years later, in 14th century Europe.

These tablets are the earliest known examples of using geometry to calculate positions in time-space and suggest that ancient Babylonian astronomers may have influenced the emergence of such techniques in Western science.

JOURNAL Science Mathieu Ossendrijver discusses the translation of four almost completely intact tablets that were most likely written in Babylon between 350 and 50 BCE. They depict two intervals from when Jupiter first appears along the horizon, calculating the planet's position at 60 and 120 days. The texts contain geometrical calculations based on a trapezoid's area, and its "long" and "short" sides; previously, it was thought that Babylonian astronomers operated exclusively with arithmetical concepts. The ancient astronomers also computed the time when Jupiter covers half of this 60-day distance by partitioning the trapezoid into two smaller ones of equal area.

While ancient Greeks used geometrical figures to describe configurations in physical space, these Babylonian tablets use geometry in an abstract sense to define time and velocity, Ossendrijver notes. These tablets redefine our history books, revealing that European scholars in Oxford and Paris in the 14th century, who were previously credited with developing such calculations, were in fact centuries behind their ancient Babylonian counterparts. This paper is featured on the cover, with a special cover caption describing how Science photo editors created a striking image of a 3-D printed replica of the ancient tablet, positioned aptly under a prominent Jupiter in the Babylonian night sky.

Wednesday, January 20, 2016

Neolithic tomb reveals community stayed together, even in death


This image shows the superposition of different layers of the Neolithic ossuary indicating the individuals with the same genetic profile.  

Credit: Graphic by Héctor Arcusa Magallón.
A Neolithic Spanish burial site contains remains of a closely-related local community from 6000 years ago, according to a study published January 20th, 2015 in the open-access journal PLOS ONE by Kurt W. Alt from Danube Private University, Austria, and colleagues.

The Neolithic people are thought to have introduced new burial rituals in the modern-day Europe. This included building megalithic tombs, which were used over an extended period of time as collective burial sites and venues for ritual acts. The authors of this study examined a megalithic tomb at Alto de Reinoso in Northern Spain to build a comprehensive picture of this community using archaeological analysis, genetics, isotope analysis, and bone analysis.

The researchers identified at least 47 adults and adolescents that had been buried in the tomb over a hundred-year period. Based on DNA and isotope analysis, the authors suggest that the tomb contained a series of families from a local close-knit group. The individuals likely farmed cereal crops, and possibly sheep and goats. The tomb comprised three distinct layers. The individuals at the bottom of the tomb were more closely related and on occasion, family members appeared to have been buried side-by-side. Above them, almost all the skeletons exhibited signs of manipulation such as missing skeletal parts, especially skulls, suggesting a shift in the use of the tomb. Although the author's conclusions rely on certain underlying assumptions about the Neolithic society at the time, the authors state that this may be the first study to provide such an in-depth picture of this community in life and death.

Kurt W. Alt notes: "All the extensive data collected, including information on life style, demographics, health status, diet and subsistence, mobility patterns as well as the genetic profile of the group fit in with the typical way of life of sedentary farming populations at this time period. The embracement of a collective burial chamber for the community members rather than individual graves indicates significant shifts in social identity."

Evidence of a prehistoric massacre extends the history of warfare


This skeleton was that of a man, found lying prone in the lagoon's sediments. The skull has multiple lesions on the front and on the left side, consistent with wounds This skeleton was that of a man, found lying prone in the lagoon's sediments. The skull has multiple lesions on the front and on the left side, consistent with wounds from a blunt implement, such as a club. 

Credit: Marta Mirazon Lahr
The fossilised bones of a group of prehistoric hunter-gatherers who were massacred around 10,000 years ago have been unearthed 30km west of Lake Turkana, Kenya, at a place called Nataruk.
Researchers from Cambridge University's Leverhulme Centre for Human Evolutionary Studies found the partial remains of 27 individuals, including at least eight women and six children.

Twelve skeletons were in a relatively complete state, and ten of these showed clear signs of a violent death: including extreme blunt-force trauma to crania and cheekbones, broken hands, knees and ribs, arrow lesions to the neck, and stone projectile tips lodged in the skull and thorax of two men.

Several of the skeletons were found face down; most had severe cranial fractures. Among the in situ skeletons, at least five showed "sharp-force trauma", some suggestive of arrow wounds. Four were discovered in a position indicating their hands had probably been bound, including a woman in the last stages of pregnancy. Foetal bones were uncovered.

The bodies were not buried. Some had fallen into a lagoon that has long since dried; the bones preserved in sediment.

The findings suggest these hunter-gatherers, perhaps members of an extended family, were attacked and killed by a rival group of prehistoric foragers. Researchers believe it is the earliest scientifically-dated historical evidence of human conflict - an ancient precursor to what we call warfare.

The origins of warfare are controversial: whether the capacity for organised violence occurs deep in the evolutionary history of our species, or is a symptom of the idea of ownership that came with the settling of land and agriculture.

The Nataruk massacre is the earliest record of inter-group violence among prehistoric hunter-gatherers who remained largely nomadic.

"The deaths at Nataruk are testimony to the antiquity of inter-group violence and war," said Dr Marta Mirazon Lahr, from Cambridge's LCHES, who directs the IN-AFRICA Project and led the Nataruk study, published today in the journal Nature.

"These human remains record the intentional killing of a small band of foragers with no deliberate burial, and provide unique evidence that warfare was part of the repertoire of inter-group relations among some prehistoric hunter-gatherers," she said.

The site was first discovered in 2012. Following careful excavation, the researchers used radiocarbon and other dating techniques on the skeletons - as well as on samples of shell and sediment surrounding the remains - to place Nataruk in time. They estimate the event occurred between 9,500 to 10,500 years ago, around the start of the Holocene: the geological epoch that followed the last Ice Age.

Now scrubland, 10,000 years ago the area around Nataruk was a fertile lakeshore sustaining a substantial population of hunter-gatherers. The site would have been the edge of a lagoon near the shores of a much larger Lake Turkana, likely covered in marshland and bordered by forest and wooded corridors.

This lagoon-side location may have been an ideal place for prehistoric foragers to inhabit, with easy access to drinking water and fishing - and consequently, perhaps, a location coveted by others. The presence of pottery suggests the storage of foraged food occurred.

"The Nataruk massacre may have resulted from an attempt to seize resources - territory, women, children, food stored in pots - whose value was similar to those of later food-producing agricultural societies, among whom violent attacks on settlements became part of life," said Mirazon Lahr.

"This would extend the history of the same underlying socio-economic conditions that characterise other instances of early warfare: a more settled, materially richer way of life. However, Nataruk may simply be evidence of a standard antagonistic response to an encounter between two social groups at that time."

Antagonism between hunter-gatherer groups in recent history often resulted in men being killed, with women and children subsumed into the victorious group. At Nataruk, however, it seems few, if any, were spared.

Of the 27 individuals recorded, 21 were adults: eight males, eight females, and five unknown. Partial remains of six children were found co-mingled or in close proximity to the remains of four adult women and of two fragmentary adults of unknown sex.

No children were found near or with any of the men. All except one of the juvenile remains are children under the age of six; the exception is a young teenager, aged 12-15 years dentally, but whose bones are noticeably small for his or her age.

Ten skeletons show evidence of major lesions likely to have been immediately lethal. As well as five - possibly six - cases of trauma associated with arrow wounds, five cases of extreme blunt-force to the head can be seen, possibly caused by a wooden club. Other recorded traumas include fractured knees, hands and ribs.

Three artefacts were found within two of the bodies, likely the remains of arrow or spear tips. Two of these are made from obsidian: a black volcanic rock easily worked to razor-like sharpness. "Obsidian is rare in other late Stone Age sites of this area in West Turkana, which may suggest that the two groups confronted at Nataruk had different home ranges," said Mirazon Lahr.

One adult male skeleton had an obsidian 'bladelet' still embedded in his skull. It didn't perforate the bone, but another lesion suggests a second weapon did, crushing the entire right-front part of the head and face. "The man appears to have been hit in the head by at least two projectiles and in the knees by a blunt instrument, falling face down into the lagoon's shallow water," said Mirazon Lahr.

Another adult male took two blows to the head - one above the right eye, the other on the left side of the skull - both crushing his skull at the point of impact, causing it to crack in different directions.
The remains of a six-to-nine month-old foetus were recovered from within the abdominal cavity of one of the women, who was discovered in an unusual sitting position - her broken knees protruding from the earth were all Mirazon Lahr and colleagues could see when they found her. The position of the body suggests that her hands and feet may have been bound.

While we will never know why these people were so violently killed, Nataruk is one of the clearest cases of inter-group violence among prehistoric hunter-gatherers, says Mirazon Lahr, and evidence for the presence of small-scale warfare among foraging societies.

For study co-author Professor Robert Foley, also from Cambridge's LCHES, the findings at Nataruk are an echo of human violence as ancient, perhaps, as the altruism that has led us to be the most cooperative species on the planet.

"I've no doubt it is in our biology to be aggressive and lethal, just as it is to be deeply caring and loving. A lot of what we understand about human evolutionary biology suggests these are two sides of the same coin," Foley said.

Ancient genomes reveal that the English are one-third Anglo-Saxon

For the first time, researchers have been able to directly estimate the Anglo-Saxon ancestry of the British population from ancient skeletons, showing how Anglo-Saxon immigrants mixed with the native population.

Human remains excavated from burial sites near Cambridge provided the material for the first whole-genome sequences of ancient British DNA. Using a new analysis method to compare these ancient genomes with modern-day sequences, researchers have estimated that approximately a third of British ancestors were Anglo-Saxon immigrants.

What was the scale of the Anglo-Saxons migrations, how did they mix with the native population and how did they contribute to British ancestry? This has been a long-standing topic of debate amongst historians and archaeologists. Recently excavated skeletons dating to the late Iron Age and from the Anglo-Saxon period gave researchers the opportunity to solve this question with genomics.

"By sequencing the DNA from ten skeletons from the late Iron Age and the Anglo-Saxon period, we obtained the first complete ancient genomes from Great Britain," said Dr Stephan Schiffels, first author from the Wellcome Trust Sanger Institute, Cambridgeshire and the Max Plank Institute in Germany. "Comparing these ancient genomes with sequences of hundreds of modern European genomes, we estimate that 38% of the ancestors of the English were Anglo-Saxons. This is the first direct estimate of the impact of immigration into Britain from the 5th to 7th Centuries AD and the traces left in modern England."

Previous DNA studies have relied entirely on modern DNA and suggested anything between 10% and 95% contribution to the population. One such study suggested that Anglo Saxons didn't mix with the native population, staying segregated. However, this newly published study uses ancient genetic information and disproves the earlier idea, showing just how integrated the people of Britain were. The ancient skeletons from Cambridgeshire were carbon dated, proving they were from the late Iron Age (approximately 50BC) and from the Anglo-Saxon era (around 500-700 AD). Complete genome sequences were then obtained for selected DNA samples to determine the genetic make-up of these Iron Age Britons and Anglo-Saxons.

"Combining archaeological findings with DNA data gives us much more information about the early Anglo-Saxon lives. Genome sequences from four individuals from a cemetery in Oakington indicated that, genetically, two were migrant Anglo-Saxons, one was a native, and one was a mixture of both. The archaeological evidence shows that these individuals were treated the same way in death, and proves they were all well integrated into the Oakington Anglo-Saxon Community despite their different biological heritage." said Dr Duncan Sayer, archaeologist and author on the paper from University of Central Lancashire.

Modern British and continental European genomes from the UK10K project and the 1000 Genomes Project were compared with the genomes from the ancient skeletons. Researchers discovered that the Anglo-Saxon immigrants were genetically very similar to modern Dutch and Danish, and that they contributed 38% of the DNA of modern people from East England, and 30% for modern Welsh and Scottish. The Anglo-Saxons first settled in the South East of England so this pattern is consistent with their migration pattern.

The genomes of northern European populations are similar and it is difficult to accurately distinguish between them. To help solve this problem, the study developed a sensitive new method, called rarecoal, which could identify subtle genetic traces in individuals, using rare genetic variants identified in hundreds of present-day people. Earlier methods of mapping ancient DNA looked at common genetic variants from the very distant past, which are present in most people. The new rarecoal method did exactly the opposite, allowing researchers to map more recent events and unravel very closely related populations.

"We wanted to determine where ancient DNA samples would fit with respect to a modern population model and to map individuals into that model. This study, using whole-genome sequencing, allowed us to assign DNA ancestry at extremely high resolution and accurately estimate the Anglo-Saxon mixture fraction for each individual," said Richard Durbin, senior author at the Sanger Institute. "More full genome sequences and further improvements in methodology will allow us to resolve migrations in even more detail in the future."

Thursday, January 14, 2016

Mammoth injuries indicate humans occupied Arctic earlier than thought

Excavations of the carcass from channel deposits unit. In this photo, Sergey Gorbunov is excavating the mammoth carcass. This material relates to a paper that appeared in the Jan. 15, 2016, issue of Science, published by AAAS. The paper, by V.V. Pitulko at Russian Academy of Sciences in St. Petersburg, Russia, and colleagues was titled, "Early human presence in the Arctic: Evidence from 45,000-year-old mammoth remains."


Pitulko et al., Science (2016)

The carcass of a frozen mammoth with signs of weapon-inflicted injuries suggests humans were present in the Eurasian Arctic ten millennia earlier than previously thought. These results, which provide perhaps the oldest known story of human survival in the Arctic region, date human presence there to roughly 45,000 years ago, instead of 35,000 years ago, as previously thought.

Paleolithic records of humans in the Eurasian Arctic are scarce. In 2012, a team led by Alexei Tikhonov excavated a partial carcass of a male woolly mammoth from frozen sediments in a coastal bluff on the eastern shore of Yenisei Bay, in the central Siberian Arctic. Through radiocarbon dating of the animal's tibia bone and surrounding materials, the researchers dated it at 45,000 years old. The mammoth's bones exhibited a number of unusual injuries on the ribs, right tusk and mandible. Tikhonov, Vladimir Pitulko and colleagues analyzed these injuries. They include dents likely from sharp weapon tips such as thrusting spears and damage to the tusk suggestive of human attempts to separate the outside of the tusk by chopping.

These findings leave no doubt, say the study's authors, that people were present in the central Siberian Arctic by about 45,000 years ago. Advancements in mammoth hunting probably allowed people to survive and spread widely across northernmost Arctic Siberia at this time, the researchers say, representing an important cultural shift - one that likely facilitated the arrival of humans in the area close to the Bering land bridge, providing them an opportunity to enter the New World before the Last Glacial Maximum.

New discoveries concerning Ötzi's history

Scientists are continually unearthing new facts about Homo sapiens from the mummified remains of Ötzi, the Copper Age man, who was discovered in a glacier in 1991. Five years ago, after Ötzi's genome was completely deciphered, it seemed that the wellspring of spectacular discoveries about the past would soon dry up. An international team of scientists working with paleopathologist Albert Zink and microbiologist Frank Maixner from the European Academy (EURAC) in Bozen/Bolzano have now succeeded in demonstrating the presence of Helicobacter pylori in Ötzi's stomach contents, a bacterium found in half of all humans today. The theory that humans were already infected with this stomach bacterium at the very beginning of their history could well be true. The scientists succeeded in decoding the complete genome of the bacterium.

When EURAC's Zink and Maixner first placed samples from the Iceman's stomach under the microscope in their ancient DNA Lab at EURAC, almost three years ago, they were initially sceptical.

"Evidence for the presence of the bacterium Helicobacter pylori is found in the stomach tissue of patients today, so we thought it was extremely unlikely that we would find anything because Ötzi's stomach mucosa is no longer there," explains Zink. Together with colleagues from the Universities of Kiel, Vienna and Venda in South Africa as well as the Max Planck Institute for the Science of Human History in Jena, the scientists tried to find a new way to proceed. "We were able to solve the problem once we hit upon the idea of extracting the entire DNA of the stomach contents," reports Maixner. "After this was successfully done, we were able to tease out the individual Helicobacter sequences and reconstruct a 5,300 year old Helicobacter pylori genome."

The scientists found a potentially virulent strain of bacteria, to which Ötzi's immune system had already reacted. "We showed the presence of marker proteins which we see today in patients infected with Helicobacter," said the microbiologist.

A tenth of infected people develop further clinical complications, such as gastritis or stomach ulcers, mostly in old age. "Whether Ötzi suffered from stomach problems cannot be said with any degree of certainty," says Zink, "because his stomach tissue has not survived and it is in this tissue that such diseases can be discerned first. Nonetheless, the preconditions for such a disease did in fact exist in Ötzi."

After completing their stomach biopsy, the two EURAC scientists transferred the genome data for analysis by their colleague Thomas Rattei from the University of Vienna. Rattei, in collaboration with geneticists from the USA, South Africa and Germany, came to a surprising conclusion: "We had assumed that we would find the same strain of Helicobacter in Ötzi as is found in Europeans today," explains the computational biologist. "It turned out to be a strain that is mainly observed in Central and South Asia today."

The scientists assume that there were originally two strain types of the bacterium, an African and an Asian one, which at some point recombined into today's European version. Since bacteria are usually transmitted within the family, the history of the world's population is closely linked to the history of bacteria. Up till now, it had been assumed that Neolithic humans were already carrying this European strain by the time they stopped their nomadic life and took up agriculture. Research on Ötzi, however, demonstrates that this was not the case.

"The recombination of the two types of Helicobacter may have only occurred at some point after Ötzi's era, and this shows that the history of settlements in Europe is much more complex than previously assumed," says Maixner.


New research at the European Academy of Bolzano/Bozen (EURAC) further clarifies the genetic history of man who lived in the Eastern Alps over 5,300 years ago. In 2012 a complete analysis of the Y chromosome (transmitted from fathers to their sons) showed that Ötzi's paternal genetic line is still present in modern-day populations. In contrast, studies of mitochondrial DNA (transmitted solely via the mother to her offspring) left many questions still open. To clarify whether the genetic maternal line of the Iceman, who lived in the eastern Alps over 5,300 years ago, has left its mark in current populations, researchers at the European Academy of Bolzano/Bozen (EURAC) have now compared his mitochondrial DNA with 1,077 modern samples. The study concluded that the Iceman's maternal line -- named K1f -- is now extinct. A second part of the study, a comparison of genetic data of the mummy with data from other European Neolithic samples, provided information regarding the origin of K1f: researchers postulate that the mitochondrial lineage of the Iceman originated locally in the Alps, in a population that did not grow demographically. The study, which also clarifies Ötzi's genetic history in the context of European demographic changes from Neolithic times onwards, was published in Scientific Reports, an open access journal of the Nature group.

"The mummy's mitochondrial DNA was the first to be analysed, in 1994." says Valentina Coia, a biologist at EURAC and first author of the study. "It was relatively easy to analyse and -- along with the Y chromosome -- allows us to go back in time, telling us about the genetic history of an individual. Despite this, the genetic relationship between the Iceman's maternal lineage and lineages found in modern populations was not yet clear." The most recent study regarding the analysis of Ötzi's complete mitochondrial DNA, conducted in 2008 by other research teams showed that the Iceman's maternal lineage -- named K1f -- was no longer traceable in modern populations. The study did not make clear, however, whether this was due to an insufficient number of comparison samples or whether K1f was indeed extinct.

Valentina Coia explains further: "The first hypothesis could not be ruled out given that the study considered only 85 modern comparison samples from the K1 lineage -- the genetic lineage that also includes that of Ötzi -- which comprised few samples from Europe and especially none from the eastern Alps, which are home to populations that presumably have a genetic continuity with the Iceman. To test the two hypotheses, we needed to compare Ötzi's mitochondrial DNA with a larger number of modern samples." The EURAC research team, in collaboration with the Sapienza University of Rome and the University of Santiago de Compostela, thus compared the mitochondrial DNA of the Iceman with that from 1,077 individuals belonging to the K1 lineage, of which 42 samples originated from the eastern Alps and were for the first time analysed in this study. The new comparison showed that neither the Iceman's lineage nor any other evolutionarily close lineages are present in modern populations: the researchers therefore lean towards the hypothesis that Ötzi's maternal genetic branch has died out.

It remains to be explained why Ötzi's maternal lineage has disappeared, while his paternal lineage-- named G2a--still exists in Europe. To clarify this point, researchers at EURAC compared Ötzi's mitochondrial DNA and Y chromosome with available data from numerous ancient samples found at 14 different archaeological sites throughout Europe. The results showed that the paternal lineage of Ötzi was very common in different regions in Europe during the Neolithic age, while his maternal lineage probably existed only in the Alps.

Putting together the genetic data on the ancient and modern samples, namely those already present in the literature and those analysed in this study, researchers have now proposed the following scenario to explain the Iceman's genetic history: Ötzi's paternal lineage, G2a, is part of an ancient genetic substrate that arrived in Europe from the Near East with the migrations of the first Neolithic peoples some 8,000 years ago. Additional migrations and other demographic events occurring after the Neolithic Age in Europe then partially replaced G2a with other lineages, except in geographically isolated areas such as Sardinia. In contrast, the Iceman's maternal branch originated locally in the eastern Alps at least 5,300 years ago. The same migrations that have replaced only in part his paternal lineage caused the extinction of his maternal lineage that was inherited in a small and demographic stationary population. The groups from the eastern Alps in fact significantly increased in size only from the Bronze Age onwards, as evidenced by archaeological studies conducted in the territory inhabited by the Iceman.

Thursday, January 7, 2016

Neanderthal genes gave modern humans an immunity boost, allergies

This world map shows the frequencies of Neandertal-like TLR DNA in a 1000 Genomes dataset. The size of each pie is proportional to the number of individuals within a population.
Dannemann et al./American Journal of Human Genetics 2016

When modern humans met Neanderthals in Europe and the two species began interbreeding many thousands of years ago, the exchange left humans with gene variations that have increased the ability of those who carry them to ward off infection. This inheritance from Neanderthals may have also left some people more prone to allergies.

The discoveries reported in two independent studies in the American Journal of Human Genetics on January 7 add to evidence for an important role for interspecies relations in human evolution and specifically in the evolution of the innate immune system, which serves as the body's first line of defense against infection.

"We found that interbreeding with archaic humans--the Neanderthals and Denisovans--has influenced the genetic diversity in present-day genomes at three innate immunity genes belonging to the human Toll-like-receptor family," says Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

"These, and other, innate immunity genes present higher levels of Neanderthal ancestry than the remainder of the coding genome," adds Lluis Quintana-Murci of the Institut Pasteur and the CNRS in Paris. "This highlights how important introgression events [the movement of genes across species] may have been in the evolution of the innate immunity system in humans."

Earlier studies have shown that one to six percent of modern Eurasian genomes were inherited from ancient hominins, such as Neanderthal or Denisovans. Both new studies highlight the functional importance of this inheritance on Toll-like receptor (TLR) genes--TLR1, TLR6, and TLR10. These TLR genes are expressed on the cell surface, where they detect and respond to components of bacteria, fungi, and parasites. These immune receptors are essential for eliciting inflammatory and anti-microbial responses and for activating an adaptive immune response.

Quintana-Murci and his colleagues set out to explore the evolution of the innate immune system over time. They relied on vast amounts of data available on present-day people from the 1000 Genomes Project together with the genome sequences of ancient hominins. Quintana-Murci's team focused on a list of 1,500 genes known to play a role in the innate immune system. They then examined patterns of genetic variation and evolutionary change in those regions relative to the rest of the genome at an unprecedented level of detail. Finally, they estimated the timing of the changes in innate immunity and the extent to which variation in those genes had been passed down from Neanderthals.

These investigations revealed little change over long periods of time for some innate-immunity genes, providing evidence of strong constraints. Other genes have undergone selective sweeps in which a new variant came along and quickly rose to prominence, perhaps because of a shift in the environment or as a result of a disease epidemic. Most adaptations in protein-coding genes occurred in the last 6,000 to 13,000 years, as human populations shifted from hunting and gathering to farming, they report.

But, Quintana-Murci says, the biggest surprise for them "was to find that the TLR1-6-10 cluster is among the genes presenting the highest Neanderthal ancestry in both Europeans and Asians."

Kelso and her colleagues came to the same conclusion, but they didn't set out to study the immune system. Their interest was in understanding the functional importance of genes inherited from archaic humans more broadly. They screened present-day human genomes for evidence of extended regions with high similarity to the Neanderthal and Denisovan genomes,then examined the prevalence of those regions in people from around the world. Those analyses led them to the same three TLR genes.

Two of those gene variants are most similar to the Neanderthal genome, whereas the third is most similar to the Denisovan genome, Kelso's group reports. Her team also provides evidence that these gene variants offered a selective advantage. The archaic-like variants are associated with an increase in the activity of the TLR genes and with greater reactivity to pathogens. Although this greater sensitivity might protect against infection, it might also increase the susceptibility of modern-day people to allergies.

"What has emerged from our study as well as from other work on introgression is that interbreeding with archaic humans does indeed have functional implications for modern humans, and that the most obvious consequences have been in shaping our adaptation to our environment - improving how we resist pathogens and metabolize novel foods," Kelso says.

As surprising as it may seem, it does make a lot of sense, she adds. "Neanderthals, for example, had lived in Europe and Western Asia for around 200,000 years before the arrival of modern humans. They were likely well adapted to the local climate, foods, and pathogens. By interbreeding with these archaic humans, we modern humans gained these advantageous adaptations."

Wednesday, January 6, 2016

Neolithic and Bronze Age migration to Ireland

Modern Europe has been shaped by two episodes in prehistory, the advent of agriculture and later metallurgy. These innovations brought not only massive cultural change but also, in certain parts of the continent, a change in genetic structure. The manner in which these transitions affected the islands of Ireland and Britain on the northwestern edge of the continent remains the subject of debate. The first ancient whole genomes from Ireland, demonstrate that large-scale genetic shifts accompanied both transitions.  A new PNAS Online study also observe a strong signal of continuity between modern day Irish populations and the Bronze Age individuals, one of whom is a carrier for the hemochromatosis mutation, which has its highest frequencies in Ireland today.
The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. 

New discoveries about Knossos, Europe's oldest city

Recent fieldwork at the ancient city of Knossos on the Greek island of Crete finds that during the early Iron Age (1100 to 600 BC), the city was rich in imports and was nearly three times larger than what was believed from earlier excavations. The discovery suggests that not only did this spectacular site in the Greek Bronze Age (between 3500 and 1100 BC) recover from the collapse of the socio-political system around 1200 BC, but also rapidly grew and thrived as a cosmopolitan hub of the Aegean and Mediterranean regions. Antonis Kotsonas, a University of Cincinnati assistant professor of classics, will highlight his field research with the Knossos Urban Landscape Project at the 117th annual meeting of the Archaeological Institute of America and Society for Classical Studies. The meeting takes place Jan. 7-10, 2016 in San Francisco.
Kotsonas explains that Knossos, "renowned as a glorious site of the Greek Bronze Age, the leader of Crete and the seat of the palace of the mythical King Minos and the home of the enigmatic labyrinth," was the prosperous epicenter of Minoan culture. Scholars have studied the city's Bronze Age remains for more than a century, but more recent research has focused on the urban development of the city after it entered the Iron Age -- in the 11th century BC -- following the Bronze Age collapse of the Aegean palaces. 
The Knossos Urban Landscape Project over the past decade has recovered a large collection of ceramics and artifacts dating back to the Iron Age. The relics were spread over an extensive area that was previously unexplored. Kotsonas says that this exploration revealed considerable growth in the size of the settlement during the early Iron Age and also growth in the quantity and quality of its imports coming from mainland Greece, Cyprus, the Near East, Egypt, Italy, Sardinia and the western Mediterranean.
"No other site in the Aegean period has such a range of imports," Kotsonas says. The imports include bronze and other metals -- jewelry and adornments, as well as pottery. He adds that the majority of the materials, recovered from tombs, provide a glimpse of the wealth in the community, because status symbols were buried with the dead during this period. 
The antiquities were collected from fields covering the remains of dwellings and cemeteries. "Distinguishing between domestic and burial contexts is essential for determining the size of the settlement and understanding the demographic, socio-political and economic development of the local community," explains Kotsonas. "Even at this early stage in detailed analysis, it appears that this was a nucleated, rather densely occupied settlement extending over the core of the Knossos valley, from at least the east slopes of the acropolis hill on the west to the Kairatos River, and from the Vlychia stream on the south until roughly midway between the Minoan palace and the Kephala hill."
Kotsonas' Jan. 9, 2016 presentation is part of a colloquium themed, "Long-Term Urban Dynamics at Knossos: The Knossos Urban Landscape Project, 2005-2015." Kotsonas serves as a consultant on the project, which is dedicated to intensively surveying the Knossos valley and documenting the development of the site from 7000 BC, to the early 20th century. The project is a research partnership between the Greek Archaeological Service and the British School at Athens. Kotsonas has served as a collaborator on the project since 2009.

Monday, January 4, 2016

The first European farmers traced back to Anatolia

Human material from the Anatolian site Kumtepe was used in the study. The material was heavily degraded, but yielded enough DNA for the doctorate student Ayca Omrak to address questions concerning the demography connected to the spread of farming. She conducted her work at the Archaeological Research Laboratory.
"I have never worked with a more complicated material. But it was worth every hour in the laboratory. I could use the DNA from the Kumtepe material to trace the european farmers back to Anatolia. It is also fun to have worked with this material from the site Kumtepe, as this is the precursor to Troy", says doctorate student Ayca Omrak, at the Archaeological Research Laboratory Stockholm University.
Jan Storå, associate professor in osteoarchaeology and coauthor to the study agrees with Ayca. The results confirms Anatolias importance to Europe's cultural history. He also thinks that material from the area needs to be researched further.
"It is complicated to work with material from this region, it is hot and the DNA is degraded. But if we want to understand how the process that led from a hunter-gatherer society proceeded to a farming society, it is this material we need to exhaust", says Jan Storå, associate professor in osteoarchaeology, Stockholm University.
Anders Götherstörm who heads the archaeogenetic research at the Archaeological Research Laboratory agrees that this study indicates further possibilities:
"Our results stress the importance Anatolia has had on Europe's prehistory. But to fully understand how the agricultural development proceeded we need to dive deeper down into material from the Levant. Jan is right about that."