Monday, June 22, 2015

Human who lived in Europe about 40,000 years had recent Neanderthal ancestor

In 2002, archaeologists discovered the jawbone of a human who lived in Europe about 40,000 years ago. Geneticists have now analyzed ancient DNA from that jawbone and learned that it belonged to a modern human whose recent ancestors included Neanderthals.

Neanderthals lived in Europe until about 35,000 years ago, disappearing at the same time modern humans were spreading across the continent. The new study, co-led by Howard Hughes Medical Institute (HHMI) investigator David Reich at Harvard Medical School and Svante Pääbo at the Max Planck Institute in Germany, provides the first genetic evidence that humans interbred with Neanderthals in Europe. The scientists reported their findings in the June 22, 2015, issue of the journal Nature.

"We know that before 45,000 years ago, the only humans in Europe were Neanderthals. After 35,000 years ago, the only humans in Europe were modern humans. This is a dramatic transition," Reich says. There is archaeological evidence that modern humans interacted with Neanderthals during the time that they both lived in Europe: Changes in tool making technology, burial rituals, and body decoration imply a cultural exchange between the groups. "But we have very few skeletons from this period," Reich points out.

So the jawbone that archaeologists uncovered in Romania in 2002, which radiocarbon dating determined was between 37,000 and 42,000 years old, was an important find. "It's an amazing bone," Reich says. The jawbone was found along with the skull of another individual in a cave called Pe?tera cu Oase. No artifacts were discovered nearby, so anthropologists had no cultural clues about who the individuals were or how they lived. The physical features of the jawbone were predominantly those of modern humans, but some Neanderthal traits were also apparent, and the anthropologists proposed that the bone might have belonged to someone descended from both groups.

Pääbo and Reich teamed up to investigate that possibility by analyzing DNA from the jawbone. Trace amounts of ancient DNA can be recovered from bones as old as the Oase jawbone, but to analyze it, that ancient DNA must be sifted out of an overwhelming amount of DNA from other organisms. When Qiaomei Fu, who was a graduate student in Pääbo's lab, obtained DNA from the bone, most of it was from microbes that lived in the soil where the bone was found. Of the fraction of a percent that was human DNA, most had been introduced by people who handled the bone after its discovery.

Using methods pioneered in Pääbo's lab, Fu enriched the proportion of human DNA in the sample, using genetic probes to retrieve pieces of DNA that spanned any of 3.7 million positions in the human genome that are considered useful in evaluating variation between human populations. Most of the DNA she ended up with was human, but came from people who had handled the jawbone since 2002, rather than the jawbone itself. Fu, who is now a postdoctoral researcher in Reich's group, solved that problem by restricting her analysis to DNA with a kind of damage that deteriorates the molecule over tens of thousands of years.

Once they had discarded the contaminating DNA, Reich's team could compare the fossil's genome to genetic data from other groups. Through a series of statistical analyses, a surprising conclusion emerged. "The sample is more closely related to Neanderthals than any other modern human we've ever looked at before," Reich says. "We estimate that six to nine percent of its genome is from Neanderthals. This is an unprecedented amount. Europeans and East Asians today have more like two percent."

That suggested the Oase individual's ancestry was recent. As DNA is passed on from generation to generation, segments are broken up and recombined, so that the DNA inherited from any one individual becomes interspersed with the DNA of other ancestors. Reich found segments of intact Neanderthal DNA in the fossil that were large enough to indicate that the Oase individual had a Neanderthal ancestor just four to six generations back. That suggests that modern humans interbred with Neanderthals after they had arrived in Europe.

"It's an incredibly unexpected thing," Reich says. "In the last few years, we've documented interbreeding between Neanderthals and modern humans, but we never thought we'd be so lucky to find someone so close to that event."

The Oase individual is not responsible for passing his Neanderthal ancestry on to present day humans, however. Reich found no evidence that he is closely related to later Europeans. "This sample, despite being in Romania, doesn't yet look like Europeans today," he says. "It is evidence of an initial modern human occupation of Europe that didn't give rise to the later population. There may have been a pioneering group of modern humans that got to Europe, but was later replaced by other groups."

Thursday, June 18, 2015

Kennewick Man closely related to Native Americans, geneticists say

DNA from the 8,500-year-old skeleton of an adult man found in 1996, in Washington, is more closely related to Native American populations than to any other population in the world, according to an international collaborative study conducted by scientists at the University of Copenhagen and the Stanford University School of Medicine.

The finding challenges a 2014 study that concluded, based on anatomical data, that Kennewick Man was more related to indigenous Japanese or Polynesian peoples than to Native Americans. The study is likely to reignite a long-standing legal dispute regarding the skeleton's provenance and its eventual fate.

"Using ancient DNA, we were able to show that Kennewick Man is more closely related to Native Americans than any other population," said postdoctoral scholar Morten Rasmussen, PhD. "Due to the massive controversy surrounding the origins of this sample, the ability to address this will be of interest to both scientists and tribal members."

Rasmussen is the lead author of the research, published online June 17 in Nature. The senior author of the study is Eske Willerslev, PhD, from the University of Copenhagen's Centre for GeoGenetics. Rasmussen initiated the study at the Centre for GeoGenetics and completed the analysis of the DNA sequences at Stanford, working with Carlos Bustamante, PhD, professor of genetics.

The skeleton, known as Kennewick Man, is called the Ancient One by Native American groups, which believe the bones are those of a long-ago ancestor. In 2004, five Native American tribes of the Pacific Northwest requested repatriation of the remains for reburial, but the proceedings were halted to allow further investigation into the skeleton's origins.

Bits of ancient DNA

Now an exhaustive genetic study of the tiny bits of ancient DNA from a bone in the skeleton's hand refutes the conclusions of the 2014 study. The researchers used the latest in DNA isolation and sequencing techniques to pick out and analyze the skeleton's DNA.

"Although the exterior preservation of the skeleton was pristine, the DNA in the sample was highly degraded and dominated by DNA from soil bacteria and other environmental sources," said Rasmussen. "With the little material we had available, we applied the newest methods to squeeze every piece of information out of the bone."

The researchers compared the DNA sequences from the skeleton with those of modern Native Americans. They concluded that, although it is impossible to assign Kennewick Man to a particular tribe, he is closely related to members of the Confederated Tribes of the Colville Reservation in Washington.

Willerslev and Bustamante are well-known for their studies of ancient DNA. Willerslev and Rasmussen recently published the genome of a young child, known as the Anzick boy, buried more than 12,000 years ago in Montana. That study showed that the boy was also closely related to modern Native American groups, in particular those of South and Central America. In 2012, Bustamante and colleagues used DNA from the 5,300-year-old Iceman mummy called Otzi to show the man likely hailed from the Mediterranean island of Sardinia rather than the frigid Alps, where his body was found.

"Advances in DNA sequencing technology have given us important new tools for studying the great human diasporas and the history of indigenous populations," said Bustamante. "Now we are seeing its adoption in new areas, including forensics and archeology. The case of Kennewick Man is particularly interesting given the debates surrounding the origins of Native American populations. Morten's work aligns beautifully with the oral history of native peoples and lends strong support for their claims. I believe that ancient DNA analysis could become standard practice in these types of cases since it can provide objective means of assessing both genetic ancestry and relatedness to living individuals and present-day populations."

A Rare Inscription from the Time of King David was Discovered in the Valley of Elah

Photographic credit: Tal Rogovsky

A rare inscription from the time of King David was discovered at Khirbet Qeiyafain the Valley of Elah. A ceramic jar c. 3,000 years old that was broken into numerous sherds was discovered in 2012 in excavations carried out there by Prof. Yosef Garfinkel of the Institute of Archaeology of the Hebrew University and Saar Ganor of the Israel Antiquities Authority. Letters written in ancient Canaanite script could be discerned on several of the sherds, sparking the curiosity of researchers.

Intensive restoration work conducted in the laboratories of the Israel Antiquities Authority Artifacts Treatment Department, during which hundreds of pottery sherds were glued together to form a whole jar, solved the riddle – the jar was incised with the inscription: Eshbaʽal Ben Badaʽ. Dr. Mitka Golub and Dr. Haggai Misgav were among the team of researchers involved in deciphering the text.

According to Professor Yosef Garfinkel of the Institute of Archaeology of the Hebrew University and Saar Ganor of the IAA, "This is the first time that the name Eshbaʽal has appeared on an ancient inscription in the country. Eshbaʽal Ben Shaul, who ruled over Israel at the same time as David, is known from the Bible. Eshbaʽal was murdered by assassins and decapitated and his head was brought to David in Hebron (II Samuel, Chaps. 3-4).

It is interesting to note that the name Eshbaʽal appears in the Bible, and now also in the archaeological record, only during the reign of King David, in the first half of the tenth century BCE. This name was not used later in the First Temple period.The correlation between the biblical tradition and the archaeological finds indicates this was a common name only during that period. The name Bedaʽ is unique and does not occur in ancient inscriptions or in the biblical tradition."

According to the researchers, the fact that the name Eshbaʽal was incised on a jar suggests that he was an important person. He was apparently the owner of a large agricultural estate and the produce collected there was packed and transported in jars that bore his name. This is clear evidence of social stratification and the creation of an established economic class that occurred at the time of the formation of the Kingdom of Judah.

Garfinkel and Ganor add, "In II Samuel there was apparently reluctance to use the name Eshbaʽal, which was reminiscent of the Canaanite storm god Baʽal, and the original name was therefore changed to Ish-Bashat, but the original name of Eshbaʽal was preserved in the Book of Chronicles.  Thus, for example, the name of the warlord Gideon Ben Joash was also changed from Jerrubaal to Jerubesheth."

 Khirbet Qeiyafais identified with the biblical city Shaʽarayim. During several seasons of excavations directed by Prof. Yosef Garfinkel and Saar Ganor, a fortified city, two gates, a palace and storerooms, dwellings and cultic rooms were exposed there. The city dates from the time of David, that is, the late eleventh and early tenth centuries BCE. Unique artifacts that were previously unknown were discovered at the site. For example, in 2008 the world’s earliest Hebrew inscription was uncovered there. Now, another inscription from the same period is being published from the site.

 According to Garfinkel and Ganor,"Until about five years ago we knew of no inscriptions dating to the tenth century BCE from the Kingdom of Judah. In recent years four inscriptions have been published: two from Khirbet Qeiyafa, one from Jerusalem and one from Bet Shemesh. This completely changes our understanding of the distribution of writing in the Kingdom of Judah and it is now clear that writing was far more widespread than previously thought. It seems that the organization of the kingdom required a cadre of clerks and writers and their activity is also manifested in the appearance of inscriptions. "

Wednesday, June 17, 2015

Direct evidence of what early Palaeolithic people ate and the quality of the air they breathed

Most dentists recommend a proper teeth cleaning every six months to prevent, among other things, the implacable buildup of calculus or tartar -- hardened dental plaque. Routine calculus buildup can only be removed through the use of ultrasonic tools or dental hand instruments. But what of 400,000-year-old dental tartar?

Tel Aviv University researchers, in collaboration with scholars from Spain, the U.K. and Australia, have uncovered evidence of food and potential respiratory irritants entrapped in the dental calculus of 400,000-year-old teeth at Qesem Cave near Tel Aviv, the site of many major discoveries from the late Lower Paleolithic period. The research provides direct evidence of what early Palaeolithic people ate and the quality of the air they breathed inside Qesem Cave.

Possible respiratory irritants, including traces of charcoal found in the dental calculus, may have resulted from smoke inhalation from indoor fires used for roasting meat on a daily basis. This earliest direct evidence for inhaled environmental pollution may well have had a deleterious effect on the health of these early humans.

"Human teeth of this age have never been studied before for dental calculus, and we had very low expectations because of the age of the plaque," said Prof. Gopher. "However, our international collaborators, using a combination of methods, found many materials entrapped within the calculus. Because the cave was sealed for 200,000 years, everything, including the teeth and its calculus, were preserved exceedingly well."

In what Prof. Barkai describes as a "time capsule," the analysed calculus revealed three major findings: charcoal from indoor fires; evidence for the ingestion of essential plant-based dietary components; and fibers that might have been used to clean teeth or were remnants of raw materials.

"Prof. Karen Hardy published outstanding research on the dental calculus of Neanderthals from El Sidron cave in Spain, but these dated back just 40,000-50,000 years -- we are talking far earlier than this," said Prof. Barkai.

"This is the first evidence that the world's first indoor BBQs had health-related consequences," said Prof. Barkai. "The people who lived in Qesem not only enjoyed the benefits of fire -- roasting their meat indoors -- but they also had to find a way of controlling the fire -- of living with it.

"This is one of the first, if not the first, cases of manmade pollution on the planet. I live near power plants, near chemical factories. On the one hand, we are dependent on technology, but on the other, we are inhaling its pollutants. Progress has a price -- and we find possibly the first evidence of this at Qesem Cave 400,000 years ago."

The researchers also found minute traces of essential fatty acids, possibly from nuts or seeds, and small particles of starch in the analysed calculus. "We know that the cave dwellers ate animals, and exploited them entirely," said Prof. Barkai. "We know that they hunted them, butchered them, roasted them, broke their bones to extract their marrow, and even used the butchered bones as hammers to shape flint tools. Now we have direct evidence of a tiny piece of the plant-based part of their diet also, in addition to the animal meat and fat they consumed.

"We have come full circle in our understanding of their diet and hunting and gathering practices."

Within the calculus, the researchers also discovered small plant fibers, which they suspect may have been used to clean teeth -- prehistoric tooth picks.

"Our findings are rare -- there is no other similar discovery from this time period," said Prof. Barkai. "The charcoal and starch findings give us a more comprehensive idea of how these people lived their lives -- and this broader view came directly from their teeth."

Thursday, June 11, 2015

When modern Eurasia was born

Was it a massive migration? Or was it rather a slow and persistent seeping of people, items and ideas that laid the foundation for the demographic map of Europe and Central Asia that we see today? The Bronze Age (about 5,000 - 3,000 years ago) was a period with large cultural upheavals. But just how these upheavals came to be have remained shrouded in mystery.

Assistant Professor Morten Allentoft from the Centre for GeoGenetics at the Natural History Museum of Denmark at the University of Copenhagen is a geneticist and is first author on the paper in Nature. He says:

- Both archaeologists and linguists have had theories about how cultures and languages have spread in our part of the world. We geneticists have now collaborated with them to publish an explanation based on a record amount of DNA-analyses of skeletons from the Bronze Age.

So far the archaeologists have been divided into two different camps. Professor Kristian Kristiansen of the University of Gothenburg, who initiated the project together with Lundbeck Foundation Professor Eske Willerslev says:

- The driving force in our study was to understand the big economical and social changes that happened at the beginning of the third millennium BC, spanning the Urals to Scandinavia. The old Neolithic farming cultures were replaced by a completely new perception of family, property and personhood. I and other archaeologists share the opinion that these changes came about as a result of massive migrations.

With this new investigation the researchers confirm that the changes came about as a result of migrations. The researchers think that this is interesting also because later developments in the Bronze Age are a continuation of this new social perception. Things add up because the migrations can also explain the origin of the northern European language families. Both language and genetics have been with us all the way up to the present. Kristian Kristiansen even thinks that it was crucial events that happened during these few centuries, as crucial as the colonization of the Americas.

One of the main findings from the study is how these migrations resulted in huge changes to the European gene-pool, in particular conferring a large degree of admixture on the present populations. Genetically speaking, ancient Europeans from the time post these migrations are much more similar to modern Europeans than those prior the Bronze Age.

Mobile warrior people

The re-writing of the genetic map began in the early Bronze Age, about 5,000 years ago. From the steppes in the Caucasus, the Yamnaya Culture migrated principally westward into North- and Central Europe, and to a lesser degree, into western Siberia. Yamnaya was characterized by a new system of family and property. In northern Europe the Yamnaya mixed with the Stone Age people who inhabited this region and along the way established the Corded Ware Culture, which genetically speaking resembles present day Europeans living north of the Alps today.

Later, about 4,000 years ago the Sintashta Culture evolved in the Caucasus. This culture's sophisticated new weapons and chariots were rapidly expanding across Europe. The area east of the Urals and far into Central Asia was colonized around 3,800 years ago by the Andronovo Culture. The researchers' investigation shows that this culture had a European DNA-background.

During the last part of the Bronze Age, and at the beginning of the Iron Age, East Asian peoples arrived in Central Asia. Here it is not genetic admixture we see, but rather a replacement of genes. The European genes in the area disappear.

A new scale

These new results derive from DNA-analyses of skeletons excavated across large areas of Europe and Central Asia, thus enabling these crucial glimpses into the dynamics of the Bronze Age. In addition to the population movement insights, the data also held other surprises. For example, contrary to the research team's expectations, the data revealed that lactose tolerance rose to high frequency in Europeans, in comparison to prior belief that it evolved earlier in time (5,000 - 7,000 years ago). Co-author and Associate Professor Martin Sikora from the Centre for GeoGenetics says:

- Previously the common belief was that lactose tolerance developed in the Balkans or in the Middle East in connection with the introduction of farming during the Stone Age. But now we can see that even late in the Bronze Age the mutation that gives rise to the tolerance is rare in Europe. We think that it may have been introduced into Europe with the Yamnaya herders from Caukasus but that the selection that has made most Europeans lactose tolerant has happened at a much later time.

The paper in Nature not only gives us a new glimpse into the Bronze Age. It is also the first time an actual population evolutionary study back in time has been made to this extent. Geneticist and director of the Centre for GeoGenetics Eske Willerslev elaborates:

- Our study is the first real large-scale population genomic study ever undertaken on ancient individuals. We analysed genome sequence data from 101 past individuals. This is more than a doubling of the number of genomic sequenced individuals of pre-historic man generated to date. The study is without any comparison to anything previously made. The results show that the genetic composition and distribution of peoples in Europe and Asia today is a surprisingly late phenomenon - only a few thousand years old.