Ancient DNA reveals genetic replacement despite language continuity in the South Pacific

New genetic research reveals the complex demographic history of Vanuatu, explaining how Austronesian languages were retained throughout its history despite near-total replacement of early Austronesian-Lapita with Papuan ancestry

Young men in canoes in Northwest Malakula, Vanuatu [Credit: Russell Gray & Heidi Colleran]

The study, published in Nature Ecology & Evolution and led by a multidisciplinary research team at the Max Planck Institute for the Science of Human History (MPI-SHH) together with researchers in France, Australia, New Zealand, Germany and Vanuatu, reveals that migrations of people from the Bismarck Archipelago in Oceania to the previously settled islands of the Pacific began as early as 2,500 years ago, much earlier than previously thought. The Remote Oceanian island nation of Vanuatu is the gateway to the rest of the Pacific and understanding its demographic history is critical to uncovering that of the wider region.

The earliest inhabitants of Vanuatu, arriving about 3,000 years ago, were the Lapita peoples who spoke a form of Austronesian language and who had largely East Asian genetic ancestry. But Vanuatu's contemporary population has largely Near Oceanian heritage, showing that over time the genetic ancestry of the early inhabitants was mostly replaced by that of Bismarck Archipelago migrants, who began arriving very soon after initial settlement. Yet the original Austronesian language persisted and over 120 descendant languages continue to be spoken today, making Vanuatu the per capita most linguistically diverse place on Earth.

Vanuatu therefore presents an unprecedented case, where a population's genetic ancestry but not its languages were replaced. Through analyses of new ancient and modern genome-wide data, the researchers show that rather than occurring in one wave, the genetic replacement was long and complex, likely the result of a sustained long-distance contact between Near and Remote Oceania. This provides demographic support for a model from historical linguistics, in which the initial Austronesian language of Vanuatu survived by being continually adopted by incoming Papuan migrants.

The Austronesian Expansion, which began around 5,500 years ago likely in modern-day Taiwan, was the most geographically extensive dispersal of farming peoples in prehistory, ultimately carrying people as far west as Madagascar and all the way east to Rapa Nui. These seafaring Neolithic people initially expanded out across Island Southeast Asia, carrying farming technology and a major branch of the Austronesian language family, eventually reaching Near Oceania where they encountered the indigenous Papuan peoples of New Guinea and the Bismarck Archipelago.

Dr. Frédérique Valentin excavating at Uripiv Island, Malakula, Vanuatu [Credit: Stuart Bedford]

The initial settlement east beyond the Solomon Islands and out into Remote Oceania only began around 3,000 years ago, with Austronesian-speaking groups associated with the Lapita pottery culture rapidly expanding east out to Vanuatu, New Caledonia, Fiji and the islands of Western Polynesia. A previous ancient DNA study of Lapita burial sites has shown that these earliest inhabitants had East Asian ancestry with negligible evidence of Papuan genetic admixture. But the present-day genetic make-up of Remote Oceania suggests at least some degree of Papuan ancestry, meaning there must have been subsequent Papuan migration and admixture into the Pacific from Near Oceania.

In order to understand this previously undescribed migration, a multidisciplinary team of researchers brought together different lines of evidence from the fields of genetics, archaeology and linguistics. They generated genome-wide data from the bones and teeth of 19 ancient individuals from across Vanuatu, Tonga, French Polynesia and the Solomon Islands, a significant addition to the ancient DNA record in a region whose environmental conditions generally leads to poor ancient DNA preservation.

As co-lead author Kathrin Nägele of the MPI-SHH says, "The identification of the petrous bone, which has recently been shown to provide fantastic aDNA preservation, has been a real game changer for such regions that were previously considered to be almost inaccessible." The ancient DNA was complemented by new contemporary genome-wide data from 27 present-day inhabitants of Vanuatu, collected as part of a long-term linguistic and anthropological fieldwork project run by co-authors Professor Russell Gray and Dr. Heidi Colleran of the MPI-SHH.

The ancient DNA provided direct evidence that Papuan people began arriving in Vanuatu soon after initial settlement by Austronesians. "We found a genetically Papuan-related individual dating to around 2,500 years ago in Vanuatu, far earlier than had been previously estimated using only modern genetic data," explains co-lead author Dr. Cosimo Posth, also of the MPI-SHH. The researchers were able to show that the ancestry of the initial Austronesian inhabitants of Vanuatu has been largely replaced by ancestry from Papuan peoples coming from the Bismarck Archipelago.

Maps showing the migrations in the area, including, in the final map, the migrations
 revealed by the current study [Credit: Hans Sell, adapted from Skoglund et al. Genomic
insights into the peopling of the Southwest Pacific. Nature (2016)]

But this genetic replacement was not straightforward, as Dr. Posth says, "Our analyses show that this replacement did not occur in a one-time mass migration event but rather happened incrementally over time, suggesting an enduring long-distance network between groups in Near and Remote Oceania." The authors also directly described ancient individuals with sex-biased admixture, where Papuan males intermixed with Austronesian women, as long assumed based on analyses of the modern genetic make-up of the South Pacific.

Yet despite this genetic replacement, the people of present-day Vanuatu continue to speak languages descended from those spoken by the initial Austronesian inhabitants rather than any Papuan language of the incoming migrants. As Professor Gray, Director of the Department of Linguistic and Cultural Evolution at the MPI-SHH, says, "Population replacement with language continuity is extremely rare -- if not unprecedented -- in human history.

The linguist Bob Blust has long argued for a model in which a separate Papuan expansion reaches Vanuatu soon after initial Austronesian settlement, with the initial, and likely undifferentiated, Austronesian language surviving as a lingua franca for diverse Papuan migrant groups." Dr. Adam Powell, senior author of the study and also of the MPI-SHH, continues, "The demographic history suggested by our ancient DNA analyses provides really strong support for this historical linguistic model, with the early arrival and complex, incremental process of genetic replacement by people from the Bismarck Archipelago. This provides a compelling explanation for the continuity of Austronesian languages despite the almost complete replacement of the initial genetic ancestry of Vanuatu."

The study in particular highlights the importance of interdisciplinary work and the value that multiple lines of evidence can have in deepening our understanding of human history. As Professor Johannes Krause, a senior author and Director of the Department of Archaeogenetics at the MPI-SHH, explains, "This multidisciplinary work has begun to uncover the complex, localized demographic processes that drove the initial colonization of the wider South Pacific and formed the enduring cultural and linguistic spheres that continue to shape the Pacific today." Ongoing engagement with local communities in Vanuatu, as well as with the Vanuatu Cultural Center, has been critical to this success.

As Dr. Colleran points out, "One strength of this study is the degree to which we are collaborating with communities in Vanuatu who have a real stake in these results and who generously volunteered their data to help answer these questions. We will be back in the field very soon to share the results with those communities and to hear their thoughts on the whole process." The progress of this continuing fieldwork can be followed on the Nature Ecology & Evolution Community website.

Source: Max Planck Institute for the Science of Human History [February 27, 2018]

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Researchers sequence complete genomes of extinct and living elephants

An international team of researchers has produced one of the most comprehensive evolutionary pictures to date by looking at one of the world's most iconic animal families - namely elephants, and their relatives mammoths and mastodons-spanning millions of years.

Crushed dentine from a Woolly Mammoth for DNA extraction [Credit: JD Howell, McMaster University]

The team of scientists-which included researchers from McMaster, the Broad Institute of MIT and Harvard, Harvard Medical School, Uppsala University, and the University of Potsdam-meticulously sequenced 14 genomes from several species: both living and extinct species from Asia and Africa, two American mastodons, a 120,000-year-old straight-tusked elephant, and a Columbian mammoth.

The study, published in the Proceedings of the National Academy of Science, sheds light on what scientists call a very complicated history, characterized by widespread interbreeding. They caution, however, the behaviour has virtually stopped among living elephants, adding to growing fears about the future of the few species that remain on earth.

"Interbreeding may help explain why mammoths were so successful over such diverse environments and for such a long time, importantly this genomic data also tells us that biology is messy and that evolution doesn't happen in an organized, linear fashion," says evolutionary geneticist Hendrik Poinar, one of the senior authors on the paper and Director of the McMaster Ancient DNA Centre and principal investigator at the Michael G. DeGroote Institute for Infectious Research.

"The combined analysis of genome-wide data from all these ancient elephants and mastodons has raised the curtain on elephant population history, revealing complexity that we were simply not aware of before," he says.

Graduate student Emil Karpinski holds a tibial cross section from a Siberian Woolly Mammoth. This permafrost
preserved sample still contains fat entombed marrow [Credit: JD Howell, McMaster University]

A detailed DNA analysis of the ancient straight-tusked elephant, for example, showed that it was a hybrid with portions of its genetic makeup stemming from an ancient African elephant, the woolly mammoth and present-day forest elephants.

"This is one of the oldest high-quality genomes that currently exists for any species," said Michael Hofreiter at the University of Potsdam in Germany, a co-senior author who led the work on the straight-tusked elephant.

Researchers also found further evidence of interbreeding among the Columbian and woolly mammoths, which was first reported by Poinar and his team in 2011. Despite their vastly different habitats and sizes, researchers believe the woolly mammoths, encountered Columbians mammoths at the boundary of glacial and in the more temperate ecotones of North America.

Strikingly, scientists found no genetic evidence of interbreeding among two of the world's three remaining species, the forest and savanna elephants, suggesting they have lived in near-complete isolation for the past 500,000 years, despite living in neighbouring habitats.

These are African savanna elephants in the San Diego Zoo. In the middle is Swazi, the female elephant from
which the reference genome was sequenced [Credit: San Diego Zoo Global]

"There's been a simmering debate in the conservation communities about whether African savannah and forest elephants are two different species," said David Reich, another co-senior author at the Broad Institute who is also a professor at the Department of Genetics at Harvard Medical School (HMS) and a Howard Hughes Medical Institute Investigator. "Our data show that these two species have been isolated for long periods of time - making each worthy of independent conservation status."

Interbreeding among closely related mammals is fairly common, say researchers, who point to examples of brown and polar bears, Sumatran and Bornean orangutans, and the Eurasian gold jackal and grey wolves. A species can be defined as a group of similar animals that can successfully breed and produce fertile offspring.

"This paper, the product of a grand initiative we started more than a decade ago, is far more than just the formal report of the elephant genome. It will be a reference point for understanding how diverse elephants are related to each other and it will be a model for how similar studies can be done in other species groups," said co-senior author Kerstin Lindblad-Toh, a senior associate member of the Broad Institute and Director of the Science for Life Laboratory at Uppsala University in Sweden.

"The findings were extremely surprising to us," says Eleftheria Palkopoulou, a post-doctoral scientist in at HMS. "The elephant population relationships could not be explained by simple splits, providing clues for understanding the evolution of these iconic species."

Researchers suggest that future work should explore whether the introduction of new genetic lineages into elephant populations-both living and ancient-played an important role in their evolution, allowing them to adapt to new habitats and fluctuating climates.

Source: McMaster University [February 26, 2018]

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Geological change confirmed as a factor behind the extensive diversity in tropical rainforests

The tropical rainforests of Central and South America are home to the largest diversity of plants on this planet. Nowhere else are there quite so many different plant species in one place. However, the entire region is increasingly threatened by human activity, which is why researchers are stepping up their efforts to record this astonishing biodiversity and find out how it developed. In a project undertaken by Johannes Gutenberg University Mainz (JGU) in collaboration with Dutch research institutions, the causes of this plant diversity were investigated by studying two closely related groups of trees of the Annonaceae family.

Cremastosperma brevipes, French Guiana [Credit: Paul J. M. Maas]

The researchers identified three relevant factors: the formation of the Andes mountain range, the disappearance due to natural causes of the extensive Pebas wetlands system that once existed in the Amazon region, and the formation of a land bridge between Central and South America in the form of the Panama Isthmus.

Cremastosperma and Mosannona are two genera of the Annonaceae or custard apple family the habitat of which is neotropical rainforests, where they extend from the lowlands up to elevations of 2,000 meters. They are primarily found in the Andes region of South America, but also as far north as Central America.

Mosannona costaricensis, Costa Rica [Credit: Reinaldo Aguilar]

The team of botanists led by Dr. Michael Pirie, who joined JGU as a researcher in 2013, looked at the distributions of the various species of both genera and their phylogenetic history in order to determine the influence of the geological upheavals on the continent.

For this purpose they compiled a time-calibrated phylogenetic tree based on DNA data, using the so-called molecular clock technique which is calibrated using the ages of the available fossils. In total, they analyzed 11 species of the genus Mosannona and 24 species of the genus Cremastosperma.

Formation of the Andes, the Isthmus of Panama, and the drying-out of the Pebas wetland system all promoted diversification

The research has produced a biogeographical scenario that confirms in this context the significance of the geological history of north-western South America during the late Miocene and early Pliocene periods about 5 to 10 million years ago.

Cremastosperma yamayakatense, Peru [Credit: Michael Pirie]

"We have actually discovered that the diversification of these two plant genera took place in parallel with major geological events, namely the formation of the Andes, the drying-out of the Pebas system, and the development of a land bridge to Central America," explained Pirie. Cremastosperma species, for example, were able to spread into what is today the Amazon basin and diversify, once the wetlands had silted up due to the deposition of material from the rising Andes.

One way in which diversification can be stimulated is by migration into a new ecosystem while another is adaptation to new conditions. "Natural changes over longer periods provide plants with a chance to adapt," added Pirie. On the other hand, rapid changes, such as those that have occurred in the recent past, do not give plants sufficient time to evolve.

Cremastosperma leiophyllum, Bolivia [Credit: Lars W. Chatrou]

While the development of the two genera in line with geological conditions could be said to be more or less as might be expected, the biologists did find one clear difference between them. Although their distribution patterns mostly overlap, Cremastosperma species and Mosannona species to some extent dispersed along differing routes. In the case of Cremastosperma, colonization of an area in what is now Guyana began from north-western South America at a time before the last parts of the Andes developed and could form a barrier. Mosannona, on the other hand, began to spread here at a far later date from its base in the Amazon basin.

Taxonomic update to include five new species

Dr. Michael Pirie will be continuing his research work in 2018 with the aid of a grant from the Heisenberg Program of the German Research Foundation (DFG). This will also involve publication of an extensive monograph in which a total of 34 Cremastosperma species will be described, including five new species that Pirie and his colleagues have recently discovered.

The study is published on Royal Society Open Science.

Source: Universitat Mainz [Febraury 26, 2018]

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Ancient DNA study reveals the prehistory of Southeastern Europe

In an ancient DNA study published this week in the journal Nature, scientists and archaeologists from over 80 different institutions lift the veil on the genomic history of Southeastern Europe, a region from which very little ancient genetic data has been available until now. This is the second-largest ancient DNA study ever reported. (The largest, reported simultaneously in Nature by many of the same authors, focuses on the prehistory of Northwestern Europe.)

The burial fields of Varna, Bulgaria, is famous for its rich burial gifts. In one of the 6,500 year old graves more gold was
found than in all other graves at this time. Genetic examinations show that the DNA of the man buried there had similiarities
with the DNA of earlier European famers [Credit: © I, Yelkrokoyade, commons.wikimedia.org, CC BY-SA 3.0]

Starting around 8,500 years ago, agriculture spread into Europe from the southeast, accompanied by a movement of people from Anatolia. This study reports data from the genomes of 225 ancient people who lived both before and after this transition, and documents the interaction and mixing of these two genetically different groups of people. “Southeastern Europe was the beachhead in the spread of farming from Anatolia into Europe. This study is the first to provide a rich genetic characterization of this process by showing how the indigenous population interacted with incoming Asian immigrants at this extraordinary moment in the past,” says Songül Alpaslan-Roodenberg, a consulting anthropologist at Harvard Medical School, who identified and sampled many of the skeletons.

“In some places, hunter-gatherers and incoming farmers seem to have mixed very quickly,” says first author Iain Mathieson, a geneticist at the University of Pennsylvania, “but mostly the two groups remained isolated, at least for the first few hundred years. These hunter-gatherers had been living there for thousands of years, and it must have been quite a shock to have these new people show up—with a completely different lifestyle and appearance.”

“Three thousand years later, they were thoroughly mixed,” continues David Reich of Harvard Medical School, the Broad Institute of MIT and Harvard and the Howard Hughes Medical Institute, who co-directed the study. “Some populations derived up to a quarter of their ancestry from hunter-gatherers.” In other parts of Europe, this mixing was marked by a so-called sex bias, with most of the hunter-gatherer ancestry contributed by men. In the southeast, however, the pattern was different. “This shows that the mode of interaction between the two groups was different in different places, something we need to try to understand in the context of the archaeological evidence,” added Mathieson.

The new paper also dramatically increases the number of samples from the population of hunter-gatherers that inhabited Europe before the farmers. The study reports a particularly rich sampling of forty hunter-gatherers and early farmers from six archaeological sites from the Iron Gates region, which straddles the border of present-day Romania and Serbia. The genetic results show that the region witnessed intensive interaction between hunter-gatherers and farmers. Out of four individuals from the site of Lepenski Vir, for example, two had entirely Anatolian farmer-related ancestry, fitting with isotope evidence that they were migrants from outside the Iron Gates region, while a third individual had a mixture of ancestries and consumed aquatic resources, as expected if farmers were being integrated into hunter-gatherer groups or were adopting a hunter-gatherer lifestyle.

“These results reveal the relationship between migrations, admixture and subsistence in the this key region and show that even within early European farmers, individuals differed in their ancestry, reflecting a dynamic mosaic of hunter-farmer interbreeding,” adds Ron Pinhasi, an anthropologist at the University for Vienna, who co-directed the study.

The new paper also reports ancient DNA from the people who lived at iconic archaeological sites such as Varna, one of the first places in the world where there is evidence of extreme wealth inequality, with one individual from whom the study obtained data buried with more gold than all other known burials of the period. “The DNA from the famous Varna burial is genetically similar to that of other early European farmers. However, we also find one individual from Varna and several individuals at neighboring sites in Bulgaria who had ancestry from the eastern European steppe. This is the earliest evidence of steppe ancestry this far west—two thousand years before the mass migration from the steppe that replaced more than half of the population of northern Europe,” says Johannes Krause, Director of the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History, who led the work on Varna.

Adds Reich, “These very large ancient DNA studies, involving intense collaboration between geneticists and archaeologists, make it possible to build up a rich picture of key periods of the past that could only be weakly glimpsed before. Studies on this scale represent a coming of age for the field of ancient DNA—I look forward to what we will learn when similar approaches are applied elsewhere in the world.”

Source: Max-Planck-Gesellschaft [February 23, 2018]

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Why are there so many types of lizards?

Lizards have special superpowers. While birds can regrow feathers and mammals can regrow skin, lizards can regenerate entire structures such as their tails. Despite these differences, all have evolved from the same ancestor as lizards.

The Anolis auratus is one of several lizard species studied as part of new research comparing lizard genomes - their entire
DNA code - to those of other animals [Credit: Kenro Kusumi]

Spreading through the Americas, one lizard group, the anoles, evolved like Darwin's finches, adapting to different islands and different habitats on the mainland. Today there are more than 400 species.

Constructing a family tree for three lizard species collected in Panama at the Smithsonian Tropical Research Institute (STRI) and a fourth from the southeastern U.S., scientists at Arizona State University compared lizard genomes -- their entire DNA code -- to those of other animals.

The researchers discovered that changes in genes involved in the interbrain (the site of the pineal gland and other endocrine glands), for color vision, hormones and the colorful dewlap that males bob to attract females, may contribute to the formation of boundaries between species. Genes regulating limb development also evolved especially quickly.

"While some reptiles such as tortoises changed remarkably little over millions of years, anole lizards evolved quickly, generating a diversity of shapes and behaviors," said Kenro Kusumi, corresponding author and professor at ASU School of Life Sciences. "Now that sequencing entire genomes is cheaper and easier, we discovered molecular genetic evidence for rapid evolution that may account for striking differences between bodies of animals living in different environments."

Kusumi's lab, working with colleagues at the University of Arizona College of Medicine-Phoenix, is especially interested in how reptiles' genomes shape their ability to regenerate and to develop a diversity of body forms.

"This is the first time the complete genetic code -- the genome -- of any vertebrate species from Panama has been sequenced and analyzed," said Oris Sanjur, co-author and Associate Director for Science Administration at STRI. "Information from these three species is an important contribution to our understanding of biodiversity and the evolution of new species."

The Anolis apletophallus is one of several lizard species studied as part of new research comparing lizard genomes - their
entire DNA code - to those of other animals [Credit: Kenro Kusumi]

Scientists estimate that there are 40 species of anolid lizards living in Panama, compared to only one in the U.S. A team from ASU collected three species with permission from the Ministry of the Environment, MiAmbiente: the Central American giant anole, Anolis frenatus, lives high on tree trunks; the grass anole, A. auratus, perches on bushes or on grassy vegetation and the slender anole, A. apletophallus, found only in Panama, hangs out lower on tree trunks or on the ground.

Researchers at ASU's School of Life Sciences lined up the DNA sequences of the lizards with the DNA sequences of 31 other animals: the lobe-finned fish and the four-legged animal groups that evolved from them. They also took a careful look at genes that code for proteins: more than 22,000 genes in the green anole, A. carolinensis, versus approximately 20,000 identified each in A. auratus and A. frenatus and 13,000 in A. apletophallus.

One obvious explanation for a faster rate of evolution is the anole lizards' faster rate of reproduction. Anoles typically mate in their first year of life, while other reptiles take much longer to reach sexual maturity. They also breed with many other individuals so mutations that make it difficult for individuals to survive are eliminated fairly quickly.

The first and only other anole lizard to be sequenced previously was the green anole, A. carolinensis, the only anole species resident in the U.S. In that study from MIT, the A. carolinensis genome held evidence of more recent evolution and the loss of ancient repeated elements in the part of the DNA that does not code for proteins. In this sense, it was important to sequence the three Panamanian species, because the U.S. species may not be the most representative of the diverse anole group.

"For 15 years, an impressive amount of time and money poured into discovering the genomes of mammals, motivated by our drive to understand human evolution and to look for cures for disease. Even though the squamate reptiles include more than 10,000 species -- almost double the number of mammal species -- a single genome was not enough to understand the variability within this group," said the first author of the report, Marc Tollis, a post-doctoral fellow at ASU.

"By comparing these four anole lizard genomes, we're beginning to understand how one of the most diverse groups of vertebrates regenerate, develop and diversify," he added.

The study is published in Genome Biology and Evolution.

Source: Arizona State University [February 23, 2018]

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Pots, people and knowledge transfer

In the Late Neolithic, a new style of pottery appears among the grave goods buried with the dead in many parts of Europe. A new genetic study shows that, with one exception, its dissemination was not accompanied by large-scale migration.

"Das Bode-Becher" of Quedlinburg, Germany [Credit: K. Ulrich /Landesamt für Denkmalpflege
und Archäologie Sachsen-Anhalt]

At the end of the Neolithic, on the threshold to the Early Bronze Age, around 2600 BCE, a new set of religious beliefs began to spread across Europe. This is indicated in the archaeological record above else by the appearance of a novel form of pottery among the grave goods buried with the dead. These highly characteristic, decorated vessels are known as bell beakers, and their dissemination from Spain as far as Hungary, and across Northwestern Europe into Britain is known as the Bell Beaker phenomenon.

A team made up of geneticists and archaeologists has now explored whether the diffusion of these pots was driven by the influx of new migrants. Their findings appear in the latest issue of the journal Nature. The new study, for the first time, combines archaeological data relating to the distribution and ages of the Bell Beaker phenomenon in Europe with genetic analysis of human DNA sequences obtained from skeletal remains dated to the same period. This approach has enabled the team to compare the spread of the bell beakers (pots) with that of the migrants (people) who brought the new ideology. The results indicate that the diffusion of the pottery in continental Europe was not accompanied by large-scale migration.

"The study demonstrates that the spread of cultural elements need not involve migrational movements. In this case, it was the ideas that were propagated," says Professor Philipp Stockhammer of the Institute for Prehistoric and Protohistoric Archaeology at Ludwig-Maximilians-Universitaet (LMU) in Munich, one of the leading archaeologists among the authors. The results refute the long accepted theory that the spread of the new religion through Western and Central Europe was associated with significant incursions of migrants. Britain, however, represents a striking exception to this. Here, the appearance of the Bell Beaker phenomenon coincides with genetic evidence for the arrival of large numbers of migrants from continental Europe.

In the course of their investigation, the authors obtained DNA sequence data from 400 human skeletons, making it the largest study of ancient DNA carried out so far. This material had been excavated from 136 different sites, most of them in Britain, Spain and Germany. The new DNA samples from Germany originated from excavations carried out in the Valley of the River Lech. In a recent paper based on material from this area, Philipp Stockhammer reported evidence that reveals the surprising mobility of women in the Bronze Age.

"We will now have to compare these three regions in order to determine the degree of spatial variability in mobility across the transition from the Neolithic to the Early Bronze Age," he says. The ability to recover and analyze ancient DNA from human burials on such a large scale was made possible by the advent of new techniques. These advances will usher in "a new era in palaeogenetics," he adds.

Indeed, Stockhammer himself is among the authors of a second article in the same issue of Nature. This paper looks at the pattern of migration of farmers and herders from Anatolia into Southeastern Europe 8500 years ago. That study also uses ancient DNA to reveal how the resident hunter-gatherer population reacted to the arrival of the newcomers. In some areas the two groups lived together and in other regions, they avoided contact and lived apart for hundreds of years. In the Danube Valley, the evidence suggests that some of the new farming communities subsequently abandoned agriculture and adopted the hunter-gatherer lifestyle favored by the locals.

Source: Ludwig-Maximilians-Universitat Munchen [February 22, 2018]

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Surprising new study redraws family tree of domesticated and 'wild' horses

There are no such things as "wild" horses anymore. Research published in Science overturns a long-held assumption that Przewalski's horses, native to the Eurasian steppes, are the last wild horse species on Earth. Instead, phylogenetic analysis shows Przewalski's horses are feral, descended from the earliest-known instance of horse domestication by the Botai people of northern Kazakhstan some 5,500 years ago.

Thought to be the world's last-remaining 'wild' horse, Przewalski's horses actually descend from horses domesticated
by the Botai people about 5,500 years ago [Credit: Lee Boyd]

Further, the new paper finds that modern domesticated horses didn't descend from the Botai horses, an assumption previously held by many scientists.

"This was a big surprise," said co-author Sandra Olsen, curator-in-charge of the archaeology division of the Biodiversity Institute and Natural History Museum at the University of Kansas, who led archaeological work at known Botai villages. "I was confident soon after we started excavating Botai sites in 1993 that we had found the earliest domesticated horses. We went about trying to prove it, but based on DNA results Botai horses didn't give rise to today's modern domesticated horses -- they gave rise to the Przewalski's horse."

The findings signify there are no longer true "wild" horses left, only feral horses that descend from horses once domesticated by humans, including Przewalski's horses and mustangs that descend from horses brought to North America by the Spanish.

"This means there are no living wild horses on Earth -- that's the sad part," said Olsen. "There are a lot of equine biologists who have been studying Przewalskis, and this will be a big shock to them. They thought they were studying the last wild horses. It's not a real loss of biodiversity -- but in our minds, it is. We thought there was one last wild species, and we're only just now aware that all wild horses went extinct."

Some of the Botai horses were found to carry genetic variants causing white and leopard coat spotting patterns
[Credit: Ludovic Orlando, reworked by Sean Goddard and Alan Outram]

Many of the horse bones and teeth Olsen excavated at two Botai sites in Kazakhstan, called Botai and Krasnyi Yar, were used in the phylogenetic analysis. The international team of researchers behind the paper sequenced the genomes of 20 horses from the Botai and 22 horses from across Eurasia that spanned the last 5,500 years. They compared these ancient horse genomes with already published genomes of 18 ancient and 28 modern horses.

"Phylogenetic reconstruction confirmed that domestic horses do not form a single monophyletic group as expected if descending from Botai," the authors wrote. "Earliest herded horses were the ancestors of feral Przewalski's horses but not of modern domesticates."

Olsen said the findings give rise to a new scientific quest: locating the real origins of today's domesticated horses.

"What's interesting is that we have two different domestication events from slightly different species, or separate sub-species," she said. (The Przewalski's horse's taxonomic position is still debated.) "It's thought that modern-day domesticated horses came from Equus ferus, the extinct European wild horse. The problem is they were thought to have existed until the early 1900s. But, the remains of two individuals in St. Petersburg, Russia, are probably feral, too, or at least probably had some domesticated genes."

Olsen led excavation of Botai sites associated with the earliest-known domestication of horses
[Credit: Sandra Olsen]

Olsen began excavating Botai village sites in Kazakhstan in 1993 after the fall of the Soviet Union made the region accessible to western scientists. Some of the horse remains collected by Olsen were tested as part of the new study showing their ancestry of modern-day Przewalskis.

The Botai's ancestors were nomadic hunters until they became the first-known culture to domesticate horses around 5,500 years ago, using horses for meat, milk, work and likely transportation.

"Once they domesticated horses they became sedentary, with large villages of up to 150 or more houses," said Olsen, who specializes in zooarchaeology, or the study of animal remains from ancient human occupation sites. "They lived primarily on horse meat, and they had no agriculture. We had several lines of evidence that supported domestication. The fact the Botai were sedentary must have meant they had domesticated animals, or plants, which they didn't have. More than 95 percent of the bones from the Botai sites were from horses -- they were in a sense mono-cropping one species with an incredible focus. If they were hunting horses on foot, they would have quickly depleted bands of horses in the vicinity of the villages and would have had to go farther afield to hunt -- it wouldn't have been feasible or supported that large human population."

The KU researcher also cited bone artifacts from Botai sites used to make rawhide thongs that might have been fashioned into bridles, lassos, whips, riding crops and hobbles, as further evidence of horse domestication. Moreover, the Botai village sites include horse corrals.

The Botai buried horses with their snouts pointing southeast toward the rising sun
[Credit: Sandra Olsen]

"We found a corral that contained high levels of nitrogen and sodium from manure and urine," said Olsen. "It was very concentrated within that corral. The final smoking gun was finding residues of mares' milk in the pottery. It's commonplace today in Mongolia and Kazakhstan to milk horses -- when it's fermented it has considerable nutritional value and is very high in vitamins."

Interestingly, Olsen found that after slaughtering horses, the Botai buried some horse skulls and necks in pits with their snouts facing the southeast, toward where the sun rose in the morning in autumn. Mongols and Kazakhs slaughter most of their horses at that time of year because that is when they retain the most amount of nutritious fat in their bodies.

"It's interesting because throughout the Indo-European diaspora there's a strong connection between the sun god and the horse," she said. "It may be that Botai people spoke an early proto-Indo-European language, and they also connected the horse to the sun god. Later in time, and this idea is in the historical record for the Indo-European diaspora, it was believed the sun god was born in the east and rode across the sky in a chariot, pulled by white horses. According to the belief, he would then die in the west and be reborn every day."

The team behind the paper believe Przewalski's horses likely escaped from domestic Botai herds in eastern Kazakhstan or western Mongolia.

Excavation at the Botai site, Northern Kazakhstan, 2017
[Credit: Alan Outram/University of Exeter]

"They started developing a semi-wild lifestyle like our mustangs, but they still have a wild appearance," Olsen said. "This is partly why biologists assumed they were genuinely wild animals. They have an upright mane, something associated with wild equids. They also have a dun coat, like the ones you see in the Ice Age cave paintings in France and Spain made when horses were wild. Their size, however, is very similar to what you see at Botai and other sites."

By 1969, Przewalski's horses were declared extinct in the wild, and all living today originated from just 15 individuals captured around 1900. Today, there are approximately 2,000 Przewalski's horses, all descended from those captured horses, and they have been reintroduced on the Eurasian steppes. In a sense, the horses have fared better than the peoples who once domesticated them.

"The Botai people seem to have vanished from their homeland in northern Kazakhstan," said Olsen. "Perhaps they migrated eastward to Mongolia since the later Bronze Age people there shared the practice of ritually burying the horse's head and neck pointing toward the rising sun in the autumn, the time of year they were slaughtered. That's a very specific shared trait."

Source: University of Kansas [February 22, 2018]

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A protein that self-replicates

ETH scientists have been able to prove that a protein structure widespread in nature – the amyloid – is theoretically capable of multiplying itself. This makes it a potential predecessor to molecules that are regarded as the building blocks of life.

Lakes in volcanic surroundings could have been the breeding ground for the first biochemical compounds
around 4 to 4.5 billion years ago [Credit: Dhilung Kirat/Wikimedia, ETH Zurich]

Long regarded as a biological aberration, amyloids are fibrous aggregates of short protein fragments. Amyloids have a bad reputation because they are thought to be the cause of multiple neurodegenerative diseases, including Alzheimer’s, Parkinson’s and Creutzfeldt–Jakob disease.

It was only recently that researchers discovered that amyloids appear as structural and functional building blocks in a wide range of life forms, from bacteria, yeast and fungi to humans. In vertebrates, they play a role in the production of the pigment melanin, while yeast cells use amyloid aggregates to form a kind of molecular memory.

Catalysts in prebiotic evolution

Composed of short peptides, amyloid fibres can accelerate chemical reactions in a similar way to enzymes; they have thus been viewed for several years as candidates for the first precursor molecules of life. Until now, however, an important chemical property was lacking in the theory of amyloids role in abiogenesis: self-replication.

Left: electron micrograph of an amyloid fibre. In green is a diagram of the sheet structure characteristic
for amyloids, consisting of multiple short peptide chains [Credit: Jason Greenwald/ETH Zurich]

Early proponents of the amyloid hypothesis include ETH Professor Roland Riek and his senior assistant Jason Greenwald, from the Laboratory of Physical Chemistry. In an experiment, they have now been able to show that amyloids can serve as a chemical template for the synthesis of short peptides. And the critical point: “This ability also potentially applies to the amyloid itself – meaning the molecules can self-replicate,” says Riek. The researchers reported their findings in a study in Nature Communications.

Template for self-replication

The ability to self-replicate is regarded as an essential prerequisite for every early form of life. By proving that amyloids self-replicate, Riek and his team have not only highlighted another amazing aspect of this commonly underestimated protein, but also filled in a previously missing link in the amyloid hypothesis’ argument.

Almost two years earlier, the ETH scientists had already proven in an experiment that amyloid structures can spontaneously form with astounding ease – from simple amino acids that probably already existed when the Earth was still lifeless, and under reaction conditions that appear very plausible for the primordial soup.

The self-replication mechanism of amyloid fibres depicted schematically: piece by piece, specific amino acids (coloured
building blocks) settle at the right site and chemically combine. During the process, the growing amyloid serves
as a template for itself [Credit: Lukas Frey/ETH Zurich]

The same is true for the newly discovered peptide synthesis: “The reaction mechanism seems to be of a general nature. It is stable over a wide range of temperatures and salt concentrations, in both acidic and alkaline environments,” explains Greenwald.

This discovery strengthens the researchers’ opinion that early in evolutionary history, amyloids could have played a central role in the development of early life forms as information carriers and catalytic units.

Not just an RNA world

Until now, however, the most widespread idea for the molecular beginnings of life has been the RNA hypothesis, which sees ribonucleic acid (RNA) as the only key player in the prebiotic primordial soup. This is because, like the genetic material DNA, RNA molecules can code information, and are also able to self-replicate.

The ETH researchers are now picking away at the prevailing dogma of an RNA-based world. They think that the amyloid hypothesis is more plausible; firstly, because RNA molecules with a biological function are much larger and more complex, so they are unlikely to form spontaneously under prebiotic conditions. “Additionally, amyloids are much more stable than early nucleic acid polymers, and they have a much simpler abiotic synthesis route compared to the complexity of known catalytic RNAs,” says Greenwald.

Riek adds: “We will never be able to prove which is true – to do so, we would have to turn back the last 4 to 4.5 billion years of evolution. However, we suspect that it was not one, but multiple molecular processes with various predecessor molecules that were involved in the creation of life.”

Author: Michael Keller | Source: ETH Zurich [February 22, 2018]

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Loops, loops, and more loops: This is how your DNA gets organised

It’s so impressive: a living cell is able to neatly package a big jumble of DNA, over two meters in length, into tidy, tiny chromosomes while preparing for cell division. For over a century, it has been clear that a cell can do so, but scientists have been puzzled for decades on how the process works.

Artist impression of a condensin protein complex creating a loop in DNA
[Credit: Cees Dekker Lab TU Delft/Scixel]

Researchers from the Kavli Institute of Delft University and EMBL Heidelberg now managed for the first time to isolate and film the process, and witnessed—in real time—how a single protein complex called condensin reels in DNA to extrude a loop. By extruding many such loops in long strands of DNA, a cell effectively compacts its genome so it can be distributed evenly to its two daughter cells. The scientists published their findings online in Science.

Spaghetti

This major discovery resolves a heated debate in the field, as it finally answers a question that has been discussed in biology for over a century: Before dividing in two, DNA in a cell is comparable with spaghetti – a messy mixture of intermingled strands. The cell needs to organise this jumble in chromosomes to be able to divide its DNA neatly over both daughter cells.

For many years, it has been clear that a protein complex called ‘condensin’ plays a key role, but until now, biologists were divided on exactly how. One theory stated that condensin works like a hook that can grasp and connect DNA within the jumble of DNA, thus tying it together. Another theory suggested that the ring-shaped condensin pulls the DNA inwards to create a loop.

Motor function

In a cover article in Science last November, scientists from Delft and collaborating labs showed that condensin indeed has the motor function needed for such loop extrusion. This added an important new piece to the puzzle, but as Kim Nasmyth from Oxford University—one of the leading scientists in the field of DNA organisation—noted in the accompanying perspective in Science, “the discovery that condensin is a DNA translocase is certainly consistent with the idea that it functions as a loop extruder, but by no means proves it. The challenge will be to observe extrusion as well as translocation, to establish whether it is a property of individual or multimeric complexes, and to elucidate the molecular mechanism.”

Resolving the mystery

And this is exactly what has now been accomplished. Scientists from the Cees Dekker group at the Kavli Institute of Delft University, together with the Christian Haering group from EMBL Heidelberg who established the purification and fluorescence labeling of the protein, managed to make actual movies that caught the action of the condensin complex in the act – that is, while it was extruding a loop of DNA.

“We’ve simply proved it by filming it,” says Mahipal Ganji, a postdoc in the group of Cees Dekker at Delft. “DNA is such an entangled mishmash, that it is very difficult to isolate the process and study it in cells. In our study, the first step was to fix the two ends of a DNA molecule onto a surface and put colour dyes on the DNA and condensin. By then applying a flow in the fluid perpendicular to the molecule, we oriented the DNA in a U-shape and brought it into the focal plane of our microscope. Amazingly, we could then see a single condensin bind and start extruding a loop.”

Fuel

Prof. Cees Dekker adds, “This settles the debate. These data provide compelling evidence that condensin indeed reels in DNA to form loops. Our novel imaging approach also allows measurement of all kinds of quantitative data: the symmetry of the loop extrusion, the speed at which the loop is formed, what happens when you pull on the DNA.”

The looping speed was found to be remarkably high: up to 1500 base pairs of DNA can be reeled in by condensin per second. And it does so while consuming only a modest amount of ATP—the ‘fuel’ of the condensin motor—indicating that condensin does not step along the DNA base by base, but pulls it in large steps. When slightly pulling on the DNA, the looping process slows down. Apparently, with tension, condensin seems to struggle more to create a loop.

Unexpectedly, the loop extrusion is asymmetric: “We saw that condensin docks onto DNA and anchors itself there, and then starts reeling in DNA from one side only.” Dekker adds, “Yet another interesting finding.”

Medical relevance

The research represents a significant step in the fundamental understanding of DNA in our cells, but it is also relevant for medical research. Problems with the protein family to which condensin belongs—the SMC proteins—are related to hereditary conditions such as Cornelia de Lange Syndrome. Condensin is also crucial in the organisation of the chromosomes during cell division, and errors in the process can result in cancer. A better understanding of these processes is vital for tracking down the molecular origins of serious illnesses.

Source: Delft University of Technology [February 22, 2018]

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More on New research sheds light on prehistoric human migration in Europe

Two University of Wyoming researchers contributed to a new study in which DNA of ancient skeletal remains of people from southeastern Europe were used to determine migration patterns across Europe during prehistoric times.

This field excavation photo shows a double burial in Kargadur, located in Istria County, Croatia. The skeletal remains
 are among 225 skeletal remains sampled in a study of two major migrations across southeastern Europe
during prehistoric times [Credit: Darko Komšo]

Ivor Jankovic, an associate adjunct professor, and Ivor Karavanic, an adjunct professor, both in UW's Department of Anthropology, contributed to the new study that is highlighted in a paper, titled "The Genomic History of Southeastern Europe," published in Nature, an international weekly journal of science.

"The study confirmed that the region of southeastern Europe was a major nexus and a genetic contact zone between the East and West during prehistoric times," says Jankovic, whose full-time job is assistant director of the Institute for Anthropological Research in Zagreb, Croatia. "Two major migrations passing through southeastern Europe were confirmed by the means of archaeo-genetic studies."

The first migration was the early Neolithic Period -- 6,000 Before Common Era (BCE) -- when the first farmers, from Anatolia -- Asia Minor -- spread through Europe. The second migration occurred during the early Bronze Age (3,000-2,500 BCE) when the so-called "steppe population," from the Eurasian steppe, replaced much of northern Europe's previous population.

The first farmers of northern and western Europe passed through southeastern Europe with limited hunter-gatherer genetic admixture, which occurs when two or more previously isolated populations begin interbreeding. However, some groups that remained mixed extensively -- without the male-biased, hunter-gatherer admixture that prevailed later in the North and West, according to the paper. Southeastern Europe continued to be a nexus between East and West, with intermittent genetic contact with the Steppe people up to 2,000 years before the migrations that replaced much of northern Europe's population.

"In some places, hunter-gatherers and incoming farmers seem to have mixed very quickly," says Iain Mathieson, a geneticist at the University of Pennsylvania, who was first author of the paper. "But, mostly, the two groups remained isolated, at least for the first few hundred years. These hunter-gatherers had been living there for thousands of years, and it must have been quite a shock to have these new people show up -- with a completely different lifestyle and appearance."

Karavanic, a professor in the University of Zagreb's Department of Archaeology, was the leader of archaeological excavations of the Paleolithic/Neolithic site of Zemunica cave, from which several human remains were unearthed and used in the study. The discoveries gave needed information on origin and background research.

Jankovic, along with Mario Novak, a research associate at the Institute for Anthropological Research in Zagreb, were involved in the bio-archaeological study of human remains from several of the study samples.

The involvement of Jankovic and Karavanic in this study started through Novak, who visited UW last year to present a talk. Jankovic and James Ahern, former head of UW's Department of Anthropology and now a UW associate provost, collaborated with Novak on several previous publications.

Before the arrival of farming in southeastern Europe, the region saw interactions between diverged groups of hunter-gatherers. This interaction continued after farming arrived. After the first appearance of agriculture in the mid-seventh millennium B.C., farming spread westward via a Mediterranean route and northwestward via a Danubian route. Farming was established in both Iberia (Portugal and Spain) and central Europe by 5,600 B.C.

Ancient DNA studies have shown that the spread of farming across Europe was accompanied by a massive movement of people closely related to the farmers of northwestern Anatolia. But, nearly all of the ancient DNA from Europe's first farmers is from central and Western Europe, with only three farmers reported from southeastern Europe, the paper says.

To understand the dynamics of this migration process, Jankovic, Karovanic, Novak and many other researchers contributed to the analysis of genome-wide ancient DNA data from 225 skeletal remains of individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 B.C. These areas included the Balkan Peninsula, the Carpathian Basin, the North Pontiac Steppe and surrounding regions.

"These results reveal the relationship between migrations, admixture and subsistence in this key region and show that, even within early European farmers, individuals differed in their ancestry, reflecting a dynamic mosaic of hunter-farmer interbreeding," says Ron Pinhasi, co-director of the study and an anthropologist at the University of Vienna in Austria.

While the study has clarified the genomic history of southeastern Europe from the Mesolithic to the Bronze Age, the processes that connected these populations to those living today remain largely unknown, the paper states. An important direction for future research will be to sample populations from the Bronze Age, Iron Age, and Roman and medieval periods, and compare them to present-day populations to understand how these population transitions occurred, according to the paper.

Source: University of Wyoming [February 21, 2018]

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Ancient DNA tells tales of humans' migrant history

Scientists once could reconstruct humanity's distant past only from the mute testimony of ancient settlements, bones, and artifacts.

The use of stylized bell-shaped pots like this one from Sierentz, France spread across Europe
beginning about 4,700 years ago. DNA analysis show that this so-called Bell Beaker culture
was brought to Britain by people who largely replaced the island's existing inhabitants
 [Credit: Anthony Denaire]

No longer. Now there's a powerful new approach for illuminating the world before the dawn of written history - reading the actual genetic code of our ancient ancestors. Two papers published in the journal Nature, more than double the number of ancient humans whose DNA has been analyzed and published to 1,336 individuals - up from just 10 in 2014.

The new flood of genetic information represents a "coming of age" for the nascent field of ancient DNA, says lead author David Reich, a Howard Hughes Medical Institute investigator at Harvard Medical School - and it upends cherished archaeological orthodoxy. "When we look at the data, we see surprises again and again and again," says Reich.

Together with his lab's previous work and that of other pioneers of ancient DNA, the Big Picture message is that our prehistoric ancestors were not nearly as homebound as once thought. "There was a view that migration is a very rare process in human evolution," Reich explains. Not so, says the ancient DNA. Actually, Reich says, "the orthodoxy - the assumption that present-day people are directly descended from the people who always lived in that same area - is wrong almost everywhere."

Instead, "the view that's emerging - for which David is an eloquent advocate - is that human populations are moving and mixing all the time," says John Novembre, a computational biologist at the University of Chicago.

Stonehenge's Builders Largely Vanish

In the first new Nature paper, Reich and a cast of dozens of collaborators chart the spread of an ancient culture known by its stylized bell-shaped pots, the so-called Bell Beaker phenomenon. This culture first spread between Iberia and central Europe beginning about 4,700 years ago. By analyzing DNA from several hundred samples of human bones, Reich's team shows that only the ideas - not the people who originated them - made the move initially. That's because the genes of the Iberian population remain distinct from those of the central Europeans who adopted the characteristic pots and other artifacts.

But the story changes when the Bell Beaker culture expanded to Britain after 4,500 years ago. Then, it was brought by migrants who almost completely supplanted the island's existing inhabitants - the mysterious people who had built Stonehenge - within a few hundred years. "There was a sudden change in the population of Britain," says Reich. "It was an almost complete replacement."

For archaeologists, these and other findings from the study of ancient DNA are "absolutely sort of mind-blowing," says archaeologist Barry Cunliffe, a professor emeritus at the University of Oxford. "They are going to upset people, but that is part of the excitement of it."

Vast Migration from the Steppe

Consider the unexpected movement of people who originally lived on the steppes of Central Asia, north of the Black and Caspian seas. About 5,300 years ago, the local hunter-gatherer cultures were replaced in many places by nomadic herders, dubbed the Yamnaya, who were able to expand rapidly by exploiting horses and the new invention of the cart, and who left behind big, rich burial sites.

DNA from people from the Bell Beaker culture (illustration of one man shown) reveal that
they descended from nomadic herders who migrated from the steppes of Central Asia
[Credit: Manuel Rojo-Guerra/Luis Pascual-Repiso]

Archaeologists have long known that some of the technologies used by the Yamnaya later spread to Europe. But the startling revelation from the ancient DNA was that the people moved, too - all the way to the Atlantic coast of Europe in the west to Mongolia in the east and India in the south. This vast migration helps explain the spread of Indo-European languages. And it significantly replaced the local hunter-gatherer genes across Europe with the indelible stamp of steppe DNA, as happened in Britain with the migration of the Bell Beaker people to the island.

"This whole phenomenon of the steppe expansion is an amazing example of what ancient DNA can show," says Reich. And, adds Cunliffe, "no one, not even archeologists in their wildest dreams, had expected such a high steppe genetic content in the populations of northern Europe in the third millennium B.C."

This ancient DNA finding also explains the "strange result" of a genetic connection that had been hinted at in the genomes of modern-day Europeans and Native Americans, adds Chicago's Novembre. The link is evidence from people who lived in Siberia 24,000 years ago, whose telltale DNA is found both in Native Americans, and in the Yamnaya steppe populations and their European descendants.

New Insights from Southeastern Europe

Reich's second new Nature paper, on the genomic history of southeastern Europe, reveals an additional migration as farming spread across Europe, based on data from 255 individuals who lived between 14,000 and 2,500 years ago. It also adds a fascinating new nugget - the first compelling evidence that the genetic mixing of populations in Europe was biased toward one sex.

Hunter-gatherer genes remaining in northern Europeans after the influx of migrating farmers came more from males than females, Reich's team found. "Archaeological evidence shows that when farmers first spread into northern Europe, they stopped at a latitude where their crops didn't grow well," he says. "As a result, there were persistent boundaries between the farmers and the hunter-gatherers for a couple of thousand years." This gave the hunter-gatherers and farmers a long time to interact. According to Reich, one speculative scenario is that during this long, drawn-out interaction, there was a social or power dynamic in which farmer women tended to be integrated into hunter-gatherer communities.

So far that's only a guess, but the fact that ancient DNA provides clues about the different social roles and fates of men and women in ancient society "is another way, I think, that these data are so extraordinary," says Reich.

Advanced Machines

These scientific leaps forward have been fueled by three key developments. One is the dramatic cost reduction (and speed increase) in gene sequencing made possible by advanced machines from Illumina and other companies. The second is a discovery spearheaded by Ron Pinhasi, an archaeologist at University College Dublin. His group showed that the petrous bone, containing the tiny inner ear, harbours 100 times more DNA than other ancient human remains, offering a huge increase in the amount of genetic material available for analysis. The third is a method implemented by Reich for reading the genetic codes of 1.2 million carefully chosen variable parts of DNA (known as single nucleotide polymorphisms) rather than having to sequence entire genomes. That speeds the analysis and reduces its cost even further.

The new field made a splash when Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology, working with Reich and many other colleagues, used ancient DNA to prove that Neanderthals and humans interbred. Since then, the number of ancient humans whose DNA Reich has analyzed has risen exponentially. His lab has generated about three-quarters of the world's published data and, included unpublished data, has now reached 3,700 genomes. "Every time we jump an order of magnitude in the number of individuals, we can answer questions that we couldn't even have asked before," says Reich.

Now, with hundreds of thousands of ancient skeletons (and their petrous bones) still to be analyzed, the field of ancient DNA is poised to both pin down current questions and tackle new ones. For example, Reich's team is working with Cunliffe and others to study more than 1,000 samples from Britain to more accurately measure the replacement of the island's existing gene pool by the steppe-related DNA from the Bell Beaker people. "The evidence we have for a 90 percent replacement is very, very suggestive, but we need to test it a bit more to see how much of the pre-Beaker population really survived," explains Cunliffe.

Beyond that, ancient DNA offers the promise of studying not only the movements of our distant ancestors, but also the evolution of traits and susceptibilities to diseases. "This is a new scientific instrument that, like the microscope when it was invented in the seventeenth century, makes it possible to study aspects of biology that simply were not possible to examine before," explains Reich. In one example, scientists at the University of Copenhagen found DNA from plague in the steppe populations. If the groups that migrated to Britain after 4,500 years ago brought the disease with them, that could help explain why the existing population shrank so quickly.

With the possibility of many such discoveries still ahead, "it is a very exciting time," says Cunliffe. "Ancient DNA is going to revitalize archeology in a way that few of us could have guessed even ten years ago."

Source: Howard Hughes Medical Institute [February 21, 2018]

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Largest ever genomic study shows that first Beaker expansion was one of cultural diffusion

Prehistoric Iberians 'exported' their culture throughout Europe, reaching Great Britain, Sicily, Poland and all over central Europe in general. However, they did not export their genes. The Beaker culture, which probably originated in Iberia, left remains in those parts of the continent.

Iberian beakers [Credit: Museo de Almeria]

However, that diffusion was not due to large migrations of populations that took this culture with them. These are the conclusions of an international study in which the Spanish National Research Council (CSIC) was involved. Its findings, published in the journal Nature, indicate no evidence of any genetic outflow from Iberia to those areas has been discovered.

"Therefore, the diffusion of the Beaker culture from Iberia is the first example of a culture being transmitted as an idea, basically due to a question of social prestige (since it was associated with the virtues of being virile and of being warriors), which is why it is adopted by other populations," indicates researcher Carles Lalueza-Fox, from the Institute of Evolutionary Biology, a mixed research centre run by CSIC and the Pompeu Fabra University, in Barcelona, Spain.

Between 4,700 and 4,400 years ago, a new type of bell-shaped beaker pottery was introduced throughout western and central Europe. For more than a century, archaeologists have been trying to determine whether the spread of this beaker pottery -- and the (Beaker) culture associated with it -- represented a large-scale migration or whether it was due simply to the exchange of new ideas.

Now, this new study, which includes DNA data from 400 prehistoric skeletons collected from sites across Europe, resolves the debate of whether the spread was due to migrations or ideas, indicating that both arguments are correct. The findings show that the culture which produced these bell-shaped beakers extended from Iberia to central Europe without a significant movement of populations, although the Beaker culture would spread to other places through migrations at a later date.

The study, whose first author is the Spanish researcher Inigo Olalde, a geneticist at Harvard Medical School, shows that once the (Bell) Beaker culture reaches the centre of Europe (around Germany and its surrounding area), it expands backwards to other places, notably to the British Isles. Yet, in this case, it does represent a migration, replacing around 90% of the population with it.

"That is to say, the Neolithic people who built Stonehenge (and who had a greater genetic similarity with Neolithic Iberians than with those from Central Europe) almost disappear and are replaced by the populations from the Beaker culture from the Netherlands and Germany. This replacement is almost absolute in terms of the Y chromosome, which is transmitted by the paternal line, indicating an extreme reproductive bias, and therefore a previously unheard of social dominance. The backward flow also reaches other places such as Italy (at least in the north) and Iberia. I believe it is possible that this is also associated with the expansion of the Celtic or Proto-Celtic languages," Mr. Lalueza-Fox points out.

Coordinated by researcher David Reich from Harvard University, the study was developed by an international team of 144 archaeologists and geneticists from institutions in Europe and the United States.

Source: Spanish National Research Council [February 21, 2018]

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