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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