Ancient DNA from Rapa Nui (Easter Island) refutes best-selling population collapse theory

Rapa Nui or Te Pito o Te Henua (the navel of the world), also known as Easter Island, is one of the most isolated inhabited places in the world. Located in the Pacific, it lies over 1,900 km east of the closest inhabited Polynesian island and 3,700 km west of South America. Although the island, its inhabitants and their rich culture have been extensively studied by archaeologists, anthropologists and geneticists, two key elements of Rapanui history remain very controversial to this day. One of these is the theory of population collapse through "ecocide" in the 1600s, thought to be the result of overpopulation and resource mismanagement. The other major contention is whether the Polynesian ancestors of the Rapanui interacted with Indigenous Americans before contact with Europeans in 1722.

This week's issue of Nature features a genetic study that sheds light on these two debates related to Rapanui history by examining the genomes of 15 Rapanui individuals who lived between 1670 and 1950. The remains of these 15 individuals are currently hosted at the Musée de l'Homme, in Paris. The new study was carried out by an international team of scientists and was spearheaded by Assistant Professor Víctor Moreno-Mayar from the Globe Institute at the University of Copenhagen (Denmark), and PhD student Bárbara Sousa da Mota and Associate Prof. Anna-Sapfo Malaspinas from the Faculty of Biology and Medicine at the University of Lausanne (Switzerland), in close collaboration with colleagues in Rapa Nui as well as in Austria, France, Chile, Australia and U.S.A.

The collapse that never happened

The story of the Rapanui has often been presented as a warning tale against humanity's over-exploitation of resources. After Polynesians from the west peopled the island by 1250, the landscape on Rapa Nui changed drastically. Towering stone statues -- the moai -- were carved and placed in all corners of the island, while its original forest of millions of palm trees dwindled and, by the 1600s, was all but gone. According to the "ecocide" theory, a population of over 15,000 Rapanui individuals triggered these changes that led to a period of resource scarcity, famine, warfare and even cannibalism culminating in a catastrophic population collapse.

"While it is well established that the environment of Rapa Nui was affected by anthropogenic activity, such as deforestation, we did not know if or how these changes led to a population collapse," comments Anna-Sapfo Malaspinas, Assoc. Professor at the University of Lausanne and group leader at the SIB Swiss Institute of Bioinformatics, Switzerland, last author of the study.

The researchers looked into the genomes of the Ancient Rapanui individuals expecting to find a genetic signature of a population collapse such as a sudden drop in genetic diversity. But surprisingly, the data did not contain any evidence of a population collapse in the 1600s.

"Our genetic analysis shows a stably growing population from the 13th century through to European contact in the 18th century. This stability is critical because it directly contradicts the idea of a dramatic pre-contact population collapse," says Bárbara Sousa da Mota, a researcher at the Faculty of Biology and Medicine at University of Lausanne and first author of the study.

Through their genetic analysis, Moreno-Mayar, Sousa da Mota, Malaspinas and their colleagues have not only provided evidence against the collapse theory, but also stress the resilience of the Rapanui population facing environmental challenges over several centuries until the colonial disruptions that European contact brought after 1722.

Did Polynesians reach the Americas?

Another debate that has tantalized researchers for decades is whether Polynesians ever reached the Americas. Although long-distance maritime navigation using wooden watercraft likely halted after the Rapa Nui forest disappeared, archaeological and genetic evidence from contemporary individuals hints that voyages to the Americas did occur. However, previous studies looking at small amounts of DNA from ancient Polynesians had rejected the hypothesis that transpacific voyages took place. Thus, these findings have put into question whether Polynesians reached the Americas and have suggested that the inferred contact based on present-day genetic data was mediated by European colonial activity after 1722.

By generating high-quality ancient genomes from the 15 Rapanui individuals, the team substantially increased the amount of genomic data from the island and found that about ten percent of the Rapanui gene pool has an Indigenous American origin. But more importantly, they were able to infer both populations met before Europeans arrived in the island and in the Americas.

"We looked into how the Indigenous American DNA was distributed across the Polynesian genetic background of the Rapanui. This distribution is consistent with a contact occurring between the 13th and the 15th centuries, " says first author Víctor Moreno-Mayar, Asst. Professor at the Globe Institute's Section for Geogenetics, University of Copenhagen.

"While our study cannot tell us where this contact occurred, this might mean that the Rapanui ancestors reached the Americas before Christopher Columbus," says Malaspinas.

Altogether, the results from the new study help settle longstanding debates that have led to years of speculation surrounding Rapanui history.

"Personally, I believe the idea of the ecocide is put together as part of a colonial narrative. That is this idea that these supposedly primitive people could not manage their culture or resources, and that almost destroyed them. But the genetic evidence shows the opposite. Although we have to acknowledge that the arrival of humans dramatically changed the ecosystem, there is no evidence of a population collapse before the Europeans arrived on the island. So we can put those ideas to rest now," says Moreno-Mayar.

"Many thought that present-day Rapanui carry Indigenous American genetic ancestry due to European colonial activity. But instead, the data strongly suggests that Rapanui and Indigenous Americans met and admixed centuries before Europeans made it to Rapa Nui or the Americas. We believe this means that Rapanui were capable of even more formidable voyages across the Pacific than previously established, " adds Sousa da Mota.

Future repatriation efforts

Importantly, the scientists held face-to-face discussions with members of the Rapanui community and the "Comision Asesora de Monumentos Nacionales" in Rapa Nui (CAMN). These discussions allowed to steer the research and to define a set of research questions that were equally of high interest to the scientists and the community. For instance, the team was able to show that the populations closest to the ancient Rapanui are indeed those currently living on the island.

"We have seen that museum archives contain mistakes and mislabels. Now that we have established that these 15 individuals were in fact Rapanui we know that they belong back in the island," says Moana Gorman Edmunds, an archaeologist in Rapa Nui and co-author of the study.

Furthermore, when ongoing results were presented to representatives of the Rapanui community, the need to repatriate their ancestors was discussed as a central goal for immediate future efforts.

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Ancient DNA reveals Down syndrome in past human societies

By analysing ancient DNA, an international team of researchers have uncovered cases of chromosomal disorders, including what could be the first case of Edwards syndrome ever identified from prehistoric remains.

The team identified six cases of Down syndrome and one case of Edwards syndrome in human populations that were living in Spain, Bulgaria, Finland, and Greece from as long ago as 4,500 years before today.

The research indicated that these individuals were buried with care, and often with special grave goods, showing that they were appreciated as members of their ancient societies.

The global collaborative study, led by first author Dr Adam "Ben" Rohrlach of the University of Adelaide, and senior author Dr Kay Prüfer of the Max Planck Institute for Evolutionary Anthropology, involved screening DNA from approximately 10,000 ancient and pre-modern humans for evidence of autosomal trisomies, a condition where people carry an extra (third) copy of one of the first 22 chromosomes.

"Using a new statistical model, we screened the DNA extracted from human remains from the Mesolithic, Neolithic, Bronze and Iron Ages all the way up to the mid-1800s. We identified six cases of Down syndrome," says Dr Rohrlach, a statistician from the University of Adelaide's School of Mathematical Sciences.

"While we expected that people with Down syndrome certainly existed in the past, this is the first time we've been able to reliably detect cases in ancient remains, as they can't be confidently diagnosed by looking at the skeletal remains alone."

Down syndrome occurs when an individual carries an extra copy of chromosome 21. The researchers were able to find these six cases using a novel Bayesian approach to accurately and efficiently screen tens of thousands of ancient DNA samples.

"The statistical model identifies when an individual has approximately 50 per cent too much DNA that comes from one specific chromosome," says Dr Patxuka de-Miguel-Ibáñez of the University of Alicante, and lead osteologist for the Spanish sites.

"We then compared the remains of the individuals with Down syndrome for common skeletal abnormalities such as irregular bone growth, or porosity of the skull bones, which may help to identify future cases of Down syndrome when ancient DNA can't be recovered."

The study also uncovered one case of Edwards syndrome, a rare condition caused by three copies of chromosome 18, that comes with far more severe symptoms than Down syndrome.

The remains indicated severe abnormalities in bone growth, and an age of death of approximately 40 weeks gestation.

All of the cases were detected in perinatal or infant burials, but from different cultures and time periods.

"These individuals were buried according to either the standard practices of their time or were in some way treated specially. This indicates that they were acknowledged as members of their community and were not treated differently in death," says Dr Rohrlach.

"Interestingly, we discovered the only case of Edwards syndrome, and a noticeable increase in cases of Down syndrome, in individuals from the Early Iron Age in Spain. The remains could not confirm that these babies survived to birth, but they were among the infants buried within homes at the settlement, or within other important buildings," says Professor Roberto Risch, co-author and archaeologist from The Autonomous University of Barcelona.

"We don't know why this happened, as most people were cremated during this time, but it appears as if they were purposefully choosing these infants for special burials."

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Probing the deep genetic structure of Africa

Using ancestry decomposition techniques an international research team has revealed a deeply divergent ancestry among admixed populations from the Angolan Namib desert. This unique genetic heritage brings the researchers closer to understanding the distribution of genetic variation in the broader region of southern Africa before the spread of food production.

Africa is the birthplace of modern humans and the continent with the highest level of genetic diversity. While ancient DNA studies are revealing some aspects of the genetic structure of Africa before the spread of food production, issues concerning DNA preservation have limited the insights from ancient DNA.

Hoping to find clues in modern populations, researchers from a Portuguese-Angolan TwinLab ventured into the Angolan Namib desert -- a remote, multi-ethnic region where different traditions met. "We were able to locate groups which were thought to have disappeared more than 50 years ago," states Jorge Rocha, a population geneticist from Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO, University of Porto) who led the fieldwork, together with Angolan anthropologists Samuel and Teresa Aço from the Centro de Estudos do Deserto (CEDO).

Among the communities the team encountered are the Kwepe, a pastoral group who used to speak a language known as Kwadi. "Kwadi was a click-language that shared a common ancestor with the Khoe languages spoken by foragers and herders across southern Africa," explains Anne-Maria Fehn, a linguist from CIBIO who participated in the fieldwork and was able to interview what may well be the last two speakers of Kwadi. "Khoe-Kwadi languages have been linked to a prehistoric migration of eastern African pastoralists," adds Rocha, whose research focuses on southern African population history. In addition, the team contacted Bantu-speaking groups that are part of the dominant pastoral tradition of southwest Africa, as well as marginalized groups whose origins have been associated with a foraging tradition, distinct from that of the neighboring Kalahari peoples, and whose original language was supposedly lost.

Modern DNA research can complement ancient DNA studies

The team's new study shows that the inhabitants of the Angolan Namib are quite divergent from other modern populations but also highly structured among themselves. "In agreement with our previous studies on the maternally-inherited DNA, most genome-wide diversity segregates according to socio-economic status. A lot of our efforts were placed in understanding how much of this local variation and global excentricity was caused by genetic drift -- a random process that disproportionally affects small populations -- and by admixture from vanished populations," says Sandra Oliveira, a researcher at the University of Bern in Switzerland who worked with these populations during her PhD and post-doc studies with Rocha and Mark Stoneking at CIBIO and the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) in Leipzig, Germany. The team demonstrated that besides the high impact of genetic drift, which contributed to differences among neighboring groups of different socio-economic status, the descendants of Kwadi speakers and the marginalized communities of the Namib Desert retain a unique Pre-Bantu ancestry that is only found in populations from the Namib desert.

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Researchers extract ancient DNA from a 2,900-year-old clay brick, revealing a time capsule of plant life

Currently housed at the National Museum of Denmark, the clay brick originates from the palace of Neo-Assyrian king Ashurnasirpal II, in the ancient city of Kalhu. Known today as the North-West palace in Nimrud (modern-day northern Iraq), its construction began around 879 BCE. The brick has a cuneiform inscription (written in the now extinct Semitic language Akkadian) stating that it is 'The property of the palace of Ashurnasirpal, king of Assyria.' This makes it possible to date the brick precisely to within a decade (879 BCE to 869 BCE).

During a digitalization project at the Museum in 2020, the group of researchers were able to obtain samples from the inner core of the brick -- meaning that there was a low risk of DNA contamination since the brick was created. The team extracted DNA from the samples by adapting a protocol previously used for other porous materials, such as bone.

After the extracted DNA had been sequenced, the researchers identified 34 distinct taxonomic groups of plants. The plant families with the most abundant sequences were Brassicaceae (cabbage) and Ericaceae (heather). Other represented families were Betulaceae (birch), Lauraceae (laurels), Selineae (umbellifiers) and Triticeae (cultivated grasses).

With the interdisciplinary team comprising assyriologists, archaeologists, biologists, and geneticists, they were able to compare their findings with modern-day botanical records from Iraq as well as ancient Assyrian plant descriptions.

The brick would have been made primarily of mud collected near the local Tigris river, mixed with material such as chaff or straw, or animal dung. It would have been shaped in a mould before being inscribed with cuneiform script, then left in the sun to dry. The fact that the brick was never burned, but left to dry naturally, would have helped to preserve the genetic material trapped within the clay.

Dr Sophie Lund Rasmussen (Wildlife Conservation Research Unit, Department of Biology, University of Oxford), joint first author of the paper, said: 'We were absolutely thrilled to discover that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2,900-year-old clay brick. This research project is a perfect example of the importance of interdisciplinary collaboration in science, as the diverse expertise included in this study provided a holistic approach to the investigation of this material and the results it yielded.'

In addition to the fascinating insight this individual brick revealed, the research serves as a proof of concept and method which could be applied to many other archaeological sources of clay from different places and time periods around the world, to identify past flora and fauna. Clay materials are nearly always present in any archaeological site around the world, and their context means they can often be dated with high precision.

This study only described the plant DNA extracted, as these were the most prevalent and best-preserved specimens. However, depending on the sample, all taxa could potentially be identified, including vertebrates and invertebrates. The ability to provide accurate descriptions of ancient biodiversity would be a valuable tool to better understand and quantify present day biodiversity loss, and to gain a deeper understanding of ancient and lost civilisations.

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Ancient DNA reveals diverse community in 'Lost City of the Incas'

Who lived at Machu Picchu at its height? A new study, published today in Science Advances, used ancient DNA to find out for the first time where workers buried more than 500 years ago came from within the lost Inca Empire.

Researchers, including Jason Nesbitt, associate professor of archaeology at Tulane University School of Liberal Arts, performed genetic testing on individuals buried at Machu Picchu in order to learn more about the people who lived and worked there.

Machu Picchu is a UNESCO World Heritage Site located in the Cusco region of Peru. It is one of the most well-known archaeological sites in the world and attracts hundreds of thousands of visitors every year. It was once part of a royal estate of the Inca Empire.

Like other royal estates, Machu Picchu was home not only to royalty and other elite members of Inca society, but also to attendants and workers, many of whom lived in the estate year-round. These residents did not necessarily come from the local area, though it is only in this study that researchers have been able to confirm, with DNA evidence, the diversity of their backgrounds. "It's telling us, not about elites and royalty, but lower status people," Nesbitt said. "These were burials of the retainer population."

This DNA analysis works in much the same way that modern genetic ancestry kits work. The researchers compared the DNA of 34 individuals buried at Machu Picchu to that of individuals from other places around the Inca Empire as well as some modern genomes from South America to see how closely related they might be.

The results of the DNA analysis showed that the individuals had come from throughout the Inca Empire, some as far away as Amazonia. Few of them had shared DNA with each other, showing that they had been brought to Machu Picchu as individuals rather than as part of a family or community group.

"Now, of course, genetics doesn't translate into ethnicity or anything like that," said Nesbitt of the results, "but that shows that they have distinct origins within different parts of the Inca Empire."

"The study does really reinforce a lot of other types of research that have been done at Machu Picchu and other Inca sites," Nesbitt said. The DNA analysis supports historical documentation and archaeological studies of the artifacts found associated with the burials.

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Scientists recover an ancient woman's DNA from a 20,000-year-old pendant

Artefacts made of stone, bones or teeth provide important insights into the subsistence strategies of early humans, their behavior and culture. However, until now it has been difficult to attribute these artefacts to specific individuals, since burials and grave goods were very rare in the Palaeolithic. This has limited the possibilities of drawing conclusions about, for example, division of labor or the social roles of individuals during this period.

In order to directly link cultural objects to specific individuals and thus gain deeper insights into Paleolithic societies, an international, interdisciplinary research team, led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, has developed a novel, non-destructive method for DNA isolation from bones and teeth. Although they are generally rarer than stone tools, the scientists focused specifically on artefacts made from skeletal elements, because these are more porous and are therefore more likely to retain DNA present in skin cells, sweat and other body fluids.

A new DNA extraction method

Before the team could work with real artefacts, they first had to ensure that the precious objects would not be damaged. "The surface structure of Paleolithic bone and tooth artefacts provides important information about their production and use. Therefore, preserving the integrity of the artefacts, including microstructures on their surface, was a top priority" says Marie Soressi, an archaeologist from the University of Leiden who supervised the work together with Matthias Meyer, a Max Planck geneticist.

The team tested the influence of various chemicals on the surface structure of archaeological bone and tooth pieces and developed a non-destructive phosphate-based method for DNA extraction. "One could say we have created a washing machine for ancient artifacts within our clean laboratory," explains Elena Essel, the lead author of the study who developed the method. "By washing the artifacts at temperatures of up to 90°C, we are able to extract DNA from the wash waters, while keeping the artifacts intact."

Early setbacks

The team first applied the method to a set of artefacts from the French cave Quinçay excavated back in the 1970s to 1990s. Although in some cases it was possible to identify DNA from the animals from which the artefacts were made, the vast majority of the DNA obtained came from the people who had handled the artefacts during or after excavation. This made it difficult to identify ancient human DNA.

To overcome the problem of modern human contamination, the researchers then focused on material that had been freshly excavated using gloves and face masks and put into clean plastic bags with sediment still attached. Three tooth pendants from Bacho Kiro Cave in Bulgaria, home to the oldest securely dated modern humans in Europe, showed significantly lower levels of modern DNA contamination; however, no ancient human DNA could be identified in these samples.

A pendant from Denisova Cave

The breakthrough was finally enabled by Maxim Kozlikin and Michael Shunkov, archaeologists excavating the famous Denisova Cave in Russia. In 2019, unaware of the new method being developed in Leipzig, they cleanly excavated and set aside an Upper Paleolithic deer tooth pendant. From this, the geneticists in Leipzig isolated not only the DNA from the animal itself, a wapiti deer, but also large quantities of ancient human DNA. "The amount of human DNA we recovered from the pendant was extraordinary" says Elena Essel, "almost as if we had sampled a human tooth."

Based on the analysis of mitochondrial DNA, the small part of the genome that is exclusively inherited from the mother to their children, the researchers concluded that most of the DNA likely originated from a single human individual. Using the wapiti and human mitochondrial genomes they were able to estimate the age of the pendant at 19,000 to 25,000 years, without sampling the precious object for C14 dating.

In addition to mitochondrial DNA, the researchers also recovered a substantial fraction of the nuclear genome of its human owner. Based on the number of X chromosomes they determined that the pendant was made, used or worn by a woman. They also found that this woman was genetically closely related to contemporaneous ancient individuals from further east in Siberia, the so called 'Ancient North Eurasians' for whom skeletal remains have previously been analyzed. "Forensic scientists will not be surprised that human DNA can be isolated from an object that has been handled a lot" says Matthias Meyer, "but it is amazing that this is still possible after 20,000 years."

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Ancient DNA reveals Asian ancestry introduced to East Africa in early modern times

While serfs toiled and knights jousted in Europe and samurai and shoguns rose to power in Japan, the medieval peoples of the Swahili civilization on the coast of East Africa lived in multicultural, coral-stone towns and engaged in trade networks spanning the Indian Ocean.

Archaeologists, anthropologists, and linguists have been locked in a century-long debate about how much people from outside Africa contributed to Swahili culture and ancestry. Swahili communities have their own histories, and evidence points in multiple directions.

The largest-yet analysis of ancient DNA in Africa, which includes the first ancient DNA recovered from members of the Swahili civilization, has now broken the stalemate.

The study reveals that a significant number of people from Southwest Asia moved to the Swahili coast in medieval and early modern times and had children with the people living there. Yet the research also shows that hallmarks of the Swahili civilization predated those arrivals.

"Archaeological evidence overwhelmingly showed that the medieval Swahili civilization was an African one, but we still wanted to understand and contextualize the nonlocal heritage," said co-senior author Chapurukha Kusimba, professor of anthropology at the University of South Florida.

"Taking a genetics pathway to find the answers took courage and opened doors beyond which lie answers that force us to think in new ways," he said.

The analyses, published online March 29 in Nature, included the newly sequenced ancient DNA of 80 individuals from the Swahili coast and inland neighbors dating from 1300 CE to 1900 CE.

They also included new genomic sequences from 93 present-day Swahili speakers and previously published genetic data from a variety of ancient and present-day eastern African and Eurasian groups.

The international team was led by Kusimba and David Reich, professor of genetics in the Blatavnik Institute at Harvard Medical School and professor of human evolutionary biology at Harvard University.

Mixing between Asia and Africa

The study revealed that around 1000 CE, a stream of migrants from Southwest Asia intermingled with African people at multiple locations along the Swahili coast, contributing close to half of the ancestry of the analyzed ancient individuals.

"The results provide unambiguous evidence of ongoing cultural mixing on the East African coast for more than a millennium, in which African people interacted and had families with immigrants from other parts of Africa and the Indian Ocean world," said Reich.

The study confirmed that the bedrock of Swahili culture remained unchanged even as the newcomers arrived and Islam became a dominant regional religion, said Kusimba; the primary language, tomb architecture, cuisine, material culture, and matrilocal marriage residence and matriarchal kinship remained African and Bantu in nature.

The findings contradict one widely discussed scholarly view, which held that there was little contribution from foreigners to Swahili peoples, the authors said.

The researchers added that the findings also refute a diametrically opposed viewpoint prevalent in colonial times, which held that Africans provided little contribution to the Swahili towns.

"Ancient DNA allowed us to address a longstanding controversy that could not be tested without genetic data from these times and places," Reich said.

The researchers found that the initial waves of newcomers were mainly from Persia. These findings align with the oldest Swahili oral stories, which tell of Persian (Shirazi) merchants or princes arriving on the Swahili shores.

"It was exciting to find biological evidence that Swahili oral history probably depicts Swahili genetic ancestry as well as cultural legacy," said Esther Brielle, research fellow in genetics in the Reich lab.

Brielle is co-first author of the paper with Stephanie Wynne-Jones at the University of York and Jeffrey Fleisher at Rice University.

After about 1500 CE, ancestry sources became increasingly Arabian. In later centuries, intermingling with other populations from Asia and Africa further changed the genetic makeup of Swahili-coast communities.

Ancestry contributions from women from India

Analyses also showed that the initial stream of migrants had about 90 percent ancestry from Persian men and 10 percent ancestry from Indian women.

Although South Asian-associated artifacts are well documented at Swahili archaeological sites and Indian words have been integrated into Swahili, "no one had previously hypothesized an important role for Indian people in contributing to the populations of the medieval Swahili towns," said Reich.

Extreme sex differences in genetic contributions

The predominant groups that contributed to Swahili-coast populations during the initial influx in 1000 CE were male Persians and femaleAfricans. Similar genetic signatures of sex imbalances in other populations around the world sometimes indicate that incoming men forcibly married local women, but that scenario does not align with the tradition of matriarchal Swahili societies, the authors said.

A more likely explanation, said Reich, is that "Persian men allied with and married into local trading families and adopted local customs to enable them to be more successful traders."

The authors say their hypothesis is supported by the fact that the children of Persian fathers and Swahili-coast mothers passed down the language of their mothers and that the region's matriarchal traditions did not change even after locals settled down with people from traditionally patriarchal regions in Persia and Arabia and practiced the Islamic religion of their male ancestors.

Genetics and identity

The team found that the proportion of Persian-Indian ancestry has decreased among many people of the Swahili coast in the last several centuries. Many among those in present-day Kenya who identify as Swahili and had their genomes analyzed were "genetically very different" from the people who lived in the region during medieval times, the authors found, while others retained substantial medieval ancestry.

"These results highlight an important lesson from ancient DNA: While we can learn about the past with genetics, it does not define present-day identity," said Reich.

Decolonizing history

In addition to helping to diversify the populations included in ancient DNA research, the study pushes back against "a profoundly difficult history" of more than 500 years of colonization in this region of Africa, which continues to be a major problem today, said Reich.

"The story of Swahili origins has been molded almost entirely by non-Swahili people," he said.

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Ancient DNA analysis sheds light on the early peopling of South America

The Americas were the last continent to be inhabited by humans. An increasing body of archaeological and genomic evidence has hinted to a complex settlement process. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent.

Many unanswered questions still persist, such as whether the first humans migrated south along the Pacific coast or by some other route. While there is archaeological evidence for a north-to-south migration during the initial peopling of the Americas by ancient Indigenous peoples, where these ancient humans went after they arrived has remained elusive.

Using DNA from two ancient human individuals unearthed in two different archaeological sites in northeast Brazil -- Pedra do Tubarão and Alcobaça -- and powerful algorithms and genomic analyses, Florida Atlantic University researchers in collaboration with Emory University have unraveled the deep demographic history of South America at the regional level with some unexpected and surprising results.

Not only do researchers provide new genetic evidence supporting existing archaeological data of the north-to-south migration toward South America, they also have discovered migrations in the opposite direction along the Atlantic coast -- for the first time. The work provides the most complete genetic evidence to date for complex ancient Central and South American migration routes.

Among the key findings, researchers also have discovered evidence of Neanderthal ancestry within the genomes of ancient individuals from South America. Neanderthals are an extinct population of archaic humans that ranged across Eurasia during the Lower and Middle Paleolithic.

Results of the study, published in the journal Proceedings of the Royal Society B. (Biological Sciences), suggest that human movements closer to the Atlantic coast eventually linked ancient Uruguay and Panama in a south-to-north migration route -- 5,277 kilometers (3,270 miles) apart. This novel migration pattern is estimated to have occurred approximately 1,000 years ago based on the ages of the ancient individuals.

Findings show a distinct relationship among ancient genomes from northeast Brazil, Lagoa Santa (southeast Brazil), Uruguay and Panama. This new model reveals that the settlement of the Atlantic coast occurred only after the peopling of most of the Pacific coast and Andes.

"Our study provides key genomic evidence for ancient migration events at the regional scale along South America's Atlantic coast," said Michael DeGiorgio, Ph.D., co-corresponding author who specializes in human, evolutionary, and computational genomics and is an associate professor in the Department of Electrical Engineering and Computer Science within FAU's College of Engineering and Computer Science. "These regional events likely derived from migratory waves involving the initial Indigenous peoples of South America near the Pacific coast."

Researchers also found strong Australasian (Australia and Papua New Guinea) genetic signals in an ancient genome from Panama.

"There is an entire Pacific Ocean between Australasia and the Americas, and we still don't know how these ancestral genomic signals appeared in Central and South America without leaving traces in North America," said Andre Luiz Campelo dos Santos, Ph.D., first author, an archaeologist and a postdoctoral fellow in FAU's Department of Electrical Engineering and Computer Science.

To further add to the existing complexity, researchers also detected greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Denisovans are a group of extinct humans first identified from DNA sequences from the tip of finger bone discovered around 2008.

"It's phenomenal that Denisovan ancestry made it all the way to South America," says John Lindo, Ph.D., a co-corresponding author of the article who specializes in ancient DNA analysis and is an assistant professor in the Department of Anthropology at Emory University. "The admixture must have occurred a long time before, perhaps 40,000 years ago. The fact that the Denisovan lineage persisted and its genetic signal made it into an ancient individual from Uruguay that is only 1,500 years old suggests that it was a large admixture event between a population of humans and Denisovans."

Previously at the Federal University of Pernambuco in Recife, Brazil, dos Santos and colleagues uncovered the remains of the two ancient humans from northeast Brazil, which date back to at least 1,000 years before present, and sent them to Lindo for DNA extraction and subsequent genomic sequencing and analyses. Raw data were then sent to FAU for computational analysis of the whole genome sequences from northeast Brazil.

Researchers compared the two newly sequenced ancient whole genomes from northeast Brazil with present-day worldwide genomes and other ancient whole genomes from the Americas. As of the publication date of the article, Lindo says that only a dozen or so ancient whole genomes from South America have been sequenced and published, in contrast to hundreds from Europe.

Apart from the occurrence of mass burials in the sites that yielded the samples from northeast Brazil, Uruguay, southeast Brazil and Panama, there is no other evidence in the archaeological record that indicate shared cultural features among them. Importantly, the analyzed ancient individuals from southeast Brazil are about 9,000 years older than those from northeast Brazil, Uruguay and Panama, enough time for expected and noticeable cultural divergence. Moreover, northeast Brazil, Uruguay and Panama, though more similar in age, are located thousands of kilometers apart from each other.

"This groundbreaking research involved many different fields from archaeology to biological sciences to genomics and data science," said Stella Batalama, Ph.D., dean, FAU College of Engineering and Computer Science. "Our scientists at Florida Atlantic University in collaboration with Emory University have helped to shed light on an important piece of the Americas puzzle, which could not have been solved without powerful genomic and computational tools and analysis."

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Ancient genomes reveal hidden history of human adaptation

The use of ancient DNA, including samples of human remains around 45,000 years old, has shed light on a previously unknown aspect of human evolution.

Dr Yassine Souilmi, Group Leader at the University of Adelaide's Australian Centre for Ancient DNA, co-led the new study published in Nature Ecology and Evolution.

"It was widely believed the genetics of our human ancestors didn't change due to environmental pressures as much as other animals, due to our enhanced communication skills and ability to make and use tools," Dr Souilmi said.

"However, by comparing modern genomes with ancient DNA, we discovered more than 50 cases of an initially rare beneficial genetic variant becoming prevalent across all members of ancient human groups.

"In contrast to many other species, evidence for this type of adaptive genetic change has been inconsistent in humans. This discovery consequently challenges the prevailing view of human adaptation, and gives us a new and exciting insight into how humans have adapted to the novel environmental pressures they encountered as we spread across the planet."

Co-lead author Dr Ray Tobler -- an Adjunct Fellow at the University of Adelaide and a DECRA fellow at the Australian National University -- said examining ancient DNA has been critical in unlocking the secrets of human evolution.

"We believed historical mixing events between human groups might have hidden signs of genetic changes in modern human genomes," Dr Tobler said.

"We examined DNA from more than 1,000 ancient genomes, the oldest which was around 45,000 years old, to see if certain types of genetic adaptation had been more common in our history than studies of modern genomes had suggested."

Professor Christian Huber, a senior author of the research paper, is an Adjunct Fellow at the University of Adelaide and an Assistant Professor at Penn State University.

"The use of ancient genomes was crucial because they preceded major historical mixing events that have radically reshaped modern European genetic ancestry," Professor Huber said.

"This allowed the recovery of historical signs of adaptation that are invisible to standard analysis of modern genomes."

Established in 2005, the Australian Centre for Ancient DNA is a world leader in the research and development of advanced ancient DNA approaches for evolutionary, environmental and conservation applications.

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Geneticists discover new wild goat subspecies via ancient DNA

Geneticists from Trinity College Dublin, together with a team of international collaborators, have discovered a previously unknown lineage of wild goats over ten millennia old. The research was subject to open peer review and recommendation at PCI Genomics and has just been published in the journal eLife.

The new goat type, discovered from genetic screening of bone remains and referred to as "the Taurasian tur," likely survived the Last Glacial Maximum (the ice age), which stranded their ancestors in the high peaks of the Taurus Mountains in Turkey where their remains were found.

A chance discovery at Direkli Cave

Over 12,000 years ago, hunter-gatherers in the Taurus Mountains of southern Turkey relied heavily on local game for food and subsistence. Located near the present-day village of Döngel and at an elevation of ~1,100 m above sea level, Direkli Cave was used for roughly three millennia (~14,000-11,000 years ago) as a seasonal camp for these hunters and may have been inhabited year-round.

"Among the artefacts found at Direkli Cave were large amounts of bone remains with distinct processing marks, indicating that wild goats were butchered there for consumption," says Dr Kevin Daly, from Trinity's School of Genetics and Microbiology, who is first author of the research article.

"With the cave surrounded by high peaks, reaching ~2,200 m, the wild goat or bezoar ibex (Capra aegagrus) that inhabit the region today were likely the target of these Late Pleistocene hunters."

During genetic screening of goat bone remains from Direkli, the geneticists noticed something unusual: many of the goats carried mitochondrial genomes similar to a different species of wild goat.

Whereas the domestic goat is derived from the bezoar ibex, other species of wild goat are still alive today and are found in relatively restricted regions. These include the East and West Caucasus tur, two sister species (or subspecies) of wild goat now found only in the Caucasus Mountains in Georgia. Many of the Direkli Cave samples carried mitochondria related to these Caucasus tur, despite Direkli Cave being around 800 km from their current habitat.

Dr Daly added: "An even greater surprise came when we examined the Direkli Cave goats' nuclear genomes: while most looked like the bezoar ibex, as expected, one sample appeared different from the rest. This sample, Direkli4, showed more ancestral genetic variants than other Direkli goats, indicating it might have been a different species than the others."

To better understand this, the Trinity team collaborated with researchers from Muséum national d'Histoire naturelle of Paris to generate genetic data from other species in the Capra group.

A new lineage of Tur

The team was surprised to see that the Direkli4 sample in fact grouped with the Caucasian tur -- appearing to be a sister group to both East and West types. Intrigued, the team screened more material from Direkli Cave and found an additional two samples with a "tur-like" genome, suggesting that a population of these tur relatives lived in the Taurus Mountains close to local bezoar ibex, with both hunted by humans in pre-historic times.

The team suggest a name for the discovered Taurasian tur: Capra taurensis or Capra caucasica taurensis; researchers still classify living tur as either subspecies or two distinct species.

As tur are larger and heavier than other wild goats, with a distinctive horn shape, it should be possible to identify a group of tur relatives in animal remains. Horn remains are absent at Direkli Cave, despite the large numbers of remains -- possibly pointing to these being a valuable prize among hunters. But archaeozoologists in the team showed there were a lot of large-bodied goats at Direkli Cave -- and possibly at other mountainous locations in southwest Asia.

"We hope that this will encourage re-evaluation and analysis of faunal remains in the region as there could be some exciting discoveries still to be found," added Dr Daly.

A victim of climatic change and human activity?

The team suggest that the ancestors of tur lived across a broader geographical area over the past 100,000 years, from the Caucasus Mountains to the Taurus Mountains by the Mediterranean -- and that climate change may have caused habitat fragmentation.

Dr Daly said: "The Last Glacial Maximum, or ice age, may have made many areas inhospitable, forcing these goats to compete with other species. The Taurasian tur may have been a leftover group, restricted to the peaks in the Taurus Mountains. Increasing human activity would have placed additional pressure on the Taurasian tur, with hunting evidenced at Direkli Cave.

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100,000-year-old polar bear genome reveals ancient hybridization with brown bears

An analysis of ancient DNA from a 100,000-year-old polar bear has revealed that extensive hybridization between polar bears and brown bears occurred during the last warm interglacial period in the Pleistocene, leaving a surprising amount of polar bear ancestry in the genomes of all living brown bears.

The study, led by scientists at the University of California, Santa Cruz, was published June 16 in Nature Ecology & Evolution. The researchers obtained ancient DNA from the skull of a juvenile polar bear that was found in 2009 on the coast of the Beaufort Sea in Arctic Alaska. Scientists nicknamed the bear 'Bruno,' although DNA analysis later showed it to be a female.

"The availability of Bruno's paleogenome has made it possible to detect an ancient admixture event that impacted all living brown bears," said first author Ming-Shan Wang, a postdoctoral scientist in the UCSC Paleogenomics Lab.

Corresponding author Beth Shapiro, professor of ecology and evolutionary biology at UC Santa Cruz and an investigator at the Howard Hughes Medical Institute, said the team's genomic analyses show that Bruno belonged to a polar bear population that was ancestral to living polar bears. At some point, probably after around 125,000 years ago, she said, the polar bear lineage leading to Bruno and the brown bear lineage leading to all living brown bears crossed paths and hybridized.

As a result of this ancient admixture, polar bear ancestry accounts for as much as 10% of the genomes of brown bears living today. "We never would have seen this without Bruno's genome, because all living brown bears have that admixture as part of their genomes," Shapiro said.

Although polar bears and brown bears are distinct species with striking differences in appearance, behavior, and habitats, they are closely related and can readily hybridize when their ranges overlap. Reports of hybrids have increased in recent years as the climate warms and disappearing sea ice forces polar bears onto Arctic coastal areas, while brown bears expand their range northward.

Previous studies of ancient DNA have shown that admixture has occurred in certain populations of brown bears at least four different times between around 15,000 and 25,000 years ago. In all cases, the direction of gene flow was from polar bears into brown bears.

"The admixed individuals, if they survive, do so as brown bears, perhaps because they have difficulty hunting successfully on the sea ice if they are not completely white," Shapiro explained. "Polar bears have always been a small population with not much genetic diversity."

The new study did find some evidence of possible gene flow from brown bears into Bruno's lineage, but the absence of admixture in polar bears today supports the idea that brown bear ancestry reduces a bear's fitness for life as a polar bear. After diverging from brown bears about 500,000 years ago, polar bears evolved into highly specialized hunters of marine mammals on the Arctic sea ice. Brown bears, in contrast, are generalists ranging widely across North America, Europe, and Asia.

Bruno lived during a time of changing climate after the peak of a warm interglacial period when temperatures and sea levels were considerably higher than they are now. Similar conditions can be expected in the future as a result of rapid climate change driven by the burning of fossil fuels and other human activities. As Arctic sea ice declines, many polar bear populations are already struggling to survive.

"If the rapid, unnatural, and severe human-caused warming of the Arctic we are documenting today continues unabated, it is uncertain whether polar bears will have a sea ice habitat to return to and survive genetically," said coauthor Ian Stirling, a polar bear biologist and research scientist with Environment and Climate Change Canada.

According to Shapiro, "We shouldn't be surprised to see admixture happening again today as the climate changes and these species are overlapping and encountering each other again in the wild. Climate change allows gene flow to occur between what we think of as different species."

Climatic shifts that have brought polar bears and brown bears together in the past include glacial periods when sea ice was more extensive, allowing polar bears to mix with brown bears in southeast Alaska, the Kuril Islands, and even Ireland. The brown bears in these locations (now extinct in Ireland) acquired additional polar bear genes on top of the ancient admixture revealed by Bruno's genome.

As for what brown bears might have gained from their polar bear ancestry, scientists can only speculate. "It's possible that brown bears got something cool from polar bears, but we can't say for sure at this point," Shapiro said.

Finding Bruno's skull was serendipitous. Coauthors Pamela Groves, Daniel Mann and Michael Kunz from the University of Alaska Fairbanks were walking the Beaufort Sea coastline in 2009 surveying for recent coastal erosion when they stumbled upon the skull resting just above the high tide line.

"We weren't even looking for bones, as typically we find ancient bones a hundred miles inland where they have been stored in permafrost along sleepy rivers," said Groves. Since polar bears spend most of their lives at sea, finding any polar bear remains is extremely unusual. Bruno is the only ancient polar bear skull ever recorded and the only ancient polar bear bone known from North America.

"Understanding how past changes in climate drove interactions between organisms is critical to predicting how current changes will create new admixtures, increase disease transmission, or impact natural resources or society," said Leslie Rissler, program director at the U.S. National Science Foundation, which funded the research.

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DNA provides unique look at moa and climate change

Ancient moa DNA has provided insights into how species react to climate change, a University of Otago study has found.

By analysing ancient DNA of the extinct eastern moa, researchers from the Department of Zoology found the giant birds altered their distribution as the climate warmed and cooled.

Lead author Dr Alex Verry says the species was spread across the eastern and southern South Island during the warmer Holocene period, but was restricted to the southern South Island during the height of the last Ice Age about 25,000 years ago.

This is in comparison to the heavy-footed moa, which retreated to both southern and northern regions of the South Island, while the upland moa inhabited four different areas.

"The eastern moa's response had consequences for its population size and genetic diversity -- the last Ice Age lead to a pronounced genetic bottleneck which meant it ended up with lower genetic diversity than other moa living in the same areas," Dr Verry says.

The study, published in Biology Letters, is the first time high throughput DNA sequencing, which simultaneously sequences millions of pieces of DNA, has been used to investigate moa at the population level.

The findings highlight how past climate change impacted species in different ways and that a 'one size fits all' model is not practical.

"It makes us wonder what is going to happen to species as they attempt to adapt to climate change today and into the future? Will they also attempt to move to new areas in order to survive?

"For some species this will not be possible, some species will run out of space, such as alpine species which will have to move upward but can only go so far until there is no more 'up'," he says.

Co-author Dr Nic Rawlence, Director of Otago's Palaeogenetics Laboratory, says the research is a rare example of the impacts of past climate change on extinct megafauna from New Zealand.

It also demonstrates how fossil remains and museum collections can be used to answer new questions about the past.

"This is really bringing the power of palaeogenomics to New Zealand research questions, whereas previously most research and interest has focused on Eurasian or American species. We are really starting to build capacity for this research in New Zealand," he says.

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Solving the disappearance of bears and lions with ancient DNA

An international team of researchers led by the University of Adelaide, suggest a change in climate is the likely cause of the mysterious disappearance of ancient lions and bears from parts of North America for a thousand years or more prior to the last Ice Age.

In a study in Molecular Ecology, the researchers sequenced DNA from fossils of cave lions and bears from North America and Eurasia to better understand the timing and drivers of their past movement between continents.

Co-author, Dr Kieren Mitchell from the University of Adelaide's Australian Centre for Ancient DNA said, "There's a common perception that outside of mass extinctions or direct human interference, ecosystems tend to remain stable over thousands or even millions of years.

"As illustrated by our study of the fossil record, that's not necessarily the case.

"Previous research has shown that brown bears (or grizzly bears) disappeared from some parts of North America for thousands of years prior to the last Ice Age. They later reappeared, walking from Russia to Alaska across the Bering Land Bridge -- possibly at the same time as people moved across the Bridge into North America too.

"But no-one knows exactly why they disappeared in the first place, which is why studying this event is important."

A key finding of the new research is that cave lions from the same area became extinct more than once -- before their final extinction they also disappeared and reappeared thousands of years later, around the same time as bears. There is no evidence that people caused these temporary disappearances, and cold Ice Age conditions were not to blame.

"Instead, it looks like a smoking gun pointing to some kind of change in their ecosystem," Dr Mitchell said.

The timing of lions and bear extinction from parts of North America (specifically Alaska and the Yukon Territory) coincides with evidence of widespread vegetation change in the region. The researchers suggest that warm temperatures before the last Ice Age may have caused a change in the abundance of different kinds of plants, which had knock-on effects on herbivores and then their predators (like bears and lions).

Colder temperatures leading up to the last Ice Age might have reversed this change and made the area more hospitable for herbivores, and in turn their predators.

"Overall, these findings demonstrate just how changeable past ecosystems have been, and also how the abundance of different species can be very sensitive to changes in climate," Dr Mitchell said.

Lead author from the University of Adelaide Dr Alexander Salis said: "The shared patterns of dispersal between lions and bears correspond with the presence of the Bering Land Bridge that connected Russia and Alaska during Ice Ages.

"The Bridge was periodically exposed and inundated by changing sea levels during the last few Ice Ages, allowing intermittent dispersal of animals and people between continents and changing the faunal composition.

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Ancient DNA reveals the world’s oldest family tree

Analysis of ancient DNA from one of the best-preserved Neolithic tombs in Britain has revealed that most of the people buried there were from five continuous generations of a single extended family.

By analysing DNA extracted from the bones and teeth of 35 individuals entombed at Hazleton North long cairn in the Cotswolds-Severn region, the research team was able to detect that 27 of them were close biological relatives. The group lived approximately 5700 years ago -- around 3700-3600 BC -- around 100 years after farming had been introduced to Britain.

Published in Nature, it is the first study to reveal in such detail how prehistoric families were structured, and the international team of archaeologists and geneticists say that the results provide new insights into kinship and burial practices in Neolithic times.

The research team -- which included archaeologists from Newcastle University, UK, and geneticists from the University of the Basque Country, University of Vienna and Harvard University -- show that most of those buried in the tomb were descended from four women who had all had children with the same man.

The cairn at Hazleton North included two L-shaped chambered areas which were located north and south of the main 'spine' of the linear structure. After they had died, individuals were buried inside these two chambered areas and the research findings indicate that men were generally buried with their father and brothers, suggesting that descent was patrilineal with later generations buried at the tomb connected to the first generation entirely through male relatives.

While two of the daughters of the lineage who died in childhood were buried in the tomb, the complete absence of adult daughters suggests that their remains were placed either in the tombs of male partners with whom they had children, or elsewhere.

Although the right to use the tomb ran through patrilineal ties, the choice of whether individuals were buried in the north or south chambered area initially depended on the first-generation woman from whom they were descended, suggesting that these first-generation women were socially significant in the memories of this community.

There are also indications that 'stepsons' were adopted into the lineage, the researchers say -- males whose mother was buried in the tomb but not their biological father, and whose mother had also had children with a male from the patriline. Additionally, the team found no evidence that another eight individuals were biological relatives of those in the family tree, which might further suggest that biological relatedness was not the only criterion for inclusion. However, three of these were women and it is possible that they could have had a partner in the tomb but either did not have any children or had daughters who reached adulthood and left the community so are absent from the tomb.

Dr Chris Fowler of Newcastle University, the first author and lead archaeologist of the study, said: "This study gives us an unprecedented insight into kinship in a Neolithic community. The tomb at Hazleton North has two separate chambered areas, one accessed via a northern entrance and the other from a southern entrance, and just one extraordinary finding is that initially each of the two halves of the tomb were used to place the remains of the dead from one of two branches of the same family. This is of wider importance because it suggests that the architectural layout of other Neolithic tombs might tell us about how kinship operated at those tombs."

Iñigo Olalde of the University of the Basque Country and Ikerbasque, the lead geneticist for the study and co-first author, said: "The excellent DNA preservation at the tomb and the use of the latest technologies in ancient DNA recovery and analysis allowed us to uncover the oldest family tree ever reconstructed and analyse it to understand something profound about the social structure of these ancient groups."

David Reich at Harvard University, whose laboratory led the ancient DNA generation, added: "This study reflects what I think is the future of ancient DNA: one in which archaeologists are able to apply ancient DNA analysis at sufficiently high resolution to address the questions that truly matter to archaeologists."

Ron Pinhasi, of the University of Vienna, said: "It was difficult to imagine just a few years ago that we would ever know about Neolithic kinship structures. But this is just the beginning and no doubt there is a lot more to be discovered from other sites in Britain, Atlantic France, and other regions."

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Ancient DNA found in soil samples reveals mammoths, Yukon wild horses survived thousands of years longer than believed

Mere spoonfuls of soil pulled from Canada's permafrost are opening vast windows into ancient life in the Yukon, revealing rich new information and rewriting previous beliefs about the extinction dynamics, dates and survival of megafauna like mammoths, horses and other long-lost life forms.

In a new paper, published in the journal Nature Communications, researchers from McMaster University, the University of Alberta, the American Museum of Natural History and the Yukon government present a 30,000-year DNA record of past environments, drawn from cored permafrost sediments extracted from the Klondike region of central Yukon.

Researchers used DNA capture-enrichment technology developed at McMaster to isolate and rebuild, in remarkable detail, the fluctuating animal and plant communities at different time points during the Pleistocene-Holocene transition, an unstable climatic period 11,000-14,000 years ago when a number of large species such as mammoths, mastodons and sabre-toothed cats disappeared.

They reconstructed the ancient ecosystems using tiny soil samples which contain billions of microscopic genomic sequences from animal and plant species.

The analysis reveals that mammoths and horses were already in steep decline prior to the climatic instability, but they did not immediately disappear due to human overhunting as previously thought. In fact, the DNA evidence shows that both the woolly mammoth and North American horse persisted until as recently as 5,000 years ago, bringing them into the mid-Holocene, the interval beginning roughly 11,000 years ago that we live in today.

Through the early Holocene the Yukon environment continued to experience massive change. Formerly rich grasslands -- the "Mammoth Steppe" -- were overrun with shrubs and mosses, species no longer held in check by large grazing herds of mammoths, horses and bison. Today, grasslands do not prosper in northern North America, in part because there are no megafaunal "ecological engineers" to manage them.

"The rich data provides a unique window into the population dynamics of megafuana and nuances the discussion around their extinction through more subtle reconstructions of past ecosystems" says evolutionary geneticist Hendrik Poinar, a lead author on the paper and director of the McMaster Ancient DNA Centre.

This work builds on previous research by McMaster scientists who had determined woolly mammoths and the North American horse were likely present in the Yukon approximately 9,700 years ago. Better techniques and further investigation have since refined the earlier analysis and pushed forward the date even closer to contemporary time.

"Now that we have these technologies, we realize how much life-history information is stored in permafrost,"explains Tyler Murchie, a postdoctoral researcher in McMaster's Department of Anthropology and a lead author of the study.

"The amount of genetic data in permafrost is quite enormous and really allows for a scale of ecosystem and evolutionary reconstruction that is unparalleled with other methods to date" he says.

"Although mammoths are gone forever, horses are not" says Ross MacPhee of the American Museum of Natural History, another co-author. "The horse that lived in the Yukon 5,000 years ago is directly related to the horse species we have today, Equus caballus. Biologically, this makes the horse a native North American mammal, and it should be treated as such."

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Ancient DNA analysis sheds light on dark event in medieval Spain

An international research team led by the University of Huddersfield's Archaeogenetics Research Group, including geneticists, archaeological scientists, and archaeologists, has published the genome sequence of a unique individual from Islamic medieval Spain -- al-Andalus -- the results of which have shed light on a brutal event that took place in medieval Spain.

The individual, who was discovered in an eleventh century Islamic necropolis from the city of Segorbe, near Valencia in Spain, is known to local archaeologists as the 'Segorbe Giant' because of his unusual height.

His skeleton had suggested that he might have some African ancestry. Most of Spain had been progressively conquered by Arabs and Berbers from Northwest Africa from the eighth century onwards, creating one of the major centres of medieval European civilisation.

The ancient DNA analysis was carried out by Dr Marina Silva and Dr Gonzalo Oteo-Garcia, who had been working on the University's Leverhulme Trust doctoral scholarship programme in evolutionary genomics.

They found that the "Giant" carried highly specific North African genetic lineages on both his male and female lines of descent -- the Y-chromosome and the mitochondrial DNA -- the oldest individual known to have this particular pattern of ancestry. This suggested that his recent ancestry was indeed amongst the newly Islamicised Berber populations of medieval Northwest Africa.

But a more detailed examination revealed a more complex situation. The male and female lines of descent account for only a small fraction of our overall ancestry -- that from our father's father's father and our mother's mother's mother, and so on.

His genome-wide ancestry showed that he also carried a significant amount -- likely more than half -- of local Spanish ancestry in his chromosomes. Moreover, stable isotope analyses suggested that he most likely grew up locally meaning the "Giant's" Berber ancestry was in fact due to migration from an earlier generation. He therefore belonged to a settled community that had thoroughly intermixed local Spanish and immigrant North African ancestry.

What was especially striking revealed Professor Martin Richards, Director of the University's Evolutionary Genomics Research Centre, was that he was very unlike modern people from Valencia, who carry little or none of his Berber genetic heritage.

This can be explained by the changing political situation following the Christian reconquest of Spain as Dr Oteo-Garcia, who recently commenced work at the University of Parma, explained: "The decree of expulsion of Moriscos from the Valencia region, that is, Muslims who had already been forcibly converted to Christianity, was followed by the resettlement by people from further north, who had little North African ancestry, thereby transforming the genetic variation in the region."

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Ancient DNA rewrites early Japanese history -- modern day populations have tripartite genetic origin

Ancient DNA extracted from human bones has rewritten early Japanese history by underlining that modern day populations in Japan have a tripartite genetic origin -- a finding that refines previously accepted views of a dual genomic ancestry.

Twelve newly sequenced ancient Japanese genomes show that modern day populations do indeed show the genetic signatures of early indigenous Jomon hunter-gatherer-fishers and immigrant Yayoi farmers -- but also add a third genetic component that is linked to the Kofun peoples, whose culture spread in Japan between the 3rd and 7th centuries.

Rapid cultural transformations

The Japanese archipelago has been occupied by humans for at least 38,000 years but Japan underwent rapid transformations only in the last 3,000 years, first from foraging to wet-rice farming, and then to a technologically advanced imperial state.

The previous, long-standing hypothesis suggested that mainland Japanese populations derive dual-ancestry from the indigenous Jomon hunter-gatherer-fishers, who inhabited the Japanese archipelago from around 16,000 to 3,000 years ago, and later Yayoi farmers, who migrated from the Asian continent and lived in Japan from around 900 BC to 300 AD.

But the 12 newly sequenced ancient Japanese genomes -- which came from the bones of people living in pre- and post-farming periods -- also identify a later influx of East Asian ancestry during the imperial Kofun period, which lasted from around 300 to 700 AD and which saw the emergence of political centralisation in Japan.

Shigeki Nakagome, Assistant Professor in Psychiatry in Trinity College Dublin's School of Medicine, led the research, which brought together an interdisciplinary team of researchers from Japan and Ireland. Professor Nakagome said:

"Researchers have been learning more and more about the cultures of the Jomon, Yayoi, and Kofun periods as more and more ancient artefacts show up, but before our research we knew relatively little about the genetic origins and impact of the agricultural transition and later state-formation phase."

"We now know that the ancestors derived from each of the foraging, agrarian, and state-formation phases made a significant contribution to the formation of Japanese populations today. In short, we have an entirely new tripartite model of Japanese genomic origins -- instead of the dual-ancestry model that has been held for a significant time."

Genomic insights into key Japanese transformations

In addition to the overarching discovery, the analyses also found that the Jomon maintained a small effective population size of around 1,000 over several millennia, with a deep divergence from continental populations dated to 20,000-15,000 years ago -- a period which saw Japan become more geographically insular through rising sea-levels.

The Japanese archipelago had become accessible through the Korean Peninsula at the beginning of the Last Glacial Maximum, some 28,000 years ago, enabling movement between. And the widening of the Korea Strait 16,000 to 17,000 years ago due to rising sea-levels may have led to the subsequent isolation of the Jomon lineage from the rest of the continent. These time frames also coincide with the oldest evidence of Jomon pottery production.

"The indigenous Jomon people had their own unique lifestyle and culture within Japan for thousands of years prior to the adoption of rice farming during the subsequent Yayoi period. Our analysis clearly finds them to be a genetically distinct population with an unusually high affinity between all sampled individuals -- even those differing by thousands of years in age and excavated from sites on different islands," explained Niall Cooke, PhD Researcher at Trinity. "These results strongly suggest a prolonged period of isolation from the rest of the continent."

The spread of agriculture is often marked by population replacement, as documented in the Neolithic transition throughout most of Europe, with only minimal contributions from hunter-gatherer populations observed in many regions. However, the researchers found genetic evidence that the agricultural transition in prehistoric Japan involved the process of assimilation, rather than replacement, with almost equal genetic contributions from the indigenous Jomon and new immigrants associated with wet-rice farming.

Several lines of archaeological evidence support the introduction of new large settlements to Japan, most likely from the southern Korean peninsula, during the Yayoi-Kofun transition. And the analyses provide strong support for the genetic exchange involved in the appearance of new social, cultural, and political traits in this state-formation phase.

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Breakthrough in studying ancient DNA from Doggerland that separates the UK from Europe

Thousands of years ago the UK was physically joined to the rest of Europe through an area known as Doggerland. However, a marine inundation took place during the mid-holocene, separating the British landmass from the rest of Europe, which is now covered by the North Sea.

Scientists from the School of Life Sciences at the University of Warwick have studied sedimentary ancient DNA (sedaDNA) from sediment deposits in the southern North Sea, an area which has not previously been linked to a tsunami that occurred 8150 years ago.

The paper, led by the University of Bradford and involving Universities of Warwick, Wales St. Trinity David, St. Andrews, Cork, Aberystwyth, Tartu as well as the Smithsonian and Natural History Museum, 'Multi-Proxy Characterisation of the Storegga Tsunami and Its Impact on the Early Holocene Landscapes of the Southern North Sea', published in the Journal Geosciences, sees Life Scientists from the University of Warwick work specifically on the sedimentary ancient DNA from Doggerland.

A number of innovative breakthroughs were achieved by the University of Warwick scientists in terms of analysing the sedaDNA. One of these was the concept of biogenomic mass, where for the first time they were able to see the how the biomass changes with events, evidence of this presented in the paper refers to the large woody mass of trees from the tsunami found in the DNA of the ancient sediment.

New ways of authenticating the sedaDNA were also developed, as current methods of authentication do not apply to sedaDNA which has been damaged whilst under the sea for thousands of years because there is too little information for each individual species. Researchers therefore came up with a new way, metagenomic assessment methodology, whereby the characteristic damage found at the ends of ancient DNA molecules is collectively analysed across all species rather than one.

Alongside this a key part of analysing the sedaDNA is to determine whether or not it was deposited in situ or has moved over time. This led researchers to develop statistical methods to establish which scenario was appropriate, using stratigraphic integrity they were able to determine that the sedaDNA in the sediment deposits had not moved a massive amount since deposition by assessing the biomolecules vertical movement in the core column of the sedaDNA.

Identifying which organisms the ancient fragmented molecules of DNA came from is also challenging because often there is nothing to directly compare. In a fourth innovation the researchers refined algorithms to define these regions of "dark phylogenetic space" from where organisms must have originated overcome this issue.

Professor Robin Allaby from the School of Life Sciences at the University of Warwick comments: "This study represents an exciting milestone for sedimentary ancient DNA studies establishing a number of breakthrough methods to reconstruct an 8,150 year old environmental catastrophe in the lands that existed before the North Sea flooded them away into history."

Professor Vince Gaffney from the School of Archaeological and Forensic Sciences at the University of Bradford said: "Exploring Doggerland, the lost landscape underneath the North Sea, is one of the last great archaeological challenges in Europe. This work demonstrates that an interdisciplinary team of archaeologists and scientists can bring this landscape back to life and even throw new light on one of prehistory's great natural disasters, the Storegga Tsunami.

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