Researchers, Coast Salish people analyze 160-year-old indigenous dog pelt in the Smithsonian's collection

Researchers from the Smithsonian's National Museum of Natural History led a new analysis that sheds light on the ancestry and genetics of woolly dogs, a now extinct breed of dog that was a fixture of Indigenous Coast Salish communities in the Pacific Northwest for millennia. Anthropologist Logan Kistler and evolutionary molecular biologist Audrey Lin analyzed genetic clues preserved in the pelt of "Mutton," the only known woolly dog fleece in the world, to pinpoint the genes responsible for their highly sought-after woolly fur.

The study's findings, published today, Dec. 14, in the journal Science, include interviews contributed by several Coast Salish co-authors, including Elders, Knowledge Keepers and Master Weavers, who provided crucial context about the role woolly dogs played in Coast Salish society.

"Coast Salish traditional perspective was the entire context for understanding the study's findings," said Kistler, the museum's curator of archaeobotany and archaeogenomics.

Coast Salish tribal nations in Washington state and British Columbia bred and cared for woolly dogs for thousands of years. Prized for their thick undercoats, the dogs were sheared like sheep and often kept in pens or on islands to carefully manage their breeding and to care for the canines' health and vitality. Coast Salish weavers used the dogs' wool to craft blankets and other woven items that served a variety of ceremonial and spiritual purposes. Woolly dogs themselves possessed spiritual significance and were often treated as beloved family members. As emblems for many Coast Salish communities, woolly dogs adorned woven baskets and other art forms.

By the mid-19th century, this once thriving dog wool-weaving tradition was in decline. In the late 1850s, naturalist and ethnographer George Gibbs cared for a woolly dog named Mutton. When Mutton died in 1859, Gibbs sent his pelt to the nascent Smithsonian Institution, where the fleece has resided ever since. However, few were aware of the pelt's existence until it was rediscovered in the early 2000s.

Lin first learned about Mutton when she was a Peter Buck postdoctoral fellow at the museum in 2021.

"When I saw Mutton in person for the first time, I was just overcome with excitement," said Lin, who is now a postdoctoral researcher at the American Museum of Natural History. "I had heard from some other people that he was a bit scraggly, but I thought he was gorgeous."

She was surprised to find out that virtually no work had been done on the genetics of woolly dogs, which disappeared around the turn of the 20th century. She teamed up with Kistler and they reached out to several Coast Salish communities to gauge their interest in working together on a potential research project on woolly dogs.

Many in the Coast Salish communities were eager to share their knowledge.

"We were very excited to participate in a study that embraces the most sophisticated Western science with the most established Traditional Knowledge," said Michael Pavel, an Elder from the Skokomish/Twana Coast Salish community in Washington, who remembers hearing about woolly dogs early in his childhood. "It was incredibly rewarding to contribute to this effort to embrace and celebrate our understanding of the woolly dog."

To complement the perspectives they received from Pavel and other Coast Salish people from British Columbia and Washington state (the text from their interviews is available in the study's supplementary materials), Lin, Kistler and their colleagues began analyzing Mutton's genetic code. They sequenced the woolly dog genome and compared it with the genomes of ancient and modern breeds of dogs to determine what set woolly dogs apart. They also identified certain chemical signatures called isotopes in Mutton's pelt to determine the dog's diet and teamed up with noted natural history illustrator Karen Carr to create a life-like reconstruction of what Mutton looked like in the 1850s. Carr's work is the first in-depth reconstruction of a Coast Salish woolly dog in nearly three decades.

Based on the genetic data, the team estimated that woolly dogs diverged from other breeds up to 5,000 years ago -- a date that lines up with archaeological remains from the region. They also discovered that Mutton was genetically similar to pre-colonial dogs from Newfoundland and British Columbia. The researchers estimate that nearly 85% of Mutton's ancestry can be linked to pre-colonial dogs. This ancient ancestry is surprising because Mutton lived decades after the introduction of European dog breeds. This makes it likely that Coast Salish communities continued to maintain woolly dogs' unique genetic makeup until right before the dogs were wiped out.

In total, the team analyzed more than 11,000 different genes in Mutton's genome to determine what gave woolly dogs their fluffy fleece and wool fibers that could be spun together to create yarn. They identified 28 genes that have links to hair growth and follicle regeneration. These included a gene that causes a woolly hair phenotype in humans, and another linked to curly hair in other dogs. Similar genes were even activated in the genomes of woolly mammoths.

However, Mutton's genetics could tell the researchers little about what caused the dogs to decline. Traditionally, scholars have speculated that the arrival of machine-made blankets to the region in the early 19th century made woolly dogs expendable. But insights from Pavel and other traditional experts revealed that it was improbable that such a central part of Coast Salish society could be replaced.

Instead, woolly dogs were likely doomed by numerous factors impacting the Coast Salish tribal nations after European settlers arrived. Due to disease and colonial policies of cultural genocide, displacement and forced assimilation, it likely became increasingly difficult or forbidden for Coast Salish communities to maintain their woolly dogs.

"It was thousands of years of very careful maintenance lost within a couple of generations," Lin said.

But despite their disappearance, the memory of woolly dogs is still embedded into Coast Salish society. And Pavel thinks their understanding of woolly dogs is only getting clearer thanks to the new research effort.

"All of our communities held a certain aspect of knowledge about the woolly dog," Pavel said. "But when woven together, as a result of participating in this study, we now have a much more complete understanding."

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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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New method traces ancestry of hybrid plants and animals

If you've ever kept a garden, you're probably familiar with hybrids, from disease-resistant tomatoes to Stargazer lilies.

Hybrids -- common in agriculture as well as in nature -- have chromosomes from two or more parent species. In some cases, including strawberries, goldfish and several other species, these disparate parental chromosomes become doubled, a condition known as allopolyploidy.

In "Transposon signatures of allopolyploid subgenome evolution," a recent article published in the journal Nature Communications, Binghamton University Assistant Professor of Biological Sciences Adam Session and Daniel S. Rokhsar, a professor of genetics, evolution and development at the University of California, Berkeley, outline a way to trace these genomes back to the polypoid hybrid's parent species.

Unlike previous methods, which use comparison with related non-hybrid species to decipher polypoid ancestry, the authors' method allows them to discover distinct ancestries by looking at genomic patterns in the hybrid itself.

"Each ancestral genome carries a unique set of repetitive elements," Session explained. "So if we find sets of chromosomes in a polypoid that carry different repetitive elements, that proves hybrid ancestry and allows us to figure out which chromosomes were inherited together coming from the various progenitor species."

In the article, they apply the method to some well-studied cases of polyploid hybrids, such as tobacco, cotton and cyprinid fish, such as goldish and carp. They also use it to tease out the disputed ancestries of other hybrids, including false flax and strawberries.

"In many cases, the ancestors of living polyploids are not known. Using our method, we can figure out the ancestral origin of different chromosomes just by studying the polyploid genome itself, and divide the chromosomes into sets, or 'sub-genomes,' derived from its various ancestors," he said. "In addition to identifying the subgenomes, we can also tell you the order in which they were put together."

Polyploidization -- the duplication of genomes in a hybrid that stabilizes its ancestry -- is much more common in plants than animals, since plants can better tolerate multiple copies of their genomes, Session explained. The process of polyploidization is more involved with animal species, although it does happen in some fish and amphibians. In the case of goldfish, the authors prove for the first time that they share the same duplicated gene sequences as common carp, and thus a common hybrid ancestor.

Polyploidy is unknown in mammals, although hybridization is still possible. Take mules, for instance, which are a hybrid between horses and donkeys: Male mules are effectively sterile, although female mules can mate with either parent species. But without genomic duplication, the distinctive hybrid type cannot be stably propagated.

A tetraploid such as cotton has four copies of each chromosome, two from each of two ancestors, while hexaploids -- such as false flax -- have six chromosomes derived from three parent species. With eight copies of each chromosome, an octoploid such as strawberry ultimately has four ancestral species.

Polyploids have complex biology that is still being deciphered, and figuring out the sub-genome structure of their genomes is a step forward. Over millions of years, the genes contributed by each of the parental species evolve in their new polyploid context. Some redundant genes are lost or inactivated; others can develop new functions or novel interactions with their counterparts in the other sub-genomes. The new work argues that the order in which parental species are added to the emerging polyploid mix in a higher polyploid like strawberry can have profound impact on how these evolutionary processes occur. Sorting out the impact of these duplicated on the evolving polyploid is an ongoing challenge, the authors said.

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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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DNA from archaeological remains shows that immigration to Scandinavia was exceptional during the Viking period

A new study based on 297 ancient Scandinavian genomes analysed together with the genomic data of 16,638 present day Scandinavians resolve the complex relations between geography, ancestry, and gene flow in Scandinavia -- encompassing the Roman Age, the Viking Age and later periods. A surprising increase of variation during the Viking period indicates that gene flow into Scandinavia was especially intense during this period.

An international study coordinated from Stockholm and Reykjavik investigates the development of the Scandinavian gene pool over the latest 2000 years. In this effort the scientists relied on historic and prehistoric genomes, and from material excavated in Scandinavia. These ancient genomes were compared with genomic data from 16,638 contemporary Scandinavians. As the geographical origin and the datings were known for all these individuals, it was possible to resolve the development of the gene pool to a level never realised previously.

Dr Ricardo Rodríguez Varela at the Centre for Palaeogenetics*, who analysed all the data and extracted some of the ancient DNA used in the study, explains: "With this level of resolution we not only confirm the Viking Age migration. We are also able to trace it to the east Baltic region, the British-Irish Isles and southern Europe. But not all parts of Scandinavia received the same amounts of gene flow from these areas. For example, while British-Irish ancestry became widespread in Scandinavia the eastern-Baltic ancestry mainly reached Gotland and central Sweden."

The gene pool bounced back after the Viking period

Another new discovery in this study was what happened to the gene pool after the Viking period. The scientists were surprised to find that it bounced back in the direction of what it looked like before the Viking period migration.

Professor Anders Götherström at the Centre for Palaeogenetics, who is a senior scientist on the study, is intrigued: "Interestingly, the non-local ancestry peaks during the Viking period while being lower before and after. The drop in current levels of external ancestry suggests that the Viking-period migrants got less children, or somehow contributed proportionally less to the gene pool than the people who were already in Scandinavia."

Yet a new discovery was the history of the northern Scandinavian gene pool. There is a genetic component in northern Scandinavia that is rare in central and western Europe, and the scientists were able to track this component in northern Scandinavia through the latest 1000 years.

Dr Ricardo Rodríguez Varela comments, "We suspected that there was a chronology to the northern Scandinavian gene pool, and it did indeed prove that a more recent influx of Uralic ancestry into Scandinavia define much of the northern gene pool. But if it is recent, it is comparatively so. For example, we know that this Uralic ancestry was present in northern Scandinavia as early as during the late Viking period."

Based on well-known Swedish archaeological sites

The study is based on a number of well-known Swedish archaeological sites. For example, there are genomes from the 17th century warship Kronan, from the Viking and Vendel period boat burials in the lake Mälaren Valley, and from the migration period ring fortress Sandby borg on Öland.

Anders Götherström conclude: "We were working on a number of smaller studies on different archaeological sites. And at some point it just made sense to combine them into a larger study on the development of the Scandinavian gene pool.

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Armored worm reveals the ancestry of three major animal groups

An international team of scientists, including from the Universities of Bristol and Oxford, and the Natural History Museum, have discovered that a well-preserved fossilised worm dating from 518 million years ago resembles the ancestor of three major groups of living animals.

Measuring half-an-inch long, the fossil worm -- named Wufengella and unearthed in China -- was a stubby creature covered in a dense, regularly overlapping array of plates on its back, belonging to an extinct group of shelly organisms called tommotiids.

Surrounding the asymmetrical armour was a fleshy body with a series of flattened lobes projecting from the sides. Bundles of bristles emerged from the body in between the lobes and the armour. The many lobes, bundles of bristles and array of shells on the back are evidence that the worm was originally serialised or segmented, like an earthworm.

The findings are reported today in the journal Current Biology. Study co-author, Dr Jakob Vinther from the University of Bristol's School of Earth Sciences, said: "It looks like the unlikely offspring between a bristle worm and a chiton mollusc. Interestingly, it belongs to neither of those groups."

The animal kingdom consists of more than 30 major body plans categorised as phyla. Each phylum harbours a set of features that set them apart from one another. Only a few features are shared across more than one group, which is a testament to the very fast rate of evolution during which these major groups of animals originated, called the Cambrian Explosion, about 550 million years ago.

Brachiopods are a phylum that superficially resemble bivalves (such as clams) in having a pair of shells and living attached to the seafloor, rocks or reefs. However, when looking inside, brachiopods reveal themselves to be very different in many respects. In fact, brachiopods filter water using a pair of tentacles folded up into a horseshoe-shape organ.

Such an organ is called a lophophore and brachiopods share the lophophore with two other major groups called the phoronids ("horseshoe worms") and bryozoans ("moss animals"). Molecular studies -- which reconstruct evolutionary trees using amino acid sequences -- agree with anatomical evidence that brachiopods, bryozoans and phoronids are each other's closest living relatives, a group called Lophophorata after their filter-feeding organ.

Co-author Dr Luke Parry from the University of Oxford added: "Wufengella belongs to a group of Cambrian fossils that's crucial for understanding how lophophorates evolved. They're called tommotiids, and thanks to these fossils we have been able to understand how brachiopods evolved to have two shells from ancestors with many shell-like plates arranged into a cone or tube.

"We have known for a long time about this tommotiid group called camenellans. Palaeontologists have thought that those shells were attached to an agile organism -- crawling around -- rather than being fixed in one place and feeding with a lophophore."

The team, which consists of palaeontologists from the University of Bristol, Yunnan University, the Chengjiang Museum of Natural History, University of Oxford, the Natural History Museum in London and the Muséum national d'Histoire Naturelle in Paris, demonstrate that Wufengella is a complete camenellan tommotiid, which means that reveals what the long sought-after wormy ancestor to lophophorates looked like.

Dr Parry added: "When it first became clear to me what this fossil was that I was looking at under the microscope, I couldn't believe my eyes. This is a fossil that we have often speculated about and hoped we would one day lay eyes on."

While the fossil fulfils the palaeontological prediction that the lophophorates' ancestral lineage was an agile, armoured worm, the appearance of its soft anatomy brings into focus some hypotheses about how lophophorates may be related to segmented worms.

Dr Vinther said: "Biologists had long noted how brachiopods have multiple, paired body cavities, unique kidney structures and bundles of bristles on their back as larvae. These similarities led them to notice how closely brachiopods resemble annelid worms."

"We now can see that those similarities are reflections of shared ancestry. The common ancestor of lophophorates and annelids had an anatomy most closely resembling the annelids.

"At some point, the tommotiid ancestor to the lophophorates became sessile and evolved suspension feeding (catching particles suspended in the water). Then a long, wormy body with numerous, repeated body units became less useful and was reduced."

Co-author Greg Edgecombe from the Natural History Museum said: "This discovery highlights how important fossils can be for reconstructing evolution.

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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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Pre-historic Wallacea: A melting pot of human genetic ancestries

The Wallacean islands have always been separated from Asia and Oceania by deep-sea waters. Yet, these tropical islands were a corridor for modern humans migrating into the Pleistocene Australia-New Guinea landmass (Sahul) and have been home to modern human groups for at least 47 thousand years. The archaeological record attests a major cultural transition across Wallacea that started around 3,500 years ago and is associated with the expansion of Austronesian-speaking farmers, who intermixed with local hunter-gatherer groups. However, previous genetic studies of modern-day inhabitants have yielded conflicting dates for this intermixing, ranging from 1,100 to nearly 5,000 years ago.

To shed light on the details of this expansion and the resulting human interactions, an international team of researchers analyzed DNA from 16 ancient individuals from different islands in Wallacea, greatly increasing the amount of ancient genomic data representing this region. "We found striking differences between regions in Wallacea and surprisingly, the ancestry of ancient individuals from the southern islands cannot be simply explained by admixture between Austronesian- and Papuan-related groups," says Sandra Oliveira, one of the study's lead authors.

Early ancestry contribution from Mainland Southeast Asia

The team identified an additional ancestry contribution from Mainland Southeast Asia, closest to present-day Austroasiatic speakers, and proposed that admixture occurred first between the Mainland Southeast Asian and Papuan-related ancestry and that gene flow from Austronesian-related groups occurred only later. "That Mainland Southeast Asian component is a great mystery to me. I suspect that we might be looking at small groups, perhaps of early farmers, who travelled a long way, left no archaeological or linguistic traces along the way, but who increased their population sizes after arrival," says Peter Bellwood, an author of the study who has conducted archaeological work in Island Southeast Asia for decades.

While the identity of the people who spread this ancestry is still unclear, the discovery of the Mainland Southeast Asian ancestry and its possible antiquity in the southern Wallacean islands has major implications for the understanding of the Neolithic dispersals into Island Southeast Asia. "This finding is very important for the archaeologists in the region," adds Toetik Koesbardiati, an Indonesian anthropologist involved in the study. He adds, "We will certainly intensify our efforts to study this migration with other lines of evidence."

Multiple admixture events throughout Wallacea

This work also revealed a closer relationship between the Austronesian-related ancestry of ancient individuals from northern Wallacea and the Pacific, compared to those from southern Wallacea -- a pattern matched by linguistic evidence. Additionally, it shed light on the timing of the Asian-Papuan genetic admixture. "Previous studies based on present-day populations have reported widely different estimates, some of which preceeded the archaeological evidence for the Austronesian expansion, while others were much more recent. Since we now have ancient individuals from different time periods we can directly show that admixture occurred in multiple pulses or continuously since at least 3,000 years ago throughout Wallacea," explains Mark Stoneking, a senior author of the study. He adds, "Future studies on older genomes might extend this date even further."

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Largest ever human family tree: 27 million ancestors

Researchers from the University of Oxford's Big Data Institute have taken a major step towards mapping the entirety of genetic relationships among humans: a single genealogy that traces the ancestry of all of us. The study has been published today in Science.

The past two decades have seen extraordinary advancements in human genetic research, generating genomic data for hundreds of thousands of individuals, including from thousands of prehistoric people. This raises the exciting possibility of tracing the origins of human genetic diversity to produce a complete map of how individuals across the world are related to each other.

Until now, the main challenges to this vision were working out a way to combine genome sequences from many different databases and developing algorithms to handle data of this size. However, a new method published today by researchers from the University of Oxford's Big Data Institute can easily combine data from multiple sources and scale to accommodate millions of genome sequences.

Dr Yan Wong, an evolutionary geneticist at the Big Data Institute, and one of the principal authors, explained: "We have basically built a huge family tree, a genealogy for all of humanity that models as exactly as we can the history that generated all the genetic variation we find in humans today. This genealogy allows us to see how every person's genetic sequence relates to every other, along all the points of the genome."

Since individual genomic regions are only inherited from one parent, either the mother or the father, the ancestry of each point on the genome can be thought of as a tree. The set of trees, known as a "tree sequence" or "ancestral recombination graph," links genetic regions back through time to ancestors where the genetic variation first appeared.

Lead author Dr Anthony Wilder Wohns, who undertook the research as part of his PhD at the Big Data Institute and is now a postdoctoral researcher at the Broad Institute of MIT and Harvard, said: "Essentially, we are reconstructing the genomes of our ancestors and using them to form a vast network of relationships. We can then estimate when and where these ancestors lived. The power of our approach is that it makes very few assumptions about the underlying data and can also include both modern and ancient DNA samples."

The study integrated data on modern and ancient human genomes from eight different databases and included a total of 3,609 individual genome sequences from 215 populations. The ancient genomes included samples found across the world with ages ranging from 1,000s to over 100,000 years. The algorithms predicted where common ancestors must be present in the evolutionary trees to explain the patterns of genetic variation. The resulting network contained almost 27 million ancestors.

After adding location data on these sample genomes, the authors used the network to estimate where the predicted common ancestors had lived. The results successfully recaptured key events in human evolutionary history, including the migration out of Africa.

Although the genealogical map is already an extremely rich resource, the research team plans to make it even more comprehensive by continuing to incorporate genetic data as it becomes available. Because tree sequences store data in a highly efficient way, the dataset could easily accommodate millions of additional genomes.

Dr Wong said: "This study is laying the groundwork for the next generation of DNA sequencing. As the quality of genome sequences from modern and ancient DNA samples improves, the trees will become even more accurate and we will eventually be able to generate a single, unified map that explains the descent of all the human genetic variation we see today."

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The impacts from using genetic testing to track down relatives

Genetic genealogy has become a popular hobby over the past several years, thanks to direct-to-consumer (DTC) genetic testing and relative-finder services offered by some DTC genetic testing companies. In a paper published February 24 in the American Journal of Human Genetics, researchers report results from a survey that asked people who had participated in these services what effect the discovery of previously unknown relatives had on their lives.

Among the most important findings were that identifying a genetic relative appeared to be somewhat common. Additionally, those discoveries were generally experienced as neutral or positive and didn't appear to have a big impact on participants' lives. However, some participants learned things that could be considered significant and destabilizing -- such as that their biological parent wasn't who they thought. These participants were especially vulnerable to negative outcomes.

"Everyone on our team is involved in studying the ethical, legal, and social implications of DTC genetic testing, and we've been paying attention to stories in the media about individuals who've made surprising family discoveries from these tests and relative-matching services," says lead author Christi Guerrini of the Center for Medical Ethics and Health Policy at Baylor College of Medicine. "We wanted to understand if these and other kinds of discoveries are common, how they're experienced by those making the discoveries, and what people are doing as a result."

The investigators sent the survey to about one million DTC genetic testing customers and genetic genealogy database participants; more than 26,000 responded. The final sample for analysis consisted of 23,196 completed or substantially completed surveys. Among the reasons that respondents said they chose to participate in this type of testing were to learn more about their family or build their family trees; to search for a biological parent, child, or other relative; or to investigate a suspicion that they might not be genetically related to family members.

"It seems that many -- perhaps most -- are just curious about their families and interested in building out their family trees, but it's clear that quite a lot of participants are looking for someone or hoping to confirm something in particular," Guerrini says. "It might be that they're adopted and looking for a biological parent, or that they've always felt out of place in their family and want to see if there's something to that feeling. Or they might be looking for information about a branch of their family tree that's unknown to them, or to confirm a family story that's been passed down over the years."

Most respondents (82%) reported that they learned the identity of at least one genetic relative. Among this subpopulation, 10% identified a biological grandparent, 10% identified a full or half- sibling, and 7% identified a biological father. The survey asked whether the participant had chosen to contact any of their newly identified relatives and, if so, the reasons for doing so. It also asked whether their discoveries resulted in any life changes, including changes in health-related behaviors.

Guerrini says that the high number of people overall who identified an unknown genetic relative was not unexpected, because many of those relatives could be very distant ones. But she acknowledges that the high number of participants who found close relatives could be skewed by the type of people who choose to undergo relative matching in the first place. "Unfortunately, we can't answer that question with our data, but I'm very interested in trying to do so in future research," she says.

She adds that although these experiences appear to be interesting and enjoyable to a large number of people, it's clear that some who are participating in these services have experienced negative outcomes. "In future research, we'd like to better understand those outcomes and what resources could be helpful in managing them," she says.

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Geneticists’ new research on ancient Britain contains insights on language, ancestry, kinship, milk

New research revealing a major migration to the island of Great Britain offers fresh insights into the languages spoken at the time, the ancestry of present-day England and Wales, and even ancient habits of dairy consumption.

The findings are described in Nature by a team of more than 200 international researchers led by Harvard geneticists David Reich and Nick Patterson. Michael Isakov, a Harvard undergraduate who discovered the existence of the 3,000-year-old migration, is one of the co-first authors.

The analysis is one of two Reich-led studies of DNA data from ancient Britain that Nature published on Tuesday. Both highlight technological advances in large-scale genomics and open new windows into the lives of ancient people.

"This shows the power of large-scale genetic data in concert with archaeological and other data to get rich information about our past from a time before writing," said Reich, a professor in the Department of Human Evolutionary Biology and a professor of genetics at Harvard Medical School. "The studies are not only important for Great Britain, where we now have far more ancient DNA data than in any other region, but also because of what they show about the promise of similar studies elsewhere in the world."

The researchers analyzed the DNA of 793 newly reported individuals in the largest genome-wide study involving ancient humans. Their findings reveal a large-scale migration likely from somewhere in France to the southern part of Great Britain, or modern-day England and Wales, that eventually replaced about 50 percent of the ancestry of the island during the Late Bronze Age (1200 to 800 B.C.).

The study supports a recent theory that early Celtic languages came to Great Britain from France during the Late Bronze Age. It challenges two prominent theories: that the languages arrived hundreds of years later, in the Iron Age, or 1,500 years earlier at the dawn of the Bronze Age.

Previous research has shown that large-scale movement often accompanied language changes in pre-state societies. The Reich team argues that this untold migration event makes more sense for the spread of early Celtic languages into Britain.

"By using genetic data to document times when there were large-scale movements of people into a region, we can identify plausible times for a language shift," Reich said. "Known Celtic languages are too similar in their vocabularies to plausibly descend from a common ancestor 4,500 years ago, which is the time of the earlier pulse of large-scale migration, and very little migration occurred in the Iron Age. If you're a serious scholar, the genetic data should make you adjust your beliefs: downweighting the scenario of early Celtic language coming in the Iron Age [and early Bronze Age] and upweighting the Late Bronze Age."

As part of the genetic analysis, the researchers found that the ability to digest cow's milk dramatically increased in Britain from 1200 to 200 B.C., which is about a millennium earlier than it did in central Europe. These findings illuminate a different role for dairy consumption in Britain during this period compared with the rest of mainland Europe. More study is needed to define that role, the researchers said. Increased milk tolerance would have provided a big advantage in the former of higher survival rates among the children of people carrying this genetic adaptation.

The newly discovered ancestry change happened around 3,000 years ago, more than a millennium and a half before the Saxon period. The team was aware of a migration into England at some point during this gap because of an observation they made in research published in 2016. That study showed that contemporary English people have more DNA from early European farmers than people who lived in England about 4,000 years ago. The team set out to collect DNA from later periods to detect the shift.

The discontinuity -- a specific point in time when the percentage of farmer ancestry in English genomes changed -- was first noticed in the summer of 2019 by Isakov, an applied mathematics concentrator. He had started working as a researcher in Reich's lab the summer after his first year and was able to increase the statistical power of the group's ancestry tests. When he noticed some outliers in the data from people living 3,000 years ago, he led a closer analysis and discovered the migration.

"It's an extraordinary outcome and I'm very happy that I was able to get through it," said Isakov, who will graduate in May.

The second paper looks at kinship practices of 35 individuals who lived about 5,700 years ago and were buried in a tomb at Hazleton North in Gloucestershire, England. The researchers found a 27-person family -- three times larger than the second-largest documented ancient family -- whose kin relationships could be precisely determined by analyzing their DNA. The team created a family tree that covered five generations and found examples of polygyny, polyandry, adoption, and a key role for both patrilineal and matrilineal descent.

The lab's research illustrates the interdisciplinary collaborations that are required to tell the richest stories of the ancient past, Isakov said.

"It's sort of incredible that we have geneticists, we have statisticians, we have archaeologists, linguists, and even chemical analysis coming together. I think that the fact that we're able to like merge all these fields and have an actual insight that's culturally important is a great example of interdisciplinary science."

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Deep mantle krypton reveals Earth’s outer solar system ancestry

Krypton from the Earth's mantle, collected from geologic hot spots in Iceland and the Galapagos Islands, reveals a clearer picture of how our planet formed, according to new research from the University of California, Davis.

The different isotopes of krypton are chemical fingerprints for scientists sleuthing out the ingredients that made the Earth, such as solar wind particles and meteorites from the inner and outer solar system. The findings indicate Earth's volatile elements -- essentials such as carbon, water and nitrogen -- arrived as Earth was growing and becoming a planet. This contradicts the popular theory that Earth's volatile elements were mostly delivered near the end of Earth's formation, which is marked by the moon-forming giant impact. Instead, the krypton isotopes suggest planetesimals from the cold outer solar system bombarded the Earth early on, millions of years before the big crunch. The young Earth also hoovered up dust and gas from the solar nebula (the cloud surrounding the sun) and was bombarded by meteorites.

"Our results require concurrent delivery of volatiles from multiple sources very early in Earth's formation," said Sandrine Péron, the lead author of the study. Péron, currently a Marie Sk?odowska-Curie Actions Fellow at ETH Zürich in Switzerland, conducted the research at UC Davis as a postdoctoral fellow working with Professor Sujoy Mukhopadhyay in the Department of Earth and Planetary Sciences.

"This study provides clues for the sources and timing of volatile accretion on Earth, and will help researchers better understand how not only Earth formed, but also other planets in the solar system and around other stars," Péron said. The study is published Dec. 15 in the journal Nature.

Primordial geochemistry

The volcanic hot spots spewing lava in Iceland and the Galapagos are fed by slushy magma plumes rising from the deepest layer of the mantle, near its boundary with the Earth's iron core. The elements and minerals in this deep layer are relatively unchanged since before the moon-forming impact, like a time capsule of the early Earth's chemistry more than 4.4 billion years old.

Mukhopadhyay's lab specializes in making precise measurements of noble gases in rocks from Earth and elsewhere. To sample deep mantle krypton, the researchers collected lava at hot spot plumes. The ancient gases rise to the surface in the erupting lava, getting trapped and entombed as bubbles in a glassy matrix when the lava quenches to a solid, providing some protection from outside contamination. However, even the most abundant krypton isotopes in these bubbles amounts to only a few hundred million atoms, making their detection challenging, Mukhopadhyay said.

Péron designed a new technique for measuring mantle krypton with mass spectrometry, concentrating krypton from rock samples in an environment virtually free of air contamination and neatly separating it from argon and xenon.

"Ours is the first study to precisely measure all krypton isotopes for the mantle, including the rarest krypton isotopes, Kr-78 and Kr-80," she said.

Building a planet

The researchers discovered that the chemical fingerprint of deep mantle krypton closely resembled primitive, carbon-rich meteorites, which may have been delivered from the cold, outer reaches of the solar system. But previous work by Mukhopadhyay and others found that neon, another noble gas in the deep mantle, was derived from the sun. The two different results suggest at least two distinct volatile sources for the Earth's mantle, delivered very early in its history. The researchers also noted less of the rare isotope Kr-86 in the deep mantle compared to known meteorites. The deficit in Kr-86 suggests that known meteorites alone may not account for all the mantle's krypton.

Finally, the new results also have implications for how Earth's atmosphere arose. The ratio of different krypton isotopes in the deep mantle doesn't match the isotope ratio in Earth's atmosphere, the researchers found. This means some gases in the atmosphere, including noble gases like krypton, were delivered to Earth after the moon-forming impact. Otherwise, Earth's mantle and atmosphere would have the same isotopic composition due to isotopic equilibration following the impact, Péron said.

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DNA tool allows you to trace your ancient ancestry

Scientists at the University of Sheffield studying ancient DNA have created a tool allowing them to more accurately identify ancient Eurasian populations, which can be used to test an individual's similarity to ancient people who once roamed the earth.

Currently the study of ancient DNA requires a lot of information to classify a skeleton to a population or find its biogeographical origins.

Now scientists have defined a new concept called Ancient Ancestry Informative Markers (aAIMs) -- a group of mutations that are sufficiently informative to identify and classify ancient populations.

The research, led by Dr Eran Elhaik, from the University of Sheffield's Department of Animal and Plant Sciences, saw the identification of a small group of aAIMs that can be used to classify skeletons to ancient populations.

Dr Elhaik said: "We developed a new method that finds aAIMs efficiently and have proved that it is accurate."

AIMs (Ancestry Informative Markers) have a long history in science and have been employed for the past decade by health and forensic experts.

But Dr Elhaik said that when his team applied traditional AIMs-finding tools to ancient DNA data, they were disappointed with their low accuracy.

"Ancient populations are much more diverse than modern ones," he said. "Their diversity was reduced over the years following events such as the Neolithic revolution and the Black Death.

"Although we have many more people today they are all far more similar to each other than ancient people. In addition, the ancient data themselves are problematic due to the large amount of degraded DNA."

To overcome these challenges, Dr Elhaik developed a specialised tool that identifies aAIMs by combining traditional methodology with a novel one that takes into account a mixture.

"Ancient genomes typically consist of hundreds of thousands and sometimes millions of markers. We demonstrated that only 13,000 markers are needed to make accurate population classifications for ancient genomes and while the field of ancient forensics does not exist yet, these aAIMs can help us get much closer to ancient people."

He added: "Until now you couldn't test people for ancient DNA ancestry because commercial microarrays, such as the ones used for genetic genealogy, don't have a lot of markers relevant for paleogenomics -- people could not study their primeval origins.

"This finding of aAIMs is like finding the fingerprints of ancient people. It allows testing of a small number of markers -- that can be found in a commonly available array -- and you can ask what part of your genome is from Roman Britons or Viking, or Chumash Indians, or ancient Israelites, etc.

"We can ask any question we want about these ancient people as long as someone sequenced these ancient markers. So this paper brings the field of paleogenomics to the public."

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