Friday, October 13, 2017

40,000-year-old man in China reveals complicated genetic history of Asia Chinese Academy

The biological makeup of humans in East Asia is shaping up to be a very complex story, with greater diversity and more distant contacts than previously known, according to a new study in Current Biology analyzing the genome of a man that died in the Tianyuan Cave near Beijing, China 40,000 years ago. His bones had enough DNA molecules left that a team led by Professor FU Qiaomei, at the Molecular Paleontology Lab at the Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), could use advanced ancient DNA sequencing techniques to retrieve DNA from him that spans the human genome.

Though several ancient humans have been sequenced in Europe and Siberia, few have been sequenced from East Asia, particularly China, where the archaeological record shows a rich history for early modern humans. This new study on the Tianyuan man marks the earliest ancient DNA from East Asia, and the first ancient genome-wide data from China.

The Tianyuan man was studied in 2013 by the same lab. Then, they found that he showed a closer relationship to present-day Asians than present-day Europeans, suggesting present-day Asian history in the region extends as far back as 40,000 years ago. With new molecular techniques only published in the last two years, Professor FU and her team, in a joint collaboration with experts at the Max Planck Institute of Evolutionary Anthropology and UC Berkeley, sequenced and analyzed more regions of the genome, particularly at positions also sequenced in other ancient humans.

Since 2013, DNA generated from ancient Europeans has shown that all present-day Europeans derive some of their population history from a prehistoric population that separated from other early non-African populations soon after the migration out of Africa. The mixed ancestry of present-day Europeans could bias tests of genetic similarity, including the results found for the Tianyuan man. With the newly published data, however, the Fu lab showed that his genetic similarity to Asians remained in comparisons including ancient Europeans without mixed ancestry. They confirmed that the closest relationship he shares is with present-day Asians. That was not, however, the most exciting result they found.

With a close relationship to present-day Asians, they expected him to act similarly to present-day Asian populations with respect to Europeans. It was a surprise when they found that a 35,000-year-old individual from Belgium, GoyetQ116-1, who in other ways behaved as an ancient European, shared some genetic similarity to the Tianyuan individual that no other ancient Europeans shared. It is unlikely that this is due to direct interactions between populations near the east and west coasts of Eurasia, since other ancient Europeans do not show a similar result. Instead, the researchers suggested that the two populations represented by the Tianyuan and GoyetQ116-1 individuals derived some of their ancestry from the same sub-population prior to the European-Asian separation. The genetic relationship observed between these two ancient individuals is direct evidence that European and Asian populations have a complex history.

A second unexpected result shed some light on human genetic diversity in prehistoric East Asia. In 2015, a study comparing present-day populations in Asia, the Pacific and the Americas showed that some Native American populations from South America had an unusual connection to some populations south of mainland Asia, most notably the Melanesian Papuan and the Andamanese Onge.
That study proposed that the population that crossed into the Americas around 20,000 years ago could not be thought of as a single unit. Instead, one or more related but distinct populations crossed at around the same time period, and at least one of these groups had additional ties to an Asian population that also contributed to the present-day Papuan and Onge.

No trace of this connection is observed in present-day East Asians and Siberians, but unlike them, the Tianyuan man also possesses genetic similarities to the same South Americans, in a pattern similar to that found for the Papuan and Onge. The new study directly confirms that the multiple ancestries represented in Native Americans were all from populations in mainland Asia. What is intriguing, however, is that the migration to the Americas occurred approximately 20,000 years ago, but the Tianyuan individual is twice that age. Thus, the population diversity represented in the Americas must have persisted in mainland Asia in two or more distinct populations since 40,000 years ago.

The Tianyuan man is only one individual, but the deeper sequencing of his genome by Professor FU and her team reveals a complicated separation for ancient Europeans and Asians and hints at a diverse genetic landscape for humans in East Asia. Their study also showed that he derives from a population that is related to present-day East Asians, but is not directly ancestral to these populations, further suggesting that multiple genetically distinct populations were located in Asia from 40,000 years ago until the present.

The Tianyuan man shows us that between 40,000 years ago and the present, there are many unanswered questions about the past populations of Asia, and ancient DNA will be the key solving those questions.

Thursday, October 12, 2017

Indigenous people have been on the far northeastern edge of Canada for most of the last 10,000 years, moving in shortly after the ice retreated from the Last Glacial Maximum. Archaeological evidence suggests that people with distinct cultural traditions inhabited the region at least three different times with a possible hiatus for a period between 2,000 and 3,000 years ago.

  • This schematic shows the settlement history of Newfoundland encompassing occupations by at least three distinct cultural groups: MA, Dorset Palaeoeskimo, and Beothuk.
  • Credit

  • Produced by Deirdre Elliott with QGIS 2.18.44, and data from Stephen Hull and Natural Earth.

Now, researchers who've examined genetic evidence from mitochondrial DNA provide evidence that two of those groups, known as the Maritime Archaic and Beothuk, brought different matrilines to the island, adding further support to the notion that those groups had distinct population histories. The findings are published in Current Biology on October 12.

"Our paper suggests, based purely on mitochondrial DNA, that the Maritime Archaic were not the direct ancestors of the Beothuk and that the two groups did not share a very recent common ancestor," says Ana Duggan of McMaster University. "This in turn implies that the island of Newfoundland was populated multiple times by distinct groups."

The relationship between the older Maritime Archaic population and Beothuk hadn't been clear from the archaeological record. With permission from the current-day indigenous community, Duggan and her colleagues, led by Hendrik Poinar, examined the mitochondrial genome diversity of 74 ancient remains from the island together with the archaeological record and dietary isotope profiles. All samples were collected from tiny amounts of bone or teeth.

The sample set included a Maritime Archaic subadult more than 7,700 years old found in the L'Anse Amour burial mound, the oldest known burial mound in North America and one of the first manifestations of the Maritime Archaic tradition. The majority of the Beothuk samples came from the Notre Dame Bay area, where the Beothuk retreated in response to European expansions. Most of those samples are from people that lived on the island within the last 300 years. The DNA evidence showed that the two groups didn't share a common maternal ancestor in the recent past, but rather one that coalesces sometime in the more distant past.

"These data clearly suggest that the Maritime Archaic people are not the direct maternal ancestors of the Beothuk and thus that the population history of the island involves multiple independent arrivals by indigenous peoples followed by habitation for many generations," the researchers write. "This shows the extremely rich population dynamics of early peoples on the furthest northeastern edge of the continent."

No trace of early contact between Rapanui and South Americans in ancient DNA

  • IMAGE: This photograph shows moai on Rapa Nui. view more 
    Credit: Terry Hunt
Rapa Nui (Easter Island, Chile) has long been a source of intrigue and mystery. How did such a small community of people build so many impressively large statues? And what happened to cause that community to collapse? Researchers have also been curious about what kind of contact Rapa Nui's inhabitants, known as Rapanui, might have had with South Americans prior to the arrival of Europeans. Earlier evidence seemed to support early contact between the Rapanui and Native Americans .

But a new study of ancient DNA evidence collected from archaeological samples and reported in Current Biology on October 12th calls those findings back into question. The new study finds no genetic evidence that ancient inhabitants of Rapa Nui intermixed with South Americans. While the findings can't exclude the possibility that cultural contact took place between the two populations, if long-distance treks across the ocean did occur, "they did not leave genetic traces among the individual samples," said Lars Fehren-Schmitz of the University of California, Santa Cruz. "We were surprised that we didn't find any Native American admixture in our ancient Rapanui specimens."

The idea that there had been early Pacific contact with South America, or even that a Southern Pacific migration route contributed to the peopling of the Americas, has been a long-standing debate in the field. In their new study, Fehren-Schmitz and colleagues wanted to find out what DNA from ancient Rapanui samples had to say on the matter.

The researchers sequenced DNA from five individual samples representing Rapanui both before and after European contact. They report that the DNA, including both complete mitochondrial genomes and low-coverage autosomal genomes, indicates that the DNA of the sampled individuals falls within the genetic diversity of present-day and ancient Polynesians.

"We can reject the hypothesis that any of these individuals had substantial Native American ancestry," Fehren-Schmitz said. "Our data thus suggest that the Native American ancestry in contemporary Easter Islanders was not present on the island prior to European contact and may thus be due to events in more recent history."

The new study highlights the value of ancient DNA for testing hypotheses about the past. It's clear from earlier evidence that living Rapanui do have a small proportion of Native American ancestry. But, the researchers in the new study say, "it is especially difficult to disentangle movements of people in the prehistoric period from more recent times." The question remains: How and when did this population exchange happen?

The researchers say they'd now like to generate genome-wide data from additional ancient Oceania and western South American populations. The goal is to develop a more detailed picture of the populations that lived within each of these regions and potential interactions among them.

Monday, October 9, 2017

Amazon farmers discovered the secret of domesticating wild rice 4,000 years ago


Amazonian farmers discovered how to manipulate wild rice so the plants could provide more food 4,000 years ago, long before Europeans colonised America, archaeologists have discovered.

Experts from the UK and Brazil have found the first evidence that ancient South Americans learned how to grow bigger rice crops with larger grains, but this expertise may have been lost after 1492 when the indigenous population was decimated, research shows.

The evidence of the success of early rice farmers on the vast wetlands near the Guaporé River in Rondônia state, Brazil, could help modern day plant breeders develop rice crops which are less susceptible to disease and more adaptable to the effects of climate change than the Asian varieties. Different species of rice were first grown approximately 11,000 years ago in the Yangtze River, China, and around 2,000 years ago in West Africa.

The University of Exeter study, funded in part by the European Research Council, also shows how important the huge wetlands and tropical forests of lowland South America were in providing food for early human settlers in South America. Ancient inhabitants managed to domesticate cassava, peanuts and chilli peppers crops for food.

The archaeologists analysed 16 samples of microscopic plant remains from ten different time periods found during excavations during 2014 led by the University of São Paulo in South West Amazonia. More phytoliths, hard, microscopic pieces of silica made by plant cells, were found at higher ground level, suggesting rice began to play a larger role in the diet of people who lived in the area - and more was farmed - as time went on.

Changes in the ratio of husk, leaf and stem remains found at different ground levels also suggest the Amazon residents became more efficient harvesters over time, bringing more grain and fewer leaves to the site. The rice grown, Oryza sp, also became bigger over time compared to the wild rice first cultivated by the South Americans. This area has been occupied by humans for at least 10,000 years.

Professor Jose Iriarte, from the University of Exeter, who led the research, said: "This is the first study to identify when wild rice first began to be grown for food in South America. We have found people were growing crops with larger and larger seeds. Even though they were also eating wild and domesticated plants including maize, palm fruits, soursop and squash, wild rice was an important food, and people began to grow it at lake or river edges.

"During a time when the climate was getting wetter and the wetlands expanding, this critical seasonal resource that is ripe at the peak of the flooding season when other resources are dispersed and scarce, residents of Monte Castelo began to grow larger rice."

Evidence for mid-Holocene rice domestication in the Americas by Lautaro Hilbert and Jose Iriarte from the University of Exeter, Elizabeth Veasey, Carlos Augusto Zimpel, Eduardo Goes Neves and Francisco Pugliese from the Universidade de São Paulo, Bronwen S. Whitney from Northumbria University and Myrtle Shock from the Universidade Federal do Oeste de Pará, is published in the journal Nature Ecology and Evolution

Friday, October 6, 2017

More traits associated with your Neandertal DNA

After humans and Neandertals met many thousands of years ago, the two species began interbreeding. Although Neandertals aren't around anymore, about two percent of the DNA in non-African people living today comes from them. Recent studies have shown that some of those Neandertal genes have contributed to human immunity and modern diseases. Now researchers reporting in the American Journal of Human Genetics on October 5th have found that our Neandertal inheritance has contributed to other characteristics, too, including skin tone, hair color, sleep patterns, mood, and even a person's smoking status.

Inspired by an earlier study that found associations between Neandertal DNA and disease risk, Janet Kelso at the Max Planck Institute for Evolutionary Anthropology in Germany says her team was interested in exploring connections between Neandertal DNA and traits unrelated to disease. In other words, they wanted to uncover the "influence Neandertal DNA might be having on ordinary variation in people today."

Because Neandertal alleles are relatively rare, the researchers needed data representing a really large number of people. They found what they were looking for in data representing more than 112,000 participants in the UK Biobank pilot study. The Biobank includes genetic data along with information on many traits related to physical appearance, diet, sun exposure, behavior, and disease.

Earlier studies had suggested that human genes involved in skin and hair biology were strongly influenced by Neandertal DNA, Kelso says. But it hadn't been clear how.

"We can now show that it is skin tone, and the ease with which one tans, as well as hair color that are affected," Kelso says.

The researchers observe multiple different Neandertal alleles contributing to skin and hair tones. What they found somewhat surprising is that some Neandertal alleles are associated with lighter skin tones and others with darker skin tones. The same was true for hair color.

"These findings suggest that Neandertals might have differed in their hair and skin tones, much as people now do" adds Michael Dannemann, first author of the study.

Kelso notes that the traits influenced by Neandertal DNA, including skin and hair pigmentation, mood, and sleeping patterns are all linked to sunlight exposure. When modern humans arrived in Eurasia about 100,000 years ago, Neandertals had already lived there for thousands of years. They were likely well adapted to lower and more variable levels of ultraviolet radiation from the sun than the new human arrivals from Africa were accustomed to.

"Skin and hair color, circadian rhythms and mood are all influenced by light exposure," the researchers wrote. "We speculate that their identification in our analysis suggests that sun exposure may have shaped Neandertal phenotypes and that gene flow into modern humans continues to contribute to variation in these traits today."

Kelso and her colleagues say they'll continue to explore Neandertals' influence on modern-day traits as more data becomes available.

New Neandertal genomes advance our understanding of human evolution

Two new studies on ancient genomes provide valuable insights into the lives of our ancestors and their cousins, the Neandertals. First, scientists have sequenced a new genome of a female Neandertal, which is only the second genome of the species to be fully sequenced with such a high level of quality. The advancement confirms a number of theories about Neandertals, but also reveals new genetic contributions of the species to modern-day humans. Neandertals are the closest evolutionary relatives of all present-day humans and therefore provide a unique perspective on human biology and history. Five Neandertal genomes have been sequenced to date, yet only one yielded high-quality data, an individual found in Siberia known as the "Altai Neandertal."

Three less well-defined genomes come from individuals found in a cave, Vindija, in Croatia, and one from Mezmaiskaya Cave, in Russia. Here, Kay Prüfer and colleagues successfully analyzed billions of DNA fragments sampled from a new individual in the Croatian cave, dubbed Vindija 33.19, a female who lived roughly 52,000 years ago. Similar to previous findings, the genetic data suggest that Neandertals lived in small and isolated populations of about 3,000 individuals.

The previously sequenced Altai Neandertal genome suggested that the individual's parents were half-siblings, prompting scientists to wonder if Neandertals commonly interbred with family members - yet the new Vindija genome does not have similar incestual patterns, suggesting that the extreme inbreeding between the parents of the Altai Neandertal may not have been ubiquitous among Neandertals. Vindija 33.19 does appear to share a maternal ancestor with two of the three other individuals from the Croatian cave who were genetically sequenced, however.

The authors use the Vindija 33.19 genome to analyze divergences and gene flow among Neandertals, Denisovans (another extinct species of hominin), and modern humans. Among many findings, they report that early modern human gene flow into Neandertal populations occurred between 130,000 and 145,000 years ago, before the Croatian and Siberian Neandertals diverged.

Based on the new high-quality genome, the authors estimate that modern non-African populations carry between 1.8-2.6% Neandertal DNA, which is higher than previous estimates of 1.5-2.1%.

Lastly, they identify a wealth of new gene variants in the Neandertal genome that are influential in modern day humans, including variants related to plasma levels of LDL cholesterol and vitamin D, eating disorders, visceral fat accumulation, rheumatoid arthritis, schizophrenia and responses to antipsychotic drugs.

Prehistoric humans are likely to have formed mating networks to avoid inbreeding

Early humans seem to have recognised the dangers of inbreeding at least 34,000 years ago, and developed surprisingly sophisticated social and mating networks to avoid it, new research has found.
The study, reported in the journal Science, examined genetic information from the remains of anatomically modern humans who lived during the Upper Palaeolithic, a period when modern humans from Africa first colonised western Eurasia. The results suggest that people deliberately sought partners beyond their immediate family, and that they were probably connected to a wider network of groups from within which mates were chosen, in order to avoid becoming inbred.
This suggests that our distant ancestors are likely to have been aware of the dangers of inbreeding, and purposely avoided it at a surprisingly early stage in prehistory.

The symbolism, complexity and time invested in the objects and jewellery found buried with the remains also suggests that it is possible that they developed rules, ceremonies and rituals to accompany the exchange of mates between groups, which perhaps foreshadowed modern marriage ceremonies, and may have been similar to those still practised by hunter-gatherer communities in parts of the world today.

The study's authors also hint that the early development of more complex mating systems may at least partly explain why anatomically modern humans proved successful while other species, such as Neanderthals, did not. However, more ancient genomic information from both early humans and Neanderthals is needed to test this idea.

The research was carried out by an international team of academics, led by the University of Cambridge, UK, and the University of Copenhagen, Denmark. They sequenced the genomes of four individuals from Sunghir, a famous Upper Palaeolithic site in Russia, which is believed to have been inhabited about 34,000 years ago.

The human fossils buried at Sunghir represent a rare and highly valuable, source of information because very unusually for finds from this period, the people buried there appear to have lived at the same time and were buried together. To the researchers' surprise, however, these individuals were not closely related in genetic terms; at the very most, they were second cousins. This is true even in the case of two children who were buried head-to-head in the same grave.

Professor Eske Willerslev, who holds posts both as a Fellow at St John's College, Cambridge, and at the University of Copenhagen, was the senior author on the study.

What this means is that even people in the Upper Palaeolithic, who were living in tiny groups, understood the importance of avoiding inbreeding, he said.

The data that we have suggest that it was being purposely avoided.

This means that they must have developed a system for this purpose. If small hunter-gatherer bands were mixing at random, we would see much greater evidence of inbreeding than we have here.
Early humans and other hominins such as Neanderthals appear to have lived in small family units. The small population size made inbreeding likely, but among anatomically modern humans it eventually ceased to be commonplace; when this happened, however, is unclear.

Small family bands are likely to have interconnected with larger networks, facilitating the exchange of people between groups in order to maintain diversity, Professor Martin Sikora, from the Centre for GeoGenetics at the University of Copenhagen, said.

Sunghir contains the burials of one adult male and two younger individuals, accompanied by the symbolically-modified incomplete remains of another adult, as well as a spectacular array of grave goods. The researchers were able to sequence the complete genomes of the four individuals, all of whom were probably living on the site at the same time. These data were compared with information from a large number of both modern and ancient human genomes.

They found that the four individuals studied were genetically no closer than second cousins, while an adult femur filled with red ochre found in the children's' grave would have belonged to an individual no closer than great-great grandfather of the boys.

This goes against what many would have predicted, Willerslev said.

I think many researchers had assumed that the people of Sunghir were very closely related, especially the two youngsters from the same grave.

The people at Sunghir may have been part of a network similar to that of modern day hunter-gatherers, such as Aboriginal Australians and some historical Native American societies. Like their Upper Palaeolithic ancestors, these people live in fairly small groups of around 25 people, but they are also less directly connected to a larger community of perhaps 200 people, within which there are rules governing with whom individuals can form partnerships.

Most non-human primate societies are organised around single-sex kin where one of the sexes remains resident and the other migrates to another group, minimising inbreeding says Professor Marta Mirazón Lahr, from the Leverhulme Centre for Human Evolutionary Studies at the University of Cambridge.

At some point, early human societies changed their mating system into one in which a large number of the individuals that form small hunter-gatherer units are non-kin. The results from Sunghir show that Upper Palaeolithic human groups could use sophisticated cultural systems to sustain very small group sizes by embedding them in a wide social network of other groups.

By comparison, genomic sequencing of a Neanderthal individual from the Altai Mountains who lived around 50,000 years ago indicates that inbreeding was not avoided. This leads the researchers to speculate that an early, systematic approach to preventing inbreeding may have helped anatomically modern humans to thrive, compared with other hominins.

This should be treated with caution, however:

We don't know why the Altai Neanderthal groups were inbred, Sikora said.

Maybe they were isolated and that was the only option; or maybe they really did fail to develop an available network of connections. We will need more genomic data of diverse Neanderthal populations to be sure.

Willerslev also highlights a possible link with the unusual sophistication of the ornaments and cultural objects found at Sunghir. Group-specific cultural expressions may have been used to establish distinctions between bands of early humans, providing a means of identifying who to mate with and who to avoid as partners.

The ornamentation is incredible and there is no evidence of anything like that with Neanderthals and other archaic humans, Willerslev added.

When you put the evidence together, it seems to be speaking to us about the really big questions; what made these people who they were as a species, and who we are as a result.

The research paper, Ancient genomes show social and reproductive behaviour of early Upper Paleolithic foragers, is published in the October 5 issue of Science.