Archaeogenetics reveals unknown migration in the South Pacific

Archaeogenetic analysis points towards settlers from Melanesia

Only some 3500 years ago people began to colonize the South Pacific archipelagos of Oceania. An international team of researchers including scientists from the Max Planck Institute for the Science of Human History in Jena now analyzed for the first time, the genomes of the first settlers who lived on the island chains Tonga and Vanuatu 3100-2500 years ago. The results, published today in Nature contradict common assumptions about the colonization of the region and point to another large and previously unknown migration wave from Melanesia.

A group of people set out from the Solomon Island chain in the southwestern edge of the Pacific Ocean and steered their outrigger canoes toward the horizon more than 3,500 years ago. These people and their descendants were to be the first to cross more than 350 kilometer stretches of open sea into a region known as Remote Oceania. It was the last great movement of humans to unoccupied but habitable lands.

Now a scientific team led by researchers at Harvard Medical School, University College Dublin, and the Max Planck Institute for the Science of Human History in Jena for the first time have analyzed DNA from people who lived in Tonga and Vanuatu between 2,500 and 3,100 years ago, and were among the first people to live on these islands.

"This is the first genome-wide data on prehistoric humans from the hot tropics, and was made possible by improved methods for preparing skeletal remains" says Ron Pinhasi at University College Dublin, a senior author of the study. "DNA gets degrades very quickly in tropical climates, however we found that in the very dense inner ear bone, called the petrous bone, DNA is well preserved even under such adverse environmental conditions for thousands of years," says Cosimo Posth, doctoral student at the Max Planck Institute for the Science of Human History in Jena.

Genetic evidence overturn established colonization model

The result of genetic analysis was a big surprise for the research team: the ancient individuals carried no trace of ancestry from people who settled Papua New Guinea more than 40,000 years ago, in contrast to all present-day Pacific islanders who derive at least one-quarter of their ancestry from Papuans. Instead, the early islanders resemble genetically people who live in China and Taiwan. This means - contrary to previous assumptions - that the Remote Oceanian pioneers swept past the archipelago that surrounds New Guinea without much mating with local people.

"A major and not previously recognized migration must have spread the Papuan ancestry that is found everywhere in the Pacific today " says David Reich, a senior author at Harvard Medical School and at the Howard Hughes Medical Institute.

"The unexpected results about Oceanian history highlight the power of ancient DNA to overthrow established models of the human past", says Johannes Krause, Director at the Max Planck Institute for the Science of Human History in Jena.

"A particularly striking finding is the different ancestry observed on the X-chromosome, which is inherited mainly from females" says lead author Pontus Skoglund of Harvard Medical School and Stockholm University. "This reveals that the vast majority of the ancestry from these open water pioneers that survives today is derived from females, showing how DNA information can provide insights into cultural processes in ancient societies".
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Reference:

EurekAlert. 2016. “Archaeogenetics reveals unknown migration in the South Pacific”. EurekAlert. Posted: October 4, 2016. Available online: https://www.eurekalert.org/pub_releases/2016-10/m-aru100416.php

Ancient feces provides earliest evidence of infectious disease being carried on Silk Road

An ancient latrine near a desert in north-western China has revealed the first archaeological evidence that travellers along the Silk Road were responsible for the spread of infectious diseases along huge distances of the route 2,000 years ago.

Cambridge researchers Hui-Yuan Yeh and Piers Mitchell used microscopy to study preserved faeces on ancient 'personal hygiene sticks' (used for wiping away faeces from the anus) in the latrine at what was a large Silk Road relay station on the eastern margins of the Tamrin Basin, a region that contains the Taklamakan desert. The latrine is thought to date from 111 BC (Han Dynasty) and was in use until 109 AD.

They found that eggs from four species of parasitic worm (helminths) were present: roundworm (Ascaris lumbricoides), whipworm (Trichuris trichiura), tapeworm (Taenia sp.), and Chinese liver fluke (Clonorchis sinensis).

Chinese liver fluke is a parasitic flatworm that causes abdominal pain, diarrhoea, jaundice and liver cancer. It requires well-watered, marshy areas to complete its life cycle. Xuanquanzhi relay station was located at the eastern end of the arid Tamrin Basin, an area that contains the fearsome Taklamakan Desert. The liver fluke could not have been endemic in this dry region.

In fact, based on the current prevalence of the Chinese liver fluke, its closest endemic area to the latrine's location in Dunhuang is around 1,500km away, and the species is most common in Guandong Province - some 2,000km from Dunhuang.

Researchers from the University of Cambridge's Department of Archaeology and Anthropology, who conducted the study, suggest that the traveller infected with this liver fluke must have journeyed an enormous distance, and suggest the discovery provides the first reliable evidence for long distance travel with an infectious disease along the Silk Road.

The findings are published today in the Journal of Archaeological Science: Reports.

"When I first saw the Chinese liver fluke egg down the microscope I knew that we had made a momentous discovery," said Hui-Yuan Yeh, one of the study's authors. "Our study is the first to use archaeological evidence from a site on the Silk Road to demonstrate that travellers were taking infectious diseases with them over these huge distances."

The Silk Road (or Silk Route) came to prominence during the Han Dynasty in China (202 BC - AD 220) as merchants, explorers, soldiers and government officials journeyed between East Asia and the Middle East/Mediterranean region. Researchers have previously suggested that diseases such as bubonic plague, anthrax and leprosy might have been carried by ancient travellers along the legendary trading route, as similar strains have been found in China and Europe.

"Until now there has been no proof that the Silk Road was responsible for the spread of infectious diseases. They could instead have spread between China and Europe via India to the south, or via Mongolia and Russia to the north," says study lead Piers Mitchell.

The Cambridge team worked alongside Chinese researchers Ruilin Mao and Hui Wang from the Gansu Institute for Cultural Relics and Archaeology, who originally excavated the ancient latrine and relay station in Ganzu Province.

The stop was a popular one on the Silk Road with travellers staying there and government officials using the facility to change their horses and deliver letters. While excavating the latrine, the Chinese team found the personal hygiene sticks with cloth wrapped round one end.

Added Mitchell: "Finding evidence for this species in the latrine indicates that a traveller had come here from a region of China with plenty of water, where the parasite was endemic. This proves for the first time that travellers along the Silk Road really were responsible for the spread of infectious disease along this route in the past."
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Reference:

EurkAlert. 2016. “Ancient feces provides earliest evidence of infectious disease being carried on Silk Road”. EurekAlert. Posted: July 21, 2016. Available online: http://www.eurekalert.org/pub_releases/2016-07/uoc-afp071916.php

Ice age bison fossils shed light on early human migrations

Scientists using evidence from bison fossils have determined when an ice-free corridor opened up along the Rocky Mountains during the late Pleistocene. The corridor has been considered a potential route for human and animal migrations between the far north (Alaska and Yukon) and the rest of North America, but when and how it was used has long been uncertain.

The researchers combined radiocarbon dating and DNA analysis to track the movements of bison into the corridor, showing that it was fully open by about 13,000 years ago. Their findings, published in Proceedings of the National Academy of Sciences, indicate that the corridor could not account for the initial dispersal of humans south of the ice sheets, but could have been used for later movements of people and animals, both northward and southward.

Rocky Mountains corridor

In the 1970s, geological studies suggested that the corridor might have been the pathway for the first movement of humans southward from Alaska to colonize the rest of the Americas. More recent evidence, however, indicated that the Cordilleran and Laurentide ice sheets coalesced at the height of the last ice age, around 21,000 years ago, closing the corridor much earlier than any evidence of humans south of the ice sheets. The initial southward movement of people into the Americas more than 15,000 years ago now seems likely to have been via a Pacific coastal route, but the Rocky Mountains corridor has remained of interest as a potential route for later migrations.

“The opening of the corridor provided new opportunities for migration and the exchange of ideas between people living north and south of the ice sheets,” said first author Peter Heintzman, a postdoctoral researcher at UC Santa Cruz who led the DNA analysis.

Previous work by coauthor Beth Shapiro, professor of ecology and evolutionary biology at UC Santa Cruz, had shown that the bison populations north and south of the ice sheets were genetically distinct by the time the corridor opened. By analyzing bison fossils from within the corridor region, the researchers were able track the movement of northern bison southward into the corridor and southern bison northward.

Genetic analysis key

“The radiocarbon dates told us how old the fossils were, but the key thing was the genetic analysis, because that told us when bison from the northern and southern populations were able to meet within the corridor,” Heintzman said. The results showed that the southern part of the corridor opened first, allowing southern bison to start moving northward as early as 13,400 years ago, before the corridor fully opened. Later, there was some movement of northern bison southward, with the two populations overlapping in the corridor by 13,000 years ago.

“Bison fossils are the most widespread Quaternary mammal in western North America and of interest because they survived the extinctions at the end of the Pleistocene, unlike most other North American large mammals,” said coauthor Duane Froese of the University of Alberta. “We were able to sample bison fossils, largely from museum collections, including critical ones from central Alberta that dated to the initial opening of the corridor.”

According to Shapiro, archeological evidence suggests that human migration within the corridor was mostly from south to north. Sites associated with the Clovis hunting culture and its distinctive fluted point technology were widespread south of the corridor around 13,000 years ago and decline in abundance from south to north within the corridor region. A Clovis site in Alaska has been dated to no earlier than 12,400 years ago.

“When the corridor opened, people were already living south of there. And because those people were bison hunters, we can assume they would have followed the bison as they moved north into the corridor,” Shapiro said.

The steppe bison of the Pleistocene (Bison priscus) were much bigger than modern bison (Bison bison), she said. Before the corridor closed, prior to the last glacial maximum, they moved freely up and down between the ice-free regions in the north and grasslands south of the ice sheets. After the ice sheets coalesced, the population that was cut off to the south contracted, leaving one genetically distinct southern lineage.

The DNA analysis used in this study focused on mitochondrial DNA, which is easier to recover from fossils than the DNA in chromosomes, because each cell has thousands of copies of the relatively short mitochondrial DNA sequence. While Shapiro’s lab led the DNA analyses, Froese’s lab led the radiocarbon dating work.
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Reference:

Past Horizons. 2016. “Ice age bison fossils shed light on early human migrations”. Past Horizons. Posted: June 6, 2016. Available online: http://www.pasthorizonspr.com/index.php/archives/06/2016/ice-age-bison-fossils-shed-light-on-early-human-migrations

Humans in Southern Arabia 10,000 years earlier than first thought

The last Ice Age made much of the globe uninhabitable, but there were oases – or refugia – where people 20,000 years ago were able to cluster and survive. Researchers at the University of Huddersfield, who specialise in the analysis of human DNA, have found new evidence that there was one or more of these shelters in what is now Southern Arabia.

Once the Ice Age receded – with the onset of the Late Glacial period about 15,000 years ago – the people of this refugium then dispersed and populated Arabia and the Horn of Africa, and might also have migrated further afield.

Study bolsters archaeological theory

The view used to be that people did not settle in large numbers in Arabia until the development of agriculture, around 10-11,000 years ago. Now, the findings by members of the University of Huddersfield’s Archaeogenetics Research Group demonstrate that modern humans have dwelt in this territory for far longer than previously thought. The new genetic data and analysis bolsters a theory that has long been held by archaeologists, although they had little evidence to support it until now.

The new argument for an Ice Age refugium in Arabia – perhaps on the Red Sea plains – is put forward in an article published in the journal Scientific Reports(open access). Its principal author is Dr Francesca Gandini, who was based at the University of Pavia in Italy before relocating in early 2015 to the University of Huddersfield, where she is a Research Fellow in Archaeogenetics and a member of the group headed by Professor Martin Richards.

Dr Gandini is currently playing a central role in the development of an Ancient DNA lab at the University of Huddersfield, which is home to a Centre for Evolutionary Genomics. It has been awarded £1 million by the Leverhulme Trust in order to provide doctoral training to the next generations of specialists in a field that uses the latest DNA science to delve into evolutionary history.

Study of rare mitochondrial DNA lineage

The new discoveries about an Ice Age refugium in Arabia and the subsequent outward migration are based on a study of a rare mitochondrial DNA lineage named ROa, which, uniquely, is most frequent in Arabia and the Horn of Africa. Dr Gandini and her co-researchers have reached the conclusion that this lineage is more ancient than previously thought and that it has a deeper presence in Arabia than was earlier believed. This makes the case for at least one glacial refugium during the Pleistocene period, which spanned the Ice Age. The article also describes the dispersals during the postglacial period, around 11,000 years ago, of people from Arabia into eastern Africa. Moreover, there is evidence for the movement of people in the R0a haplogroup through the Middle East and into Europe and there might also have been a trading network and a “gene flow” from Arabia into the territories that are now Iran, Pakistan and India.
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Reference:

Past Horizons. 2016. “Humans in Southern Arabia 10,000 years earlier than first thought”. Past Horizons. Posted: May 12, 2016. Available online: http://www.pasthorizonspr.com/index.php/archives/05/2016/humans-in-southern-arabia-10000-years-earlier-than-first-thought

Humans have always been migrants

A short animated film commissioned by two University of Kent historians challenges the concept that migration at current levels is a new phenomenon.

With migration now a major topic of debate across Europe, Professor Ray Laurence and Dr Julie Anderson, working with the University of Reading's Dr Hella Eckardt, created a script and commissioned the film to provide the public, schools and policy makers with a better understanding of its history.

The 75 second animation draws from research on the Roman Empire and the First World War.

This includes recent developments in the chemical analysis of the teeth of skeletons from the Roman Empire period in Britain which has revealed that migrants from North Africa were living in York. The analysis also suggests up to 30% of the population in Britain came from abroad during the Roman period.

Research into the hidden histories of war graves in Britain has also identified migrants who had took part in WWI. The conversion of Brighton Pavilion into a hospital for Indian troops provides further evidence of the important role they played.

With the topic of migration now included within the GCSE History curriculum of exam board, Oxford Cambridge and RSA (OCR) the film is expected to provide children with a far more complex view of Britain's population in the past.
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Reference:

Fleming, Sandy. 2016. “Humans have always been migrants”. Phys.org. Posted: February 9, 2016. Available online: http://phys.org/news/2016-02-humans-migrants.html

Documenting the world's last nomadic tribes

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Reference:

Discovery News. 2016. “Documenting the world's last nomadic tribes”. Discovery News. Posted: October 22, 2015. Available online: http://news.discovery.com/adventure/videos/documenting-the-worlds-last-nomadic-tribes-151022.htm

Modern humans out of Africa sooner than thought

"The model that is generally accepted is that modern humans left Africa only 50,000 years ago," said Maria Martinon-Torres, a researcher at University College London and a co-author of the study.

Human teeth discovered in southern China provide evidence that our species left the African continent up to 70,000 years earlier than prevailing theories suggest, a study published on Wednesday said.

Homo sapiens reached present-day China 80,000-120,000 years ago, according to the study, which could redraw the migration map for modern humans.

"In this case, we are saying the H. sapiens is out of Africa much earlier," she told the peer-reviewed journal Nature, which published the study.

While the route they travelled remains unknown, previous research suggests the most likely path out of East Africa to east Asia was across the Arabian Peninsula and the Middle East.

The findings also mean that the first truly modern humans—thought to have emerged in east Africa some 200,000 years ago—landed in China well before they went to Europe.

There is no evidence to suggest that H. sapiens entered the European continent earlier than 45,000 years ago, at least 40,000 years after they showed up in present-day China.

The 47 teeth exhumed from a knee-deep layer of grey, sandy clay inside the Fuyan Cave near the town of Daoxian closely resemble the dental gear of "contemporary humans," according to the study.

They could only have come from a population that migrated from Africa, rather than one that evolved from an another species of early man such as the extinct Homo erectus, the authors said.

The scientists also unearthed the remains of some 38 mammals, including specimens of five extinct species, one of them a giant panda larger than those in existence today.

No tools were found.

"Judging by the cave environment, it may not have been a living place for humans," lead author Wu Liu from the Chinese Academy of Science in Beijing told AFP.

Why not Europe?

The study, published in the journal Nature, also rewrites the timeline of early man in China. Up to now, the earliest proof of H. sapiens east of the Arabian Peninsula came from the Tianyuan Cave near Beijing, and dated from no more than 40,000 years ago.

The new discovery raises questions about why it took so long for H. sapiens to find their way to nearby Europe. "Why is it that modern humans—who were already at the gates—didn't really get into Europe?", Martinon-Torres asked. Wu and colleagues propose two explanations.

The first is the intimidating presence of Neanderthal man. While this species of early human eventually died out, they were spread across the European continent up until at least some 50,000 years ago.

"The classic idea is that H. sapiens... took over the Neanderthal empire, but maybe Neanderthals were a kind of ecological barrier, and Europe was too small a place" for both, Martinon-Torres said. Another impediment might have been the cold.

Up until the Ice Age ended 12,000 years ago, ice sheets stretched across a good part of the European continent, a forbidding environment for a new species emerging from the relative warmth of East Africa.

"H. sapiens originated in or near the tropics, so it makes sense that the species' initial dispersal was eastwards rather than northwards, where winter temperatures rapidly fell below freezing," Robin Dennell of the University of Exeter said in a commentary, also in Nature.

Martinon-Torres laid out some of the questions to be addressed in future research, using both genetics and fossil records.

A near miss

"What are the origins of these populations, and what was their fate? Did they vanish? Could they be the ancestors of later and current populations that entered Europe?"

She also suggested there might have been "different movements and migrations" out of Africa, not just one. Besides the prehistoric panda, called Ailuropoda baconi, the scientists found an extinct species of a giant spotted hyaena.

An elephant-like creature called Stegodon orientalis and a giant tapir, also present, were species that may have survived into the era when the Chinese had developed writing, some 3500 years ago.

The cache of teeth nearly went unnoticed, Wu told AFP.

He and his Chinese colleagues discovered the cave—and its menagerie of long-deceased animals—in the 1980s, but had no inkling that it also contained human remains.

But 25 years later, while revisiting the site, Wu had a hunch.

"By thinking about the cave environment, we realised that human fossils might be found there," he told AFP by email. "So we started a five-year excavation."
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Reference:

Phys.Org. 2016. “Modern humans out of Africa sooner than thought”. Phys.Org. Posted: October 14, 2015. Available online: http://phys.org/news/2015-10-modern-humans-africa-sooner-thought.html

One Migration from Siberia Peopled the Americas: Study

Native American ancestors reached the New World in a single, initial migration from Siberia at most 23,000 years ago, only later differentiating into today’s distinct groups, DNA research revealed Tuesday.

Most scientists agree the Americas were peopled by forefathers who crossed the Bering land and ice bridge which connected modern-day Russia and Alaska in Earth’s last glacial period.

And it is known through archaeological finds that humans were already present in the Americas 15,000 years ago.

But there was a long list of outstanding questions.

When did the migration take place? In one or several waves? And how long did these early pioneers spend in Beringia — the then-raised land area between Asia and America?

On Tuesday, analysis of Native American and Siberian DNA, present-day and ancient, sought to fill in some of the blanks with two studies carried simultaneously in the journals Science and Nature.

The first, led by the Center for GeoGenetics at the University of Copenhagen and published in Science, found there was only one initial migration, no more than 23,000 years ago.

This ancestral pool split into two main branches about 13,000 years ago, coinciding with glacier melt and the opening of routes into the North American interior, researchers found.

These became the groups which anthropologists refer to as Amerindians (American Indians) and Athabascans (a native Alaskan people).

Previous research had suggested that Amerindian and Athabascan ancestors had crossed the strait independently.

“Our study presents the most comprehensive picture of the genetic prehistory of the Americas to date,” said Maanasa Raghavan, one of the study’s lead authors.

“We show that all Native Americans, including the major sub-groups of Amerindians and Athabascans, descend from the same migration wave into the Americas.”

This was distinct from later waves which gave rise to the Paleo-Eskimo and Inuit populations, she added.

Given that the earliest evidence for the presence of humans in the Americas dates to 15,000 years ago, the first ancestors may have remained in Beringia for about 8,000 years before their final push into the New World, the team said.

This is much shorter than the tens of thousands of years of isolation theorized by some earlier research.

But diversification into the distinct tribes we know today, happened only after arrival in the Americas, not before.

The second study showed that, surprisingly, some Amazonians descend from forefathers more closely related to the indigenous peoples of Australia, New Guinea and the Andaman Islands than present-day fellow Native Americans.

“Present-day groups in South America have a small but distinct genetic link to Australasians,” co-author Pontus Skoglund of the Harvard Medical School told AFP of the research published in Nature.

This may explain a long-standing riddle: why, if Native Americans came from Eurasia, do some early American skeletons share traits with present-day Australasians?

But how and when this forefather came to the Americas remains “an open question,” said the study.
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Reference:

Discovery News. 2015. “One Migration from Siberia Peopled the Americas: Study”. Discovery News. Posted: July 21, 2015. Available online: http://news.discovery.com/human/evolution/one-migration-from-siberia-peopled-the-americas-study-15072.htm

Utah Cave Full of Children’s Moccasins Sheds Light on Little-Known Ancient Culture

Archaeologists on the trail of a little-known ancient culture have found a cache of clues that may help unlock its secrets: a cave containing hundreds of children’s moccasins.

The cave, on the shore of Utah’s Great Salt Lake, was first excavated in the 1930s, but the artifacts found there — and the questions that they raised — were largely forgotten until recently.

Dr. Jack Ives of the University of Alberta and his colleagues resumed excavations in the cave in 2011 to better understand its occupants, some of whom Ives believes may have been part of one of the greatest human migrations in the continent’s history.

Promontory Caves — contains “exceedingly abundant” artifacts numbering in the thousands, Ives said, marking a human occupation that began rather suddenly about 850 years ago.

This wealth of artifacts may go a long way in demystifying the distinctive, little-researched populations often referred to as the Promontory Culture.

“The beauty of the Promontory Culture is, probably 99 percent of the material culture that the people used was perishable,” Ives said in an interview.

“So, normally in the archaeological record, we only see the durable items — the pottery, the stone tools, the animal bones.

“[But] we have, with the Promontory Culture, spectacularly, more material culture, so we can see all aspects of daily life, together with nuances likely to reflect different cultural identities.”

Large piles of butchered bison and elk bones, for example, suggest that the Promontory lifestyle was based, almost exclusively and quite successfully, on big-game hunting, while other groups around them were farming and foraging.

Scant ceramic sherds and basket fragments, meanwhile, bear strong signs of influence from other Great Basin cultures, including the Fremont.

But it was the staggering amount of footwear in the caves that captured the attention of archaeologists, past and present.

With soles made from a single piece of bison leather, lined with fur, and sewn together at the heel, the moccasins are made in a style typical of the Canadian Subarctic, Ives said, a fashion his team describes as being “decidedly out of place in the eastern Great Basin.”

These moccasins and other cues have led some experts to theorize that the caves’ inhabitants were part of a great migration from the far north, a wave of people who moved into the Great Basin in the 12th and 13th centuries, and eventually gave rise to cultures that include the Apache and the Navajo.

To better understand the role that the Promontory may have played in this event, Ives and his colleagues used the moccasins to gauge the size and makeup of their population.

The team studied 207 pieces of footwear excavated from the cave, both in the 1930s and the 2010s, using the moccasins’ lengths to estimate the age and stature of their owners, based on known anatomical ratios.

The results showed that the vast majority of the moccasins — just over 82 percent — were worn by children of ages 12 and under.

“One of our [paper’s] reviewers said, this isn’t like a normal family ratio — this is more like an elementary school ratio,” Ives said in an interview.

Because the moccasins were likely “cast offs” that accumulated over several decades, these figures don’t reflect the exact demographics of the Promontory community, Ives explained, but they do provide valuable insights into its general proportions.

“These numerous moccasins are telling us about the structure of the population, not necessarily specific numbers,” he said.

“But you can see that children and subadults are a very big part of the population.”

Analysis of radiocarbon dates from the samples suggests that the most intense period of the cave’s use ranged over only one or two human generations — from about 1250 to 1290 CE.

This was a time, Ives points out, when other cultures in North America’s interior were undergoing dramatic changes, as a drying climate and shifting social landscapes forced entire communities to relocate, most notably among the Ancestral Puebloans.

“It’s a tumultuous time period in which this is happening,” he said.

“We know there’s a significant environmental change going on.”

And yet, the large number of children in the Promontory population — along with other clues like the abundance of burned bones of large game — suggest that the Promontory people were “thriving,” Ives said.

“That very high proportion of kids would suggest that it’s a population that’s reproducing very well,” he said.

“We can’t get more specific than that, … but it’s suggesting that there are a lot [of children] in the society, and that implies minimally that they’re doing pretty well.

“Taking it a bit farther, they’re likely a growing population.”

This period of flourishing amid otherwise hard times may have been a pivotal chapter in what Ives calls the “immense human story” of migration from the Canadian Subarctic, one that resulted in the culturally diverse Southwest that we know today.

Ives and his colleagues plan to conduct more research on other artifacts from the caves, like stone tools, nets, and bows, that bear important similarities to Subarctic cultures.

A recent, large-scale genetic study may also provide molecular evidence of the migrant’s trans-continental journey.

But for now, the materials found in Promontory Caves stand as rare examples of perishable goods that have survived to provide glimpses into the day-to-day life during this crucial period.

“Normally [these moccasins] would be gone, but here [in the cave] they’re present in abundance, and they’re signalling: We are typical of the north. That’s what they’re signalling.

“This is not mortality data,” he added. “Some research reaches conclusions from cemetery or burial settings.

“This is vitality data — these were living children and adults that the moccasins came from.”

Ives and his colleagues report their findings in the American Journal of Physical Anthropology.
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De Pastino, Blake. 2015. “Utah Cave Full of Children’s Moccasins Sheds Light on Little-Known Ancient Culture”. Western Digs. Posted: November 17, 2014. Available online: http://westerndigs.org/utah-cave-full-of-childrens-moccasins-sheds-light-on-little-known-ancient-culture/

Migration in China: Shifting slightly, but still going strong

A new study suggests coastal areas in China are not the migration magnet they used to be

The brain drain of educated workers is still felt most severely in China's central and western provinces, since most knowledge-based industries are generally concentrated in its large coastal cities. However, low-educated migrant workers increasingly find jobs in their home provinces in the central and western regions because of changing economic and government policy. So says Ye Liu and his colleagues of The Chinese University of Hong Kong in Hong Kong and The University of Leeds in the United Kingdom, who carried out a systematic analysis of migration trends in China over the past 25 years. The article is published in Springer's journal Applied Spatial Analysis and Policy.

China's unprecedented surge of internal migration since the early 1980s is the result of unbalanced regional economic development and relaxed migration controls. In the process, 163.4 million migrant workers have moved away from the less-developed interior, mostly to China's coastal regions. Another 240 million migrants are estimated to become city dwellers by 2025. This could increase the urban population to nearly one billion people.

The spatial patterns of age, and education-specific migration mirror the geography of different forms of industries in China. For instance, knowledge-based and advanced service industries that attract educated migrants are highly concentrated in a few large coastal cities such as Beijing and Shanghai. Labor-intensive industries favoring young and low-educated migrant workers are spread across the whole coastal region, where most provinces have become major recipients of less-educated migrants.

However, as a consequence of preferential policies and increasing state investment in industrialization, some interior provinces have recently undergone higher economic growth rates than most coastal provinces. The researchers believe that coastal areas will gradually lose their comparative advantages in developing labor-intensive industries due to the rising labor costs, the evaluation of China's currency and the depletion of land resources.

The authors conclude, "Our findings suggest that massive eastward migration induced by the unbalanced development strategies and the relaxed migration controls still persisted in the first decade of the 21st century, and that the state's recent efforts to alleviate regional inequalities have not resulted in the achievement of equilibrium in China's internal migration system. Nevertheless, as a consequence of preferential policies and increasing state investment, some interior provinces have begun to undergo higher economic growth rates than most coastal provinces in recent years."

Ye and his colleagues continue to explain, "While the coastal areas have made every endeavor to upgrade their industrial structures and develop knowledge-based economies, many interior areas have undergone a tide of industrialization and received many labor-intensive industries that transferred from coastal regions. Under such circumstances, low-educated and young migrant workers increasingly opted to find jobs in their home provinces located in the central and western regions, while educated migrants continued to move towards coastal large cities."
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References:

EurekAlert. 2014. “Migration in China: Shifting slightly, but still going strong”. EurekAlert. Posted: March 13, 2014. Available online: http://www.eurekalert.org/pub_releases/2014-03/ssm-mic031314.php

Language 'evolution' may shed light on human migration out-of-Beringia: Relationship between Siberian, North American languages

Evolutionary analysis applied to the relationship between North American and Central Siberian languages may indicate that people moved out from the Bering Land Bridge, with some migrating back to central Asia and others into North America, according to a paper published in the open-access journal PLOS ONE on March 12, 2014 by Mark Sicoli, from Georgetown University and Gary Holton from University of Alaska Fairbanks.

Languages evolve slowly overtime and may even follow human migratory patterns. A proposed language family known as the Dené-Yeniseian suggests that there are common language elements between the North American Na-Dene languages and the Yeniseian languages of Central Siberia. To investigate this further, scientists employed a technique originally developed to investigate evolutionary relationships between biological species called phylogenetic analysis, where a tree is constructed to represent relationships of common ancestry based on shared traits. Scientists used linguistic phylogeny to work out how approximately 40 languages from the area diffused across North America and Asia. The authors first coded a linguistic dataset from the languages, modeled the relationship between the data, and then modeled it against migration patterns from Asia to North America, or out-of-Beringia.

Results show an early dispersal of Na-Dene along the North American coast with a Yeniseian back migration through Siberia and a later dispersal of North American interior Na-Dene languages. Sicoli explained, "we used computational phylogenetic methods to impose constraints on possible family tree relationships modeling both an Out-of-Beringia hypothesis and an Out-of-Asia hypothesis and tested these against the linguistic data. We found substantial support for the out-of-Beringia dispersal adding to a growing body of evidence for an ancestral population in Beringia before the land bridge was inundated by rising sea levels at the end of the last ice age."

Although the authors cannot conclusively determine the migration pattern just from these results, and state that this study does not necessarily contradict the popular tale of hunters entering the New World through Beringia, it at the very least indicates that migration may not have been a one-way trip. This work also helps demonstrate the usefulness of evolutionary modeling with linguistic trees for investigating these types of questions.

These finding suggest that phylogenetics may be used to explore the implications of deep linguistic relationships.
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References:

Science Daily. 2014. “Language 'evolution' may shed light on human migration out-of-Beringia: Relationship between Siberian, North American languages”. Science Daily. Posted: March 12, 2014. Available online: http://www.sciencedaily.com/releases/2014/03/140312182018.htm

Boy’s Skeleton In Siberia Raises New Questions About First Americans

Results from a DNA study of a young boy’s skeletal remains believed to be 24,000 years old could turn the archaeological world upside down – it’s been proven that nearly 30 percent of modern Native American’s ancestry came from this youngster’s gene pool, suggesting First Americans came directly from Siberia, according to a research team that includes a Texas A&M University professor.

Kelly Graf, assistant professor in the Center for the Study of First Americans and Department of Anthropology at Texas A&M, is part of an international team spearheaded by Eske Willerslev and Maanasa Raghaven from the Centre for GeoGenetics at the University of Copenhagen, Denmark and additional researchers from Sweden, Russia, United Kingdom, University of Chicago and University of California-Berkeley. Their work, funded by the Danish National Science Foundation, Lundbeck Foundation, and the National Science Foundation, is published in the current issue of Nature magazine.

Graf and Willerslev conceived the project and traveled to the Hermitage State Museum in St. Petersburg, Russia, where the remains are now housed to collect samples for ancient DNA.  The skeleton was first discovered in the late 1920s near the village of Mal’ta in south-central Siberia, and since then it has been referred to as “the Mal’ta child” because until this DNA study the biological sex of the skeleton was unknown.

“Now we can say with confidence that this individual was a male” says Graf.

Graf helped extract DNA material from the boy’s upper arm and “the results surprised all of us quite a bit,” she explains.

“It shows he had close genetic ties to today’s Native Americans and some western Eurasians, specifically some groups living in central Asia, South Asia, and Europe. Also, he shared close genetic ties with other Ice-Age western Eurasians living in European Russia, Czech Republic and even Germany. We think these Ice-Age people were quite mobile and capable of maintaining a far-reaching gene pool that extended from central Siberia all the way west to central Europe.”

Another significant result of the study is that the Mal’ta boy’s people were also ancestors of Native Americans, explaining why some early Native American skeletons such as Kennewick Man were interpreted to have some European traits.

“Our study proves that Native Americans ancestors migrated to the Americas from Siberia and not directly from Europe as some have recently suggested,” Graf explains.

The DNA work performed on the boy is the oldest complete genome of a human sequenced so far, the study shows.  Also found near the boy’s remains were flint tools, a beaded necklace and what appears to be pendant-like items, all apparently placed in the burial as grave goods.

The discovery raises new questions about the timing of human entry in Alaska and ultimately North America, a topic hotly debated in First Americans studies.

“Though our results cannot speak directly to this debate, they do indicate Native American ancestors could have been in Beringia—extreme northeastern Russia and Alaska—any time after 24,000 years ago and therefore could have colonized Alaska and the Americas much earlier than 14,500 years ago, the age suggested by the archaeological record.”

“What we need to do is continue searching for earlier sites and additional clues to piece together this very big puzzle.”
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References:

Tamu Times. 2014. “Boy’s Skeleton In Siberia Raises New Questions About First Americans”. Tamu Times. Posted: November 20, 2013. Available online: http://tamutimes.tamu.edu/2013/11/20/boys-skeleton-in-siberia-raises-new-questions-about-first-americans/#.Uq4sK4

Ancient Siberian genome reveals genetic origins of Native-Americans

The genome sequence of a 24,000-year-old Siberian individual has provided a key piece of the puzzle in the quest for Native American origins. The ancient Siberian demonstrates genomic signatures that are basal to present-day western Eurasians and close to modern Native Americans. This surprising finding has great consequences for our understanding of how and from where ancestral Native Americans descended, and also of the genetic landscape of Eurasia 24,000 years ago. The breakthrough is reported in this week's Nature (Advance Online Publication) by an international team of scientists, led by the Centre for GeoGenetics at the Natural History Museum of Denmark (University of Copenhagen).

The search for Native American ancestors has been focused in northeastern Eurasia. In late 2009, researchers sampled at the Hermitage Museum, St. Petersburg the remains of a juvenile individual (MA-1) from the Upper Palaeolithic site of Mal'ta in south-central Siberia. The MA-1 individual dated to approximately 24,000 years ago. Now, the team reports genomic results from the MA-1 individual which unravel the origins of the First Americans – ancestors of modern-day Native Americans.

"Representing the oldest anatomically modern human genome reported thus far, the MA-1 individual has provided us with a unique window into the genetic landscape of Siberia some 24,000 years ago", says Dr. Maanasa Raghavan from the Centre for GeoGenetics and one of the lead authors of the study. "Interestingly, the MA-1 individual shows little to no genetic affinity to modern populations from the region from where he originated - south Siberia."

Instead, both the mitochondrial and nuclear genomes of MA-1 indicate that he was related to modern-day western Eurasians. This result paints a picture of Eurasia 24,000 years ago which is quite different from the present-day context. The genome of MA-1 indicates that prehistoric populations related to modern western Eurasians occupied a wider geographical range into northeast Eurasia than they do today.

Dual ancestry of Native Americans

The most significant finding that the MA-1 genome reveals is its relation to modern Native Americans. This relative of present-day western Eurasians shows close affinity to modern Native Americans, but surprisingly not to East Asians who are regarded as being genetically closely related to Native Americans.

Furthermore, the team finds evidence that this genetic affinity between MA-1 and Native Americans is mediated by a gene flow event from MA-1 into the First Americans, which can explain between 14-38% of the ancestry of modern Native Americans, with the remainder of the ancestry being derived from East Asians. Supported by numerous reasons against these signatures being caused by contamination from modern DNA sources or from post-Columbian admixture (post 1492 AD), the study concludes that two distinct Old World populations led to the formation of the First American gene pool: one related to modern-day East Asians, and the other a Siberian Upper Palaeolithic population related to modern-day western Eurasians.

"The result came as a complete surprise to us. Who would have thought that present-day Native Americans, who we learned in school derive from East Asians, share recent evolutionary history with contemporary western Eurasians? Even more intriguingly, this happened by gene flow from an ancient population that is so far represented only by the MA-1 individual living some 24,000 years ago", says Professor Eske Willerslev from the Centre for GeoGenetics who led the study.

Early cosmopolitans

Additionally, results from a second south-central Siberian from Afontova Gora-2 site are presented in order to address human occupation of the region during and after the Last Glacial Maximum (LGM; ca. 26,000 to 19,000 years ago), a climatically cold period when glacial ice sheets extended to their maximum range. At approximately 17,000 years ago, this post-LGM individual demonstrates similar genomic signatures as MA-1, with close affinity to modern western Eurasians and Native Americans and none to present-day East Asians. This result indicates that genetic continuity persisted in south-central Siberia throughout this climatically harsh period, which is a significant consideration for the peopling of Beringia, and eventually the Americas some 15,000 years ago.

Dr. Pontus Skoglund from Uppsala University, and one of the lead authors of the study, explains, "Most scientists have believed that Native American lineages go back about 14,000 years ago, when the first people crossed Beringia into the New World. Our results provide direct evidence that some of the ancestry that characterizes Native Americans is at least 10,000 years older than that, and was already present in Siberia before the last Ice Age."

Professor Kelly Graf from the Center for the Study of the First Americans (Texas A&M University), who together with Professor Willerslev did the sampling, adds, "Our findings are significant at two levels. First, it shows that Upper Paleolithic Siberians came from a cosmopolitan population of early modern humans that spread out of Africa to Europe and Central and South Asia. Second, Paleoindian skeletons with phenotypic traits atypical of modern-day Native Americans can be explained as having a direct historical connection to Upper Paleolithic Siberia."

As such, results from this study contribute a major leap forward for resolving the peopling of the Americas.

Take-home messages:

• First Americans descended from the meeting and admixture of at least two populations, of which one is related to contemporary East Asians and the other to present-day western Eurasians.
• These findings may explain the presence of mitochondrial lineage X in Native Americans.
• The presence of a population related to western Eurasians further into northeast Eurasia provides a more likely explanation for the presence of non-East Asian cranial characteristics in the First Americans, rather than the Solutrean hypothesis that proposes an Atlantic route from Iberia.
• Genetic continuity in south-central Siberia before and after the LGM provides evidence for the presence of humans in the region throughout this cold phase, which is of consequence to population movements into Beringia and ultimately the Americas around 15,000 years ago.

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References:

EurekAlert. 2014. “Ancient Siberian genome reveals genetic origins of Native-Americans”. EurekAlert. Posted: November 20, 2013. Available online: http://www.eurekalert.org/pub_releases/2013-11/uoc-asg112013.php

Hitchhiking virus confirms saga of ancient human migration

A study of the full genetic code of a common human virus offers a dramatic confirmation of the "out-of-Africa" pattern of human migration, which had previously been documented by anthropologists and studies of the human genome.

The virus under study, herpes simplex virus type 1 (HSV-1), usually causes nothing more severe than cold sores around the mouth, says Curtis Brandt, a professor of medical microbiology and ophthalmology at the University of Wisconsin-Madison. Brandt is senior author of the study, now online in the journal PLOS ONE.

When Brandt and co-authors Aaron Kolb and Cécile Ané compared 31 strains of HSV-1 collected in North America, Europe, Africa and Asia, "the result was fairly stunning," says Brandt.

"The viral strains sort exactly as you would predict based on sequencing of human genomes. We found that all of the African isolates cluster together, all the virus from the Far East, Korea, Japan, China clustered together, all the viruses in Europe and America, with one exception, clustered together," he says.

"What we found follows exactly what the anthropologists have told us, and the molecular geneticists who have analyzed the human genome have told us, about where humans originated and how they spread across the planet."

Geneticists explore how organisms are related by studying changes in the sequence of bases, or "letters" on their genes. From knowledge of how quickly a particular genome changes, they can construct a "family tree" that shows when particular variants had their last common ancestor.

Studies of human genomes have shown that our ancestors emerged from Africa roughly 150,000 to 200,000 years ago, and then spread eastward toward Asia, and westward toward Europe.

Scientists have previously studied herpes simplex virus type 1 by looking at a single gene, or a small cluster of genes, but Brandt notes that this approach can be misleading. "Scientists have come to realize that the relationships you get back from a single gene, or a small set of genes, are not very accurate."

The PLOS ONE study used high-capacity genetic sequencing and advanced bioinformatics to analyze the massive amount of data from the 31 genomes.

The technology of simultaneously comparing the entire genomes of related viruses could also be useful in exploring why certain strains of a virus are so much more lethal than others. In a tiny percentage of cases, for example, HSV-1 can cause a deadly brain infection, Brandt notes.

"We'd like to understand why these few viruses are so dangerous, when the predominant course of herpes is so mild. We believe that a difference in the gene sequence is determining the outcome, and we are interested in sorting this out," he says.

For studies of influenza virus in particular, Brandt says, "people are trying to come up with virulence markers that will enable us to predict what a particular strain of virus will do."

The researchers broke the HSV-1 genome into 26 pieces, made family trees for each piece and then combined each of the trees into one network tree of the whole genome, Brandt says. "Cécile Ané did a great job in coming up with a new way to look at these trees, and identifying the most probable grouping." It was this grouping that paralleled existing analyses of human migration.

The new analysis could even detect some intricacies of migration. Every HSV-1 sample from the United States except one matched the European strains, but one strain that was isolated in Texas looked Asian. "How did we get an Asian-related virus in Texas?" Kolb asks. Either the sample had come from someone who had travelled from the Far East, or it came from a native American whose ancestors had crossed the "land bridge" across the Bering Strait roughly 15,000 years ago.

"We found support for the land bridge hypothesis because the date of divergence from its most recent Asian ancestor was about 15,000 years ago. Brandt says. "The dates match, so we postulate that this was an Amerindian virus."

Herpes simplex virus type 1 was an ideal virus for the study because it is easy to collect, usually not lethal, and able to form lifelong latent infections. Because HSV-1 is spread by close contact, kissing or saliva, it tends to run in families. "You can think of this as a kind of external genome," Brandt says.

Furthermore, HSV-1 is much simpler than the human genome, which cuts the cost of sequencing, yet its genome is much larger than another virus that also has been used for this type of study. Genetics often comes down to a numbers game; larger numbers produce stronger evidence, so a larger genome produces much more detail.

But what really jumped out of the study, Brandt says, "was clear support for the out-of-Africa hypothesis. Our results clearly support the anthropological data, and other genetic data, that explain how humans came from Africa into the Middle East and started to spread from there."

The correspondence with anthropology even extends, as before, to the details. In the virus, as in human genomes, a small human population entered the Middle East from Africa. "There is a population bottleneck between Africa and the rest of the world; very few people were involved in the initial migration from Africa," Brandt says. "When you look at the phylogenetic tree from the virus, it's exactly the same as what the anthropologists have told us."
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References:

EurekAlert. 2013. “Hitchhiking virus confirms saga of ancient human migration”. EurekAlert. Posted: October 21, 2013. Available online: http://www.eurekalert.org/pub_releases/2013-10/uow-hvc102113.php

New archaeogenetic research refutes earlier findings

Modern humans did not settle in Asia before the devastating eruption of Sumatra's volcano Mount Toba 74,000 years ago

When did modern humans settle in Asia and what route did they take from mankind's African homeland? A University of Huddersfield professor has helped to provide answers to both questions. But he has also had to settle a controversy.

Professor Martin Richards, who heads the University's Archaeogenetics Research Group, co-authors a new article in the journal Proceedings of the National Academy of Sciences of the United States of America. It refutes a recent theory, that there is archaeological evidence for the presence of modern humans in southern Asia before the super-eruption of the Mount Toba volcano in Sumatra.

One of the most catastrophic events since humans evolved, it happened approximately 74,000 years ago. In 2005, Professor Richards led research published in an article in the journal Science which used mitochondrial DNA evidence to show that anatomically modern humans dispersed from their Africa homeland via a "southern coastal route" from the Horn and through Arabia, about 60,000 years ago – after the Toba eruption.

However, a team of archaeologists excavating in India then claimed to have found evidence that modern humans were there before the eruption – possibly as early as 120,000 years ago, much earlier than Europe or the Near East were colonised. These findings, based on the discovery of stone tools below a layer of Toba ash, were published in Science in 2007.

Now Professor Richards – working principally with the archaeologist Professor Sir Paul Mellars, of the University of Cambridge and the University of Edinburgh, with a team including Huddersfield University's Dr Martin Carr and colleagues from York and Porto – has published his rebuttal of this theory. In doing so, they have been able to draw on a much greater body of DNA evidence that was available for the earlier article.

"One of the things we didn't have in 2005 was very much evidence from India in the way of mitochondrial sequences. Now, with a lot of people doing sequencing and depositing material in databases there are about 1,000 sequences from India," said Professor Richards.

By using the mitochondrial DNA of today's populations and working backwards, and by drawing on a wide variety of other evidence and research, the team was able to make much more precise estimates for the arrival of modern humans in India.

The evidence suggests dispersal from Africa and settlement in India no earlier than 60,000 years ago.

"We also argue that close archaeological similarities between African and Indian stone-tool technologies after 70,000 years ago, as well as features such as beads and engravings, suggest that the slightly later Indian material had an African source," states Professor Richards.

"There were people in India before the Toba eruption, because there are stone tools there, but they could have been Neanderthals – or some other pre-modern population," he adds.

"The replacement of the presumably archaic humans living previously in South Asia by modern people with these new technologies appears analogous to the replacement of Neanderthals by modern humans in Europe and western Asia 50-40,000 years ago."
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References:

EurekAlert. 2013. “New archaeogenetic research refutes earlier findings”. EurekAlert. Posted: June 11, 2013. Available online: http://www.eurekalert.org/pub_releases/2013-06/uoh-nar061113.php

DNA study links indigenous Brazilians to Polynesians

Sequences shared by far-away populations stir up a Palaeoamerican mystery.

Indigenous people that lived in southeastern Brazil in the late 1800s shared some genetic sequences with Polynesians, an analysis of their remains shows. The finding offers some support for the possibility that Pacific islanders traded with South America thousands of years ago, but researchers say that the distinctive DNA sequences, or haplogroups, may have entered the genomes of the native Brazilians through the slave trade during the nineteenth century.

Most scientists agree that humans arrived in the Americas between 15,000 and 20,000 years ago, probably via the Bering land bridge linking northeastern Asia with what is now Alaska. But the precise timing and the number of ‘migration waves’ is unclear, owing largely to variations in early Americans’ physical features, says Sérgio Pena, a molecular geneticist at the Federal University of Minas Gerais in Belo Horizonte, Brazil.

One broad group of these Palaeoamericans — the Botocudo people, who lived in inland regions of southeastern Brazil — stands out, having skull shapes that were intermediate between those of other Palaeoamericans and a presumed ancestral population in eastern Asia.

Now, a genetic analysis sheds light on the possible heritage of the Botocudo. Pena and his colleagues studied short stretches of mitochondrial DNA (mtDNA) in samples drilled from teeth in 14 Botocudo skulls kept in a museum collection in Rio de Janeiro. By analysing material from inside the teeth, the team minimized the possibility of contamination with DNA from the numerous people who have probably handled the skulls since they arrived at the museum in the late 1800s.

The mtDNA from 12 of the skulls matched a well-known Palaeoamerican haplogroup. But mtDNA from two of the skulls included a haplogroup commonly found in Polynesia, Easter Island and other Pacific island archipelagos, the researchers report today in Proceedings of the National Academy of Sciences1. A separate lab confirmed the result with samples from one of the skulls, indicating that the ‘Polynesian haplogroup’ did not result from contamination, the researchers contend.

“But to call that haplogroup Polynesian is a bit of a misnomer,” says Lisa Matisoo-Smith, a molecular anthropologist at the University of Otago in Dunedin, New Zealand. The haplogroup is also found — albeit at a lower frequency — in populations living as far west as Madagascar.

Nevertheless, says Pena, it is a mystery how DNA from Palaeoamericans living in southeastern Brazil could include gene sequences typically found in Pacific islanders. “We have this finding,” he says. “Now we have to explain it.”

The researchers say that it is possible — but unlikely — that the DNA could have come from Polynesians who voyaged from remote islands to the western coast of South America. Those traders or their progeny would then have made their way to southeastern Brazil and settled or interbred with natives. But that, too, is improbable, says Pena, because the Andes are a formidable barrier that west coast residents typically did not climb or cross. Although researchers have suggested that ancestors of some species of chickens made their way to Chile through trade with pre-Columbian seafarers from Polynesia2, a subsequent study3 poked holes in that conclusion.

The researchers also entertain scenarios in which the haplogroup arrived in South America via the slave trade. Around 2,000 Polynesians were brought to Peru in the 1860s, and some could have ended up in Brazil, although the researchers say that they are not aware of any evidence that this occurred. And between 1817 and 1843, approximately 120,000 slaves were shipped from Madagascar to Brazil — and some of them were probably transported to areas where the Botocudo also lived. Although the researchers consider the latter scenario to be the most probable, Pena says: “We currently don’t have enough evidence to definitively reject any of these scenarios.”

“This is a pretty exciting initial result,” says Alice Storey, an archaeologist at the University of New England in Armidale, Australia. Further studies of genetic material from the skulls, including detailed analyses of nuclear DNA (which contains much longer genetic sequences than mtDNA), could offer more insight into the mysterious ancestry of the Botocudo, she says.
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References:

Perkins, Sid. 2013. “DNA study links indigenous Brazilians to Polynesians”. Nature. Posted: April 1, 2013. Available online: http://www.nature.com/news/dna-study-links-indigenous-brazilians-to-polynesians-1.12710

Article Reference:

1. Gonçalves, V. F. et al. Proc. Natl Acad. Sci. USA http:dx.doi.org/10.1073/pnas.1217905110 (2013).

2. Storey, A. A. et al. Proc. Natl Acad. Sci. USA 104, 10335–10339 (2007).

3. Gongora, J. et al. Proc. Natl Acad. Sci. USA 105, 10308–10313 (2008).

First Migration from Africa Less Than 95,000 Years Ago: Ancient Hunter-Gatherer DNA Challenges Theory of Early Out-Of-Africa Migrations

Recent measurements of the rate at which children show DNA changes not seen in their parents -- the "mutation rate" -- have challenged views about major dates in human evolution.

In particular these measurements have made geneticists think again about key dates in human evolution, like when modern non-Africans split from modern Africans. The recent measurements push back the best estimates of these dates by up to a factor of two. Now, however an international team led by researchers at the University of Tübingen and the Max Planck Institute for Evolutionary Anthropology in Leipzig, present results that point again to the more recent dates. The new study is published in Current Biology.

The team, led by Johannes Krause from Tübingen University, was able to reconstruct more than ten mitochondrial genomes (mtDNAs) from modern humans from Eurasia that span 40,000 years of prehistory. The samples include some of the oldest modern human fossils from Europe such as the triple burial from Dolni Vestonice in the Czech Republic, as well as the oldest modern human skeletons found in Germany from the site of Oberkassel close to Bonn.

The researchers show that pre-ice age hunter-gatherers from Europe carry mtDNA that is related to that seen in post-ice age modern humans such as the Oberkassel fossils. This suggests that there was population continuity throughout the last major glaciation event in Europe around 20,000 years ago. Two of the Dolni Vestonice hunter-gatherers also carry identical mtDNAs, suggesting a close maternal relationship among these individuals who were buried together.

The researchers also used the radiocarbon age of the fossils to estimate human mutation rates over tens of thousands of year back in time. This was done by calculating the number of mutations in modern groups that are absent in the ancient groups, since they had not yet existed in the ancient population. The mutation rate was estimated by counting the number of mutations accumulated along descendent lineages since the radiocarbon dated fossils.

Using those novel mutation rates -- capitalizing on information from ancient DNA -- the authors cal-culate the last common ancestor for human mitochondrial lineages to around 160,000 years ago. In other words, all present-day humans have as one of their ancestors a single woman who lived around that time.

The authors also estimate the time since the most recent common ancestor of Africans and non-Africans to between 62,000-95,000 years ago, providing a maximum date for the mass migration of modern humans out of Africa. Those results are in agreement with previous mitochondrial dates based on archaeological and anthropological work but are at the extreme low end of the dates suggested from de-novo studies that suggest a split of non-Africans from Africans about thirty thousand years earlier.

"The results from modern family studies and our ancient human DNA studies are in conflict" says Krause. "One possibility is that mutations were missed in the modern family studies, which could lead to underestimated mutation rates." The authors argue that nuclear genomes from ancient modern humans may help to explain the discrepancies.
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References:

Science Daily. 2013. “First Migration from Africa Less Than 95,000 Years Ago: Ancient Hunter-Gatherer DNA Challenges Theory of Early Out-Of-Africa Migrations”. Science Daily. Posted: March 22, 2013. Available online: http://www.sciencedaily.com/releases/2013/03/130322114856.htm

Tracing humanity's African ancestry may mean rewriting 'out of Africa' dates

UAlberta archeologist's new research may lead to rethinking how and when our ancestors left Africa to colonize the globe

New research by a University of Alberta archeologist may lead to a rethinking of how, when and from where our ancestors left Africa.

U of A researcher and anthropology chair Pamela Willoughby's explorations in the Iringa region of southern Tanzania yielded fossils and other evidence that records the beginnings of our own species, Homo sapiens. Her research, recently published in the journal Quaternary International, may be key to answering questions about early human occupation and the migration out of Africa about 60,000 to 50,000 years ago, which led to modern humans colonizing the globe.

From two sites, Mlambalasi and nearby Magubike, she and members of her team, the Iringa Region Archaeological Project, uncovered artifacts that outline continuous human occupation between modern times and at least 200,000 years ago, including during a late Ice Age period when a near extinction-level event, or "genetic bottleneck," likely occurred.

Now, Willoughby and her team are working with people in the region to develop this area for ecotourism, to assist the region economically and create incentives to protect its archeological history.

"Some of these sites have signs that people were using them starting around 300,000 years ago. In fact, they're still being used today," she said. "But the idea that you have such ancient human occupation preserved in some of these places is pretty remarkable."

Magubike: Home to a modern Stone Age family?

Willoughby says one of the fascinating things about Magubike is the presence of a large rock shelter with an intact overhanging roof. The excavations yielded unprecedented ancient artifacts and fossils from under this roof. Samples from the site date from the earliest stages of the middle Stone Age to the Iron Age. The earlier deposits include human teeth and artifacts such as animal bones, shells and thousands of flaked stone tools.

The Iron Age finds can be dated using radiocarbon, but the older deposits must go through more specialized processes, such as electron spin resonance, to determine their age. Other parts of the Magubike rock shelter, excavated in 2006 and 2008, include occupations from after the middle Stone Age. Taken together, this information could be crucial to tracking the evolutionary development of the inhabitants.

"What's important about the whole sequence is that we may have a continuous record of human occupation," said Willoughby. "If we do—and we can prove it through these special dating techniques—then we have a place people lived in over the bottleneck."

Rugged, hilly terrain may have been key to survival

The team made similar findings at Mlambalasi, about 20 kilometres from Magubike. Among the findings at this site was a fragmentary human skeleton that probably dates to the late Pleistocene Ice Age—after the out-of-Africa expansion but at the end of the bottleneck period. The bottleneck theory explains what geneticists have found by studying the mitochondrial DNA of living people—that all non-Africans are descended from one lineage of people who left Africa about 50,000 years ago.

Reconstructions of past environments through pollen and other archeological records in Iringa suggest that people abandoned the lowland, tropical and coastal areas during that period but remained in the highlands, where vegetation has remained mostly unchanged over the last 50,000 years. Those who moved to higher ground may have found what is likely one of the few places that facilitated their survival and forced their adaptation. Further testing will determine whether these findings point to a clearer link to our African ancestors—a find Willoughby says could put that region of Tanzania on many archeologists' radar.

"It was only about 20 years ago that people recognized that modern Homo sapiens actually had an African ancestry, and everyone was focused on looking at early Homo sapiens in Europe who appeared around 40,000 years ago," she said. "But we now know that as far as back as around 200,000 years ago, Africa was inhabited by people who were already physically exactly like us today or really close to being the same as us. All of a sudden, it's not Europe in this time period that's really important, it's Africa."

Engaging community yields co-operation, opportunity

Along with its scientific significance, Willoughby's work may be a linchpin to potential economic growth for the region. Since 2005, when a local cultural officer showed her the sites, she has been sharing information about her research with local citizens, schools and government—opening up opportunities for more research and co-operation. She keeps the region informed of the team's findings through posters distributed around Iringa, and has asked for and accepted assistance from local scholars. Now the community is also looking for her help in establishing the historic sites as a tourist attraction that will benefit the region.

Willoughby says she feels fortunate to have the support of the Tanzanian people. She tells people it is a shared history she is uncovering, something she is honoured to be able to do.

"They're telling me, 'You're putting Iringa on the map,'" she said. "As long as they keep letting me work there, and keep letting the people working with me work there, we'll be happy."
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References:

EurekAlert. 2012. “Tracing humanity's African ancestry may mean rewriting 'out of Africa' dates”. EurekAlert. Posted: December 13, 2012. Available online: http://www.eurekalert.org/pub_releases/2012-12/uoa-tha121312.php

New Stanford analysis provides fuller picture of human expansion from Africa

A comprehensive analysis of the anthropological and genetic history of humans' expansion out of Africa could lead to medical advances.

A new, comprehensive review of humans' anthropological and genetic records gives the most up-to-date story of the "Out of Africa" expansion that occurred about 45,000 to 60,000 years ago.

This expansion, detailed by three Stanford geneticists, had a dramatic effect on human genetic diversity, which persists in present-day populations. As a small group of modern humans migrated out of Africa into Eurasia and the Americas, their genetic diversity was substantially reduced.

In studying these migrations, genomic projects haven't fully taken into account the rich archaeological and anthropological data available, and vice versa. This review integrates both sides of the story and provides a foundation that could lead to better understanding of ancient humans and, possibly, genomic and medical advances.

"People are doing amazing genome sequencing, but they don't always understand human demographic history" that can help inform an investigation, said review co-author Brenna Henn, a postdoctoral fellow in genetics at the Stanford School of Medicine who has a PhD in anthropology from Stanford. "We wanted to write this as a primer on pre-human history for people who are not anthropologists."

This model of the Out of Africa expansion provides the framework for testing other anthropological and genetic models, Henn said, and will allow researchers to constrain various parameters on computer simulations, which will ultimately improve their accuracy.

"The basic notion is that all of these disciplines have to be considered simultaneously when thinking about movements of ancient populations," said Marcus Feldman, a professor of biology at Stanford and the senior author of the paper. "What we're proposing is a story that has potential to explain any of the fossil record that subsequently becomes available, and to be able to tell what was the size of the population in that place at that time."

The anthropological information can inform geneticists when they investigate certain genetic changes that emerge over time. For example, geneticists have found that genes that allowed humans to tolerate lactose and gluten began to emerge in populations expanding into Europe around 10,000 years ago.

The anthropological record helps explain this: It was around this time that humans embraced agriculture, including milk and wheat production. The populations that prospered – and thus those who survived to pass on these mutations – were those who embraced these unnatural food sources. This, said Feldman, is an example of how human movements drove a new form of natural selection.

Populations that expand from a small founding group can also exhibit reduced genetic diversity – known as a "bottleneck" – a classic example being the Ashkenazi Jewish population, which has a fairly large number of genetic diseases that can be attributed to its small number of founders. When this small group moved from the Rhineland to Eastern Europe, reproduction occurred mainly within the group, eventually leading to situations in which mothers and fathers were related. This meant that offspring often received the same deleterious gene from each parent and, as this process continued, ultimately resulted in a population in which certain diseases and cancers are more prevalent.

"If you know something about the demographic history of populations, you may be able to learn something about the reasons why a group today has a certain genetic abnormality – either good or bad," Feldman said. "That's one of the reasons why in our work we focus on the importance of migration and history of mixing in human populations. It helps you assess the kinds of things you might be looking for in a first clinical assessment. It doesn't have the immediacy of prescribing chemotherapy – it's a more general look at what's the status of human variability in DNA, and how might that inform a clinician." The study is published in the current edition of the Proceedings of the National Academy of Sciences and was co-authored by Feldman's longtime collaborator, population geneticist Luigi Luca Cavalli-Sforza of Stanford and the Università Vita-Salute San Raffaele in Italy.
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References:

Carey, Bjorn. 2012. “New Stanford analysis provides fuller picture of human expansion from Africa”. Stanford University News Service. Posted: October 22, 2012. Available online: http://news.stanford.edu/pr/2012/pr-genetic-human-evolution-102212.html

Forensic science used to determine who's who in pre-Columbian Peru

Analysis of ancient mitochondrial DNA (mtDNA) has been used to establish migration and population patterns for American indigenous cultures during the time before Christopher Columbus sailed to the Americas. New research published in BioMed Central's open access journal BMC Genetics has used more detailed DNA analysis of individuals from Arequipa region to identify the family relationships and burial traditions of ancient Peru. The social unit (ayllu) of Native South Americans is thought to be based on kin relationships. The establishment of ayllu-based communities is also associated with funereal monuments (chullpas) which are thought to be important social sites not only because of their religious importance but because they housed the venerated ayllu's ancestors. Ancestor worship and a belief in a common ancestor, central to the ayllu, still exists in the traditions of the Q'ero community. Researchers from University of Warsaw, in collaboration with Universidad Catolica de Santa Maria, used DNA analysis to reconstruct the family trees of individuals buried in six chullpas near the Coropuna volcano is southern Peru. Despite prior looting, the unique nature of this site, 4000m up the Cora Cora mountain, allowed an extraordinary preservation of human remains and of DNA within both teeth and bone. mtDNA analysis showed that the groups were of Andean origin and indicated a 500 year continuity, up to modern Andeans, without any major impact by European colonisation. The social structure of an aylla was established using Y (male) chromosome and autosomal microsatellites analysis, in conjunction with the mtDNA. Family connections were clearly strongest within each chullpa, since individuals buried in the same chullpa were more closely related than those buried in different chullpas, and all males buried together shared identical Y chromosome profiles. In two of the chullpas several generations of related males were found. This matches current thought that the ancient Andians would swap women between families - so called 'sister exchange' while the men retained the ancestral land. The combinations of DNA analysis used allowed for an unprecedented level of detail in social behaviour to be discerned. In one chullpa three different Y chromosome lineages were found. Comparison of mtDNA within this chullpa suggests that two of the males had the same mother but different fathers, and the third male was related to one of the females, probably a half brother. Mateusz Baca explained, "Our results show that this community of llama and alpaca herders was (genetically) an extended patriarchal society. The use of chullpas as family graves is consistent with the idea of ayllu-based communities based around strong kinship relationships. However, the chullpa with mixed male heritage shows that this social structure could also be flexible and the strict rules governing marriage and family could be intentionally, or unintentionally, relaxed." _______________ References: EurekAlert. 2012. "Forensic science used to determine who's who in pre-Columbian Peru". EurekAlert. Posted: April 22, 2012. Available online: http://www.eurekalert.org/pub_releases/2012-04/bc-fsu042012.php Notes: 1. Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community Mateusz Baca, Karolina Doan, Maciej Sobczyk, Anna Stankovic and Piotr Weglenski BMC Genetics (in press) 2. BMC Genetics is an open access, peer-reviewed journal that considers articles on all aspects of inheritance and variation in individuals and among populations. 3. BioMed Central (http://www.biomedcentral.com/) is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector.