Here’s how genetics helped crack the history of human migration

By George Busby, University of Oxford

Over the past 25 years, scientists have supported the view that modern humans left Africa around 50,000 years ago, spreading to different parts of the world by replacing resident human species like the Neanderthals. However, rapid advances in genetic sequencing have opened up a whole new window into the past, suggesting that human history is much more complicated.

In fact, genetic studies in the last few years have revealed that since our African exodus, humans have moved and mixed a lot more than previously thought – particularly over the last 10,000 years.

The technology

Our ability to sequence DNA has increased dramatically since the human genome was first sequenced 15 years ago. In its most basic form, genetic analysis involves comparing DNA from different sets of people, whether between people with or without a particular type of cancer, or individuals from different regions of the world.

The human genome is 3 billion letters long, but as people differ at just one letter in every thousand, on average, we don’t have to look at them all. Instead, we can compare people where we know there are these differences, known as genetic markers. Millions of these markers have been discovered and, together with a genetic sequencing technology that allows us to cheaply look at these markers in lots of people, there has been an explosion in the data available to geneticists.

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Why life is not a thing but a restless manner of being

Tim Requarth writes: Mike Russell found his moment of inspiration on a warm spring evening in Glasgow in 1983, when his 11-year-old son broke a new toy. The toy in question was a chemical garden, a small plastic tank in which stalactite-like tendrils grew out of seed crystals placed in a mineral solution. Although the tendrils appeared solid from the outside, when shattered they revealed their true nature: each one was actually a network of hollow tubes, like bundles of tiny cocktail straws.

At the time, Russell, a geologist, was struggling to understand an unusual rock he had recently found. It, too, was solid on the outside but inside was full of hollow tubes, their thin walls riddled with microscopic compartments. It dawned on him then that this rock – like the formations in his son’s toy – must have formed in some unusual kind of liquid solution. Russell posited a whole new geological phenomenon to explain it: undersea hydrothermal hotspots where mineral-rich water spewed from Earth’s interior and then precipitated in the cool surrounding water, creating chemical gardens of towering, hollow rocks growing up from the ocean floor.

That was a huge intuitive leap, but it soon led Russell to an even more outlandish thought. ‘I had the epiphany that life emerged from those rocks,’ he said. ‘Many years later, people would tell me the idea was amazing, but it wasn’t to me. I was just thinking in a different realm, in the light of what I knew as a geologist. I didn’t set out to study the origin of life, but it just seemed so obvious.’

What seemed obvious to Russell was that his hypothetical chemical gardens could solve one of the deepest riddles of life’s origin: the energy problem. Then as now, many leading theories of life’s origins had their roots in Charles Darwin’s speculation of a ‘warm little pond’, in which inanimate matter, energised by heat, sunlight or lightning, formed complex molecules that eventually began reproducing themselves. For decades, most origin-of-life research has focused on how such self-replicating chemistry could have arisen. They largely brushed aside the other key question, how the first living things obtained the energy to grow, reproduce and evolve to greater complexity.

But in Russell’s mind, the origin of life and the source of the energy it needed were a single issue, the two parts inextricably intertwined. As a geologist (now working at NASA’s Jet Propulsion Laboratory in California), he came at the problem with a very different perspective from his biology-trained colleagues. Undersea chemical gardens, Russell realised, would have provided an abundant flux of matter and energy in the same place – a setting conducive for self-replicating reactions, and also a free lunch for fledgling creatures. It has long troubled researchers that the emergence of life seems to rely on highly improbable chemical events that lead toward greater complexity. By considering energy first, Russell believed he could address that. In his view, the emergence of biological complexity was not improbable but inevitable. [Continue reading…]

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New human species may rewrite history

New Scientist reports: We may have lived alongside an archaic human species just 10,500 years ago in China. Controversial bone discoveries suggest we even interbred with and cannibalised these mystery hominins.

Some think the findings could overturn our understanding of what it means to be human. “If true, this would be rather spectacular and it would make the finds of truly global importance,” says Michael Petraglia at the University of Oxford, who wasn’t involved in the discoveries.

One of the most exciting finds is a hominin femur found in Muladong cave in south-west China, alongside other human and animal bones. It shows evidence of having been burned in a fire that was used for cooking other meat, and has marks consistent with it being butchered. It has also been broken in a way that is used to access bone marrow. Unusually, it has been painted with a red clay called ochre, associated with burial rituals (PLoS One, doi.org/97c).

Things got more interesting when the team tried to identify the bone. “Our work shows clearly that the femur resembles archaic humans,” says Darren Curnoe of the University of New South Wales in Sydney, Australia, who led the team behind the discoveries. Yet the sediment the bone was found in dates to just 14,000 years ago. This would make it the most recent human species to go extinct. [Continue reading…]

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The migrant roots of ancient European ancestry

University of Cambridge

The first sequencing of ancient genomes extracted from human remains that date back to the Late Upper Palaeolithic period over 13,000 years ago has revealed a previously unknown “fourth strand” of ancient European ancestry.

This new lineage stems from populations of hunter-gatherers that split from western hunter-gatherers shortly after the ‘out of Africa’ expansion some 45,000 years ago and went on to settle in the Caucasus region, where southern Russia meets Georgia today.

Here these hunter-gatherers largely remained for millennia, becoming increasingly isolated as the Ice Age culminated in the last ‘Glacial Maximum’ some 25,000 years ago, which they weathered in the relative shelter of the Caucasus mountains until eventual thawing allowed movement and brought them into contact with other populations, likely from further east.

This led to a genetic mixture that resulted in the Yamnaya culture: horse-borne Steppe herders that swept into Western Europe around 5,000 years ago, arguably heralding the start of the Bronze Age and bringing with them metallurgy and animal herding skills, along with the Caucasus hunter-gatherer strand of ancestral DNA – now present in almost all populations from the European continent.

The research was conducted by an international team led by scientists from Cambridge University, Trinity College Dublin and University College Dublin. The findings were published last month in the journal Nature Communications.

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Humans sleep less but more deeply than any other primate

Carl Zimmer writes: Over the past few million years, the ancestors of modern humans became dramatically different from other primates. Our forebears began walking upright, and they lost much of their body hair; they gained precision-grip fingers and developed gigantic brains.

But early humans also may have evolved a less obvious but equally important advantage: a peculiar sleep pattern. “It’s really weird, compared to other primates,” said Dr. David R. Samson, a senior research scientist at Duke University.

In the journal Evolutionary Anthropology, Dr. Samson and Dr. Charles L. Nunn, an evolutionary biologist at Duke, reported that human sleep is exceptionally short and deep, a pattern that may have helped give rise to our powerful minds. [Continue reading…]

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6,000 years ago humans upturned 300 million years of evolution

Smithsonian.com reports: It’s hard to imagine a global force strong enough to change natural patterns that have persisted on Earth for more than 300 million years, but a new study shows that human beings have been doing exactly that for about 6,000 years.

The increase in human activity, perhaps tied to population growth and the spread of agriculture, seems to have upended the way plants and animals distribute themselves across the land, so that species today are far more segregated than they’ve been at any other time.

That’s the conclusion of a study appearing this week in the journal Nature, and the ramifications could be huge, heralding a new stage in global evolution as dramatic as the shift from single-celled microbes to complex organisms.

A team of researchers led by S. Kathleen Lyons, a paleobiologist at the Evolution of Terrestrial Ecosystems (ETE) program in the Smithsonian’s National Museum of Natural History, examined the distribution of plants and animals across landscapes in the present and back through the fossil record in search of patterns.

Mostly they found randomness, but throughout time, there was always a small subset of plants and animals that showed up in relationship to one another more often than can be attributed to chance. That relationship either meant that pairs of species occur together, so when you find one, you usually find the other. Or it meant the opposite: when you find one, the other is usually not present, in which case they’re considered segregated. [Continue reading…]

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A new field called paleoepigenetics is probing how evolution responds to sudden stress

Ferris Jabr writes: Every year the paleontologist Alan Cooper meets up with a band of miners in the Yukon. As the miners go about their work, spraying massive jets of water at frozen mud and silt to excavate gold, they also expose animal remains from the Pleistocene, between 2 million and 12,000 years ago. Back then, North America was a riot of big mammals. Antelope, camels, llamas, and indigenous horses roamed the vast plains; lions, saber-toothed cats, and dire wolves prowled for prey; and giant ground sloths lumbered along, stripping tree branches of leaves and fruit.

But, by the time the planet transitioned to the current geological epoch, the Holocene, the vast majority of those species had gone extinct, most likely due to climate change or hunting by humans. Climate change in the Pleistocene was “huge, frequent, and rapid,” says Cooper, director of the Australian Centre for Ancient DNA at the University of Adelaide. “Sometimes a change of 10 degrees centigrade over a space of a decade or two.” It’s difficult for animals to cope with such dramatic shifts through standard evolution by natural selection, which often takes decades — even millennia — to spread advantageous genetic mutations and hone adaptations. [Continue reading…]

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The red wolf and a new theory about how evolution actually works

Ben Crair writes: Since the red wolf was originally classified as an endangered species, biologists have studied it intensely — sequencing its DNA, scrutinizing its morphology, and piecing together its evolutionary history. And they’ve put forward a compelling new theory: The red wolf, an animal the U.S. government has spent decades and millions of dollars attempting to save from extinction, may not actually be a distinct species at all.

The implications of this idea extend far beyond the swamps and farms of North Carolina, threatening the very foundations of biology itself. “Not to have a natural unit such as the species would be to abandon a large part of biology into free fall, all the way from the ecosystem down to the organism,” the noted biologist and theorist E.O. Wilson wrote in his 1992 book The Diversity of Life. And yet, the research into the red wolf challenges our accepted notions about how species are defined—and about how evolution actually works. [Continue reading…]

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Evidence that first toolmakers predated the genus Homo

Discover reports: Thanks to a wrong turn, a stroke of luck and keen eyes, husband and wife research partners Sonia Harmand and Jason Lewis of Stony Brook University could rewrite our understanding of tool use among hominins. With their team from the West Turkana Archaeological Project, the pair have found evidence that a species predating the genus Homo may have made the first stone tools.

In July 2011, Harmand and Lewis and their colleagues were scouting for sites in the area around northern Kenya’s Lake Turkana. There are no roads in this remote region, so Harmand was forced to drive in dry creek beds while Lewis navigated with a GPS device. It’s all too easy to become disoriented in this kind of terrain; at a certain juncture where the GPS indicated a right turn, she mistakenly went left. They soon found the way blocked by bushes. Unable to drive farther, they climbed a small hill to get their bearings. From the top of the rise, the team gazed down on what Harmand describes as a uniquely beautiful landscape.

“I felt certain it contained hidden areas waiting to be explored,” she says. Everyone fanned out to investigate. “We were only 10 people, working far from each other with walkie-talkies. Around 9 in the morning, we had a call from our local Turkana team member, Sammy Lokorodi. He said, ‘You should come where I am because I think I’ve spotted something very interesting.’ ”

He found stone tools sticking out of an eroding creek bed. The surface above had a dark, weathered patina, but the areas around the rocks were light, suggesting they had been only recently exposed. Harmand knew at once this was an important find because the layers in which the tools were embedded were dated to more than 2.7 million years old.

Paleomagnetic dating — matching magnetic properties in the sediments surrounding a fossil or artifact to ancient reversals in the Earth’s magnetic poles to determine age — later determined the tools had to have been made 3.3 million years ago. Despite the tools’ simple form and huge size, some almost 8 inches across, the angle and patterns on the rocks’ edges showed repetitive strikes that could not have resulted from erosion or other natural processes. Publishing the discovery in Nature in May, Harmand and Lewis dubbed the assemblage the Lomekwi 3, after the area where the tools were found. [Continue reading…]

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DNA evidence reveals that the people who civilized Europe were migrants

The New York Times reports: Before the rise of agriculture, Europe was home to a population of hunter-gatherers. Then a wave of people arrived whose DNA resembles that of people in the Near East. It’s likely that they brought agriculture with them.

Finally, about 4,500 years ago, a nomadic population from the steppes of Russia, known as the Yamnaya, swept into Europe.

The analyses that revealed these migrations were based on dozens of ancient European genomes. But in a study published Monday in Nature, David Reich, a geneticist at Harvard Medical School, and his colleagues analyzed the genomes of 230 people who lived between 8,500 and 2,300 years ago.

The enormous sample size has provided enough data to track individual genetic variations as they become more or less common through the history of ancient Europe.

The remains that Dr. Reich and his colleagues analyzed DNA from span the entire continent of Europe. They also include the Yamnaya as well as 21 people who lived in a region of Turkey called Anatolia 8,500 years ago. The study marks the first time scientists have been able to analyze the DNA of the people who brought farming to Europe. [Continue reading…]

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How the Western diet has derailed our evolution

Moises Velesquez-Manoff writes: For the microbiologist Justin Sonnenburg, that career-defining moment — the discovery that changed the trajectory of his research, inspiring him to study how diet and native microbes shape our risk for disease — came from a village in the African hinterlands.

A group of Italian microbiologists had compared the intestinal microbes of young villagers in Burkina Faso with those of children in Florence, Italy. The villagers, who subsisted on a diet of mostly millet and sorghum, harbored far more microbial diversity than the Florentines, who ate a variant of the refined, Western diet. Where the Florentine microbial community was adapted to protein, fats, and simple sugars, the Burkina Faso microbiome was oriented toward degrading the complex plant carbohydrates we call fiber.

Scientists suspect our intestinal community of microbes, the human microbiota, calibrates our immune and metabolic function, and that its corruption or depletion can increase the risk of chronic diseases, ranging from asthma to obesity. One might think that if we coevolved with our microbes, they’d be more or less the same in healthy humans everywhere. But that’s not what the scientists observed. [Continue reading…]

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Why we think the very first farmers were small groups with property rights

By Elizabeth Gallagher, UCL

For 95% of the history of modern humans we were exclusively hunter gatherers. Then suddenly about 12,000 years ago, something happened that revolutionised the way humans lived and enabled the complex societies we have today: farming.

But what triggered this revolution? Understanding this is incredibly challenging – because this occurred so far in the past, there are many factors to consider. However, by simulating the past using a complex computational model, we found that the switch from foraging to farming most likely began with very small groups of people that were using the concept of property rights.

Farming: an unlikely choice

It may seem obvious why we switched from foraging to farming: it made it possible to stay in one place, feed larger populations, have greater food security and build increasingly complex societies, political structures, economies and technologies. However, these advantages took time to develop and our early farmer ancestors would not have seen these coming.

Indeed, archaeological research suggests that when farming began it was not a particularly attractive lifestyle. It involved more work, a decrease in the quality of nutrition and health, an increase in disease and infection, and greater challenges in defending resources. For a hunter-gatherer at the cusp of the “agricultural revolution”, a switch to farming wasn’t the obvious choice.

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In a society where everyone is ready to defend the common good, corruption doesn’t pay

Suzanne Sadedin writes: By making a few alterations to the composition of the justice system, corrupt societies could be made to transition to a state called ‘righteousness’. In righteous societies, police were not a separate, elite order. They were everybody. When virtually all of society stood ready to defend the common good, corruption didn’t pay.

Among honeybees and several ant species, this seems to be the status quo: all the workers police one another, making corruption an unappealing choice. In fact, the study showed that even if power inequalities later re-appeared, corruption would not return. The righteous community was extraordinarily stable.

Not all societies could make the transition. But those that did would reap the benefits of true, lasting harmony. An early tribe that made the transition to righteousness might out-compete more corrupt rivals, allowing righteousness to spread throughout the species. Such tribal selection is uncommon among animals other than eusocial insects, but many researchers think it could have played a role in human evolution. Hunter-gatherer societies commonly tend toward egalitarianism, with social norms enforced by the whole group rather than any specially empowered individuals. [Continue reading…]

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How did complex creatures evolve from simple single-celled organisms?

Emily Singer writes: In September 2014, Christa Schleper embarked on an unusual hunting expedition in Slovenia. Instead of seeking the standard quarry of deer or wild boar, Schleper was in search of Lokiarchaeota, or Loki, a newly discovered group of organisms first identified near deep-sea vents off the coast of Norway. The simple, single-celled creatures have captured scientists’ interest because they are unlike any other organism known to science. They belong to an ancient group of creatures known as archaea, but they seem to share some features with more complex life-forms, including us.

Though little is known about Loki, scientists hope that it will help to resolve one of biology’s biggest mysteries: how life transformed from simple single-celled organisms to the menagerie of complex life known as eukaryotes — a category that includes everything from yeast to azaleas to elephants. “Next to the origins of life, there’s probably no bigger mystery in the history of life,” said John Archibald, an evolutionary biologist at Dalhousie University in Nova Scotia.

The jump from single cells to complex creatures is so puzzling because it represents an enormous evolutionary gulf. “How do you make a eukaryote, that’s a big question,” said Schleper, a microbiologist at the University of Vienna in Austria. “It’s a huge transition.”

Though single-celled organisms blanket the Earth and are capable of impressive biochemistry — some can eat nuclear waste, for example — their structure and shape remain simple. Cells from animals, plants and fungi, which make up the eukaryotes, are much more sophisticated. They possess a suite of features lacking in their simpler brethren: a nucleus that houses DNA; an energy-producing device known as the mitochondrion; and molecular architecture, known as the cytoskeleton, that controls cell shape and movement.

Most biologists agree that at some point around two billion years ago, one featureless cell swallowed another, and the two began to work together as one. But the details of this process — whether this symbiosis jump-started an evolutionary process, or whether it happened midway along the path to eukaryotes — continue to drive huge disputes in the field. [Continue reading…]

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Competition in Cambrian seas 542 million years ago helped cause an explosion in animal diversity

Brooke Borel writes: Battles fought 542 million years before today helped fuel a blast that brought humans and most animals into existence. The great Cambrian Explosion was a period of unprecedented one-upmanship. Beastly claws crushed through thin skin, and soft-bodied creatures evolved shells shaped like scythes, sickles, and shields.

For about a billion years prior, the cells and genes that would later create animals were evolving in microscopic organisms who inhabited the oceans of Earth. These essential molecular changes may only be inferred today because they’re not preserved in fossils. The earliest traces of animals, about 580 million years old, appear soft, with no sign of claws, teeth, limbs, or brains. Then, within 54 million years (a relative blink but still, 270 times the duration of humans’ existence thus far), most of the main animal groups around today originated. This rapid rate of increase in animal architectures has never since been repeated.

A simple species count does not do justice to the power of the Cambrian Explosion. Species have continuously formed over time. A new type of moth may have antennae that are furrier than its sisters; a new species of dinosaur may be distinguished by clawed wings and vicious front fangs. But a new phylum — a major branch on the tree of life, the upper-level ranking that separates an insect from a pterodactyl — is rarely born.

Most of today’s 30 to 40 animal phyla originated in the Cambrian, and have persisted through time with hundreds of variations on a theme. [Continue reading…]

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