December 4, 2013
Since its discovery in 1990, La Sima de los Huesos, an underground cave in Northern Spain’s Atapuerca Mountains, has yielded more than 6,000 fossils from 28 individual ancient human ancestors, making it Europe’s most significant site for the study of ancient humans. But despite years of analysis, the exact age and even the species to which these individuals belonged has been in doubt.
Now, though, an international group of scientists has extracted and sequenced DNA from the fossilized femur of one of these individuals for the first time. The resulting data—which represent the oldest genetic material ever sequenced from a hominin, or ancient human ancestor—finally give us an idea of the age and lineage of these mysterious individuals, and it’s not what many scientists expected.
The fossilized bone tested, a femur, is roughly 400,000 years old. But the big surprise is that, although scientists had previously believed the fossils belonged to Neanderthals because of their anatomical appearance, the DNA analysis actually shows they’re more closely related to Denisovans, a recently-discovered third lineage of human ancestors known only from DNA isolated from a few fossils found in Siberia in 2010. The findings, published today in Nature, will force anthropologists to further reconsider how the Denisovans, Neanderthals and the direct ancestors of modern-day humans fit together in a complicated family tree.
The analysis was enabled by recent advances in methods for recovering ancient DNA fragments developed at the Max Planck Institute for Evolutionary Anthropology in Germany, previously used to analyze the DNA of a cave bear fossil found in the same cave. “This wouldn’t have been possible just two years ago,” says Juan Luis Arsuaga, a paleontologist at the University of Madrid who led the initial excavations of the cave and collaborated on the new study. “And even given these new methods, we still didn’t expect these bones to preserve DNA, because they’re so old—ten times older than some of the oldest Neanderthals from whom we’ve taken DNA.”
After extracting a two grams of crushed bone from the femur, a group of scientists led by Matthias Meyer isolated the mitochondrial DNA (mtDNA), a pool of genetic material that’s distinct from the DNA in the chromosomes located in our cells’ nuclei. Instead, this mtDNA lives in our cells’ mitochondria—microscopic organelles responsible for cellular respiration—and is much shorter in length than nuclear DNA.
There’s another quirk of mtDNA that makes it especially valuable as a means of studying the evolution of ancient humans: Unlike your nuclear DNA, which is a mix of DNA from both your parents, your mtDNA comes solely from your mother, because most of a sperm’s mitochondria are found in its tail, which it sheds after fertilization. As a result, mtDNA is nearly identical from generation to generation, and a limited number of distinct sequences of mtDNA (called haplogroups) have been observed in both modern humans and ancient human ancestors. Unlike anatomical characteristics and nuclear DNA, which can vary within a group and make it difficult to confidently distinguish one from another, mtDNA is generally consistent, making it easier to link a particular specimen with a lineage.
Which is why, when the researchers compared the femur’s mtDNA to previously sequenced samples from Neanderthals, from a Denisovan finger bone and tooth found in Siberia and from many different modern humans, they found it so surprising that it more closely resembled the Denisovans. “This was really unexpected,” Arsuaga says. “We had to think really hard to come up with a few scenarios that could potentially explain this.”
Anthropologists had already known that all three lineages (humans, Neanderthals and Denisovans) shared a common ancestor, but it’s far from clear how all three groups fit together, and the picture is further clouded by the fact that interbreeding may have occurred between them after they diverged. Helpfully, comparing the femur’s mtDNA to the Neanderthal, Denisovan and modern human samples allowed the researchers to estimate its age—based upon known rates of mtDNA mutation, the previously established ages of the other samples, and the degree of difference between them—leading to the 400,000 year figure.
To explain how a Neanderthal-looking individual could come to have Denisovan mtDNA during this time period, the scientists present several different hypothetical scenarios. It’s possible, for instance, that the fossil in question belongs to a lineage that served as ancestors of both Neanderthals and Denisovans, or more likely, one that came after the split between the two groups (estimated to be around 1 million years ago) and was closely related to the latter but not the former. It’s also a possibility that the femur belongs to a third, different group, and that its similarities to Denisovan mtDNA are explained by either interbreeding with the Denisovans or the existence of yet another hominin lineage that bred with both Denisovans and the La Sima de los Huesos population and introduced the same mtDNA to both groups.
If this sounds like a complicated family tree to you, you’re not alone. This analysis, along with earlier work, adds further mystery to an already puzzling situation. Initial testing on the Denisovan finger bone found in Siberia, for instance, found that it shared mtDNA with modern humans living in New Guinea, but nowhere else. Meanwhile, it was previously thought that Neanderthals had settled in Europe and Denisovans further east, on the other side of the Ural Mountains. The new analysis complicates that idea.
For now, the researchers believe the most plausible scenario (illustrated below) is the femur belongs to a lineage that split off from Denisovans sometime after they diverged from the common ancestor of both Neanderthals and modern humans. But perhaps the most exciting conclusion to come out of this work is that it proves that genetic material can survive for at least 400,000 years, and can be analyzed even after that amount of degradation. Armed with this knowledge and the new techniques, anthropologists can now attempt to genetically survey many other ancient specimens in hopes of better understanding our family tree.
December 2, 2013
It’s a platitude that we’ve all heard dozens of times, whether to justify our treatment of other species or simply to celebrate a carnivorous lifestyle: humans are the top of the food chain.
Ecologists, though, have a statistical way of calculating a species’ trophic level—its level, or rank, in a food chain. And interestingly enough, no one ever tried to rigorously apply this method to see exactly where humans fall.
Until, that is, a group of French researchers recently decided to use food supply data from the U.N Food and Agricultural Organization (FAO) to calculate human tropic level (HTL) for the first time. Their findings, published today in the Proceedings of the Natural Academy of Sciences, might be a bit deflating for anyone who’s taken pride in occupying the top position.
On a scale of 1 to 5, with 1 being the score of a primary producer (a plant) and 5 being a pure apex predator (a animal that only eats meat and has few or no predators of its own, like a tiger, crocodile or boa constrictor), they found that based on diet, humans score a 2.21—roughly equal to an anchovy or pig. Their findings confirm common sense: We’re omnivores, eating a mix of plants and animals, rather than top-level predators that only consume meat.
To be clear, this doesn’t imply that we’re middle-level in that we routinely get eaten by higher-level predators—in modern society, at least, that isn’t a common concern—but that to be truly at the “top of the food chain,” in scientific terms, you have to strictly consume the meat of animals that are predators themselves. Obviously, as frequent consumers of rice, salad, bread, broccoli and cranberry sauce, among other plant products, we don’t fit that description.
The researchers, led by Sylvain Bonhommeau of the French Research Institute for Exploitation of the Sea, used FAO data to construct models of peoples’ diets in different countries over time, and used this to calculate HTL in 176 countries from 1961 to 2009. Calculating HTL is fairly straightforward: If a person diet is made up of half plant products and half meat, his or her trophic level will be 2.5. More meat, and the score increases; more plants, and it decreases.
With the FAO data, they found that while the worldwide HTL is 2.21, this varies widely: The country with the lowest score (Burundi) was 2.04, representing a diet that was 96.7 percent plant-based, while the country with the highest (Iceland) was 2.54, reflecting a diet that contained slightly more meats than plants.
On the whole, since 1961, our species’ overall HTL has increased just slightly—from 2.15 to 2.21—but this averaged number obscures several important regional trends.
A group of 30 developing nations in Southeast Asia and Sub-Saharan Africa (shown in red)—including Indonesia, Bangladesh and Nigeria, for example—have had HTLs below 2.1 during the entire period. But a second group of developing countries that includes India and China (shown in blue) has slightly higher HTL measures that have consistently risen over time, going from around 2.18 to over 2.2. The HTLs of a third group, shown in green (including Brazil, Chile, South Africa and several countries in Southern Europe), have risen further, from around 2.28 to 2.33.
By contrast, HTL in the world’s wealthiest countries (shown in purple)—including those in North America, Northern Europe and Australia—was extremely high for most of the study period but decreased slightly starting during the 1990s, going from around 2.42 to 2.4. A fifth group of small, mostly island countries with limited access to agricultural products (shown in yellow, including Iceland and Mauritania) has seen more dramatic declines, from over 2.6 to less than 2.5.
These trends closely correlate, it turns out, with a number of World Bank development indicators, such as gross domestic product, urbanization and education level. The basic trend, in other words, is that as people become wealthier, they eat more meat and fewer vegetable products.
That has translated to massive increases in meat consumption in many developing countries, including China, India, Brazil and South Africa. It also explains why meat consumption has leveled off in the world’s richest countries, as gains in wealth leveled off as well. Interestingly, these trends in meat consumption also correlate with observed and projected trends in trash production—data indicate that more wealth means more meat consumption and more garbage.
But the environmental impacts of eating meat go far beyond the trash thrown away afterward. Because of the quantities of water used, the greenhouse gases emitted and the pollution generated during the meat production process, it’s not a big leap to speculate that the transition of huge proportions of the world’s population from a plant-based diet to a meat-centric one could have dire consequences for the environment.
Unfortunately, like the garbage problem, the meat problem doesn’t hint at an obvious solution. Billions of people getting wealthier and having more choice over the diet they eat, on a basic level, is a good thing. In an ideal world, we’d figure out ways to make that transition less damaging while still feeding huge populations. For example, some researchers have advocated for offbeat food sources like meal worms as a sustainable meat, while others are trying to develop lab-grown cultured meat as an environmentally-friendly alternative. Meanwhile, some in Sweden are proposing a tax on meat to curb its environmental cost while government officials in the UK are urging consumers to cut back on their demand for meat to increase global food security and to improve health. Time will tell which approaches stick.
In the meantime, simply keeping track of the amount of meat we’re eating as a society via HTL could provide a host of useful baseline information. As the authors write, “HTL can be used by educators to illustrate the ecological position of humans in the food web, by policy makers to monitor the nutrition transition at global and national scales and to analyze the effects of development on dietary trends, and by resource managers to assess the impacts of human diets on resource use.”
In other words, monitoring the intricacies of our middling position on the food chain may yield scientific fodder to tackle problems like food security, obesity, malnutrition and environmental costs of the agricultural industry. A heavy caseload for a number that ranks us on the same trophic level as anchovies.
November 29, 2013
A few years ago, University of Maryland PhD student Nathan Jud was routinely examining a batch of ancient plant fossils in the Smithsonian Natural History Museum‘s collections when one in particular caught his eye.
“It looked sort of like a little piece of fern, so I tried to remove a bit of the rock that was covering it to get a sense of what type of fern it was,” he says. “But the more of the rock I would lift off the surface, the more fossil I found buried. What I thought had been one little piece of a leaf actually turned out to be two, connected to each other.”
As he labored to carefully flake the rock without defacing the fossil, he noticed a series of curious characteristics that suggested the preserved plant was no ordinary fern: It had a closed network of veins, rather than a series of branching ones that split off from each other without coming back together, and at its tips, there were tiny structures called glandular teeth, used to shed excess water.
“Eventually, I realized this wasn’t a fern at all, but some kind of early flowering plant,” he says. Its features wouldn’t be at all out of the ordinary in a plant growing outside today. The fact that they occur in a fossil from the Early Cretaceous period, though, is remarkable. At somewhere between 125 and 115 million years old, this fossil, described in a paper Jud published today in the American Journal of Botany, is among the oldest flowering plants ever found in North America.
Flowering plants—which replicate with sexual structures (i.e. flowers) to produce seeds—now dominate the planet, but for the first 300 million years or so of plant existence, beginning around 450 million years ago, the only types of vegetation belonged to older, more primitive families, such as algae, mosses and ferns, which all reproduce with spores rather than seeds, or gymnosperms, which produce seeds but not flowers.
During the Early Cretaceous, some of the first primitive flowering plants began to evolve. Researchers know that the layer in which this new fossil was found dates to this time period due to a few factors: Pollen analysis (which considers the chemical makeup of pollen embedded in the surrounding rock) and as well as study of the surrounding sediment itself. The same layer has previously produced several other flowering plant fossils of a similar age—together, they’re the oldest ever discovered in North America—but this is the oldest example of a eudicot, a group that includes roughly 70 percent of flowering plants worldwide today that share a distinctively-shaped pollen structure.
Compared to the other fossils found in the same layer, this one is especially remarkable for its derived traits, anatomical characteristics that were previously thought to have developed much more recently in flowers. Their existence so long ago suggests that some early plants were actually quite complex.
“When I compared it to living plants, I realized it was remarkably similar to the leaves of a certain group of modern poppies,” Jud says. “I didn’t expect to see a group that seemingly modern in a collection that old.” The fact that these features existed so long ago, both in this plant and other ancient fossils recently excavated in China, tells us that the evolution of flowering plants (which Charles Darwin famously called an “abominable mystery“) did not happen gradually, but instead occurred very rapidly during a narrow time interval in the Early Cretaceous period between when flowering plants first emerged and the date of this fossil.
There’s also a much more recent history of this fossil that’s just as fascinating. Jud did a bit of research and found that it’d been excavated in 1971 by a former Smithsonian curator, Leo Hickey, who went on to Yale and died in February before working with Jud to re-analyze the fossil after all these years. Hickey had found it during a dig at the Dutch Gap, in Virginia, in sediments that were exposed over a century earlier, by freed slaves who were forcibly taken from the Roanoke Island Freedmen’s Colony by Union troops and forced to dig a canal in August 1864.
While digging, they exposed ancient fossil-filled rocks, and a few decades later, in the 1870s and 1880s, scientists worked there to collect fossils and create some of the Smithsonian’s first fossil collections. Later, Hickey and other researchers returned to collect remaining specimens.
Jud honored this recent history in naming the ancient species that this specimen represents. “Potomac refers to the Potomac Group beds where the fossil was found, capnos is a reference to living poppies that are quite similar to the fossil and apeleutheron is the Greek word for freedmen,” he says. “So the new plant will be named Potomacapnos apeleutheron: roughly, ‘freedmen’s poppy of the Potomac.’”
November 27, 2013
When we think of ants as builders, we normally imagine them digging intricate tunnel networks as part of underground colonies.
But David Hu, Nathan Mlot and a team of other researchers at Georgia Tech are studying a very different type of building behavior specific to one ant species: The ability of Solenopsis invicta to construct bridges, rafts and even temporary shelters using their own bodies as building material.
“Fire ants are capable of building what we call ‘self-aggregations,’” Hu says. “They can build little boats, little houses called bivouacs and even bridges to cross streams by being the building material, linking their bodies together and forming strong networks.”
The ants are now considered an invasive species in 25 states, Asia and Australia, but their unusual behavior is a survival strategy shaped by their native environment: a particular area of wetlands in western Brazil that are flooded frequently. “The ants live underground, but when it begins to flood, they have to gather the colony members, pull them out of the ground and build a floating raft,” Hu says.
When this raft hits land, the ants keep building. To cross small streams during their subsequent migration, they make living bridges that allow the entire colony to scramble to safety. Afterward, using their bodies, they construct a temporary aboveground encampment to provide shelter for the few days it takes to re-dig underground tunnels. All the while, the ants that form the temporary shelter are continuously moving, but still preserving the structure. “It’s really living architecture—it has well-constructed, organized tunnels, brooding rooms,” Hu says. At least for the ants in the inside, this provides protection against hostile weather or predators.
Hu, an engineer, is primarily interested in studying the swarming ants as a novel material with unprecedented characteristics. As part of his group’s recent research, presented yesterday at an annual meeting of the American Physical Society, he and colleagues considered the ants within the context of other “active materials”—substances that can respond to changing conditions, such as self-healing cements that can use the energy in sunlight to expand and fill their own fractures.
“We wanted to characterize what kind of material it is—is it a fluid, or is it a solid, and how does it respond to stress?” he says. “In nature, for instance, these rafts might float down a river and bump into rocks, or raindrops might hit them.”
To test these self-aggregations, Hu’s team used a few techniques, comparing live ant structures to clumped dead ants as a control. Using a rheometer—a device that can precisely measure the stress response and flow of a fluid, and is often applied in industrial situations (such as the development of a new shampoo)—they found that the ants continuously reorganize their structure to maintain stability.
Many materials behave like a solid when stressed by forces moving at certain speeds, and a fluid when stressed by slowed ones. Water, for instance, behaves like a fluid when you stick your hand in it, but a solid when hit by a human body jumping off a diving board—the reason that a belly flop hurts so much.
But the ant structures are a combination of solid and fluid when stressed by forces at all speeds, the researchers found. They actively deform their structure to accommodate a stress (like a fluid) but then bounce back into place afterward (like a solid). Check out what happens when one of their structures is compressed by a petri dish, for instance:
“This makes sense, based on their natural environment,” Hu says. “If they’re floating in a raft down a river, they have no control over where it floats, so if there’s something in the way—say, a twig—you see respond and flow around the twig, kind of like an amoeba.”
The ants’ sheer resiliency and buoyancy is also remarkable. When the researchers tried to push the floating rafts below the water’s surface, they found they could resist a significant amount of force and float back up:
This is enabled, in part, by the ants’ exoskeletons, which are naturally hydrophobic (i.e. they chemically repel water). When many ants clump together to form a structure, water doesn’t penetrate into the gaps between then, so when they’re forced underwater, the air that remains in these cavities helps them float.
Perhaps the biggest mystery of these ants’ remarkable living structures is how the creatures communicate to build them. Most ant communication is based on trails of pheromones left on the ground, but in such an interconnected form, that type of communication seems unlikely. Microscopic examination reveals that the ants grasp each other using both their jaws and little claws on the end of their legs. Noting this, Hu adds, ”We think they’re communicating through touch, but we really don’t understand it yet.”
November 12, 2013
In the summer of 2010, husband-and-wife paleobiologist team Z. Jack Tseng and Juan Liu traveled to the Zanda Basin in western Tibet with a group of colleagues. The remote area, a week’s drive from Beijing and near the border of Pakistan and China, is “basically badlands everywhere, with deeply cut valleys throughout,” Tseng says.
To explore the valleys, the team drove up dirt trail after dirt trail before coming upon a dense patch of fossils sticking out of the ground halfway up a hill. “In the little concentration of fossils, there were lots of limb bones from antelopes and horses obscuring everything else,” says Tseng, who was then a graduate student at USC and is now with the American Museum of Natural History. “It wasn’t until we started lifting things up, one by one, that we saw the top of a skull, and we thought, from the shape, that it looked something like a cat.”
After a few years of analysis, Tseng’s team has discovered that the skull doesn’t belong to any old cat. As they’ve documented in a study published today in Proceedings of the Royal Society B, the skull and six associated fossilized jawbone fragments are the first evidence of a newly discovered species, which they’ve called Panthera blytheae. The discovery represents the oldest “big cat” (a group that includes large predatory cats like lions, jaguars, tigers and leopards) ever found by a wide margin.
The sediments that make up the basin as a whole range from 6 million to 400,000 years in age, so the group dated the fossil by analyzing the age of the particular rock layers it was buried in. This involved using techniques of magnetostratigraphy, in which scientists analyze the magnetic orientation of the rocks and compare it to known reversals of the Earth’s magnetic field. This method can only provide rough estimates for an item’s age, but it revealed that the skull is between 4.10 and 5.95 million years old. Previously, the oldest known big cat fossils—a number of tooth fragments found in Tanzania—were 3.6 million years old.
The new find fills a gap in the evolutionary record of big cats. By analyzing the DNA of living species, scientists had previously estimated that big cats had split from the Felinae subfamily—which includes smaller wild cats, like cougars, lynxes, along with domestic cats—about 6.37 million years ago. The very existence of P. blytheae confirms that the split happened prior to when this big cat roamed.
But how much earlier? The find could suggest, Tsang says, that big cats branched off from smaller cats much farther back than thought. By comparing the skull’s characteristics with fossils from other extinct big cats, the anatomy of living cat species, and DNA samples taken from both living cats and a few recently extinct, Ice Age-era species (known as cave lions), the researchers assembled a new evolutionary family tree for all big cats. Using known rates of anatomical changes over time and the observed anatomy of P. blytheae, they projected backwards, and estimated that the earliest big cats likely branched off from the Felinae subfamily between 10 and 11 million years ago.
The new fossil also solves a geological mystery. Previously, using DNA analysis of all living big cats and mapping the the fossils excavated from various sites around the world, researchers had determined it was most likely that their common ancestor had lived in Asia. The oldest known specimens, however, were found in Africa. The new species provides the first direct evidence that central Asia was indeed the big cats’ ancestral home, at least as far back as the current fossil record currently goes.
From the fragmented fossils, it’s hard to know much about the extinct species’ behavior and lifestyle, but the researchers were able to make some basic extrapolations from the skull’s anatomy. “It’s not a huge cat, like a lion or a tiger, but closer to a leopard,” Tsang says. The creature’s habitat was likely similar to the current Tibetan plateau, so Tseng speculates that, like the snow leopards that currently live in the area, this species did not hunt on the open plains, but rather cliffs and valleys. Tooth wear patterns also suggest similarities with current snow leopards—the rear teeth, likely used for cutting soft tissue, remain sharp, whereas the front teeth are heavily worn, perhaps reflecting their use in prying open carcasses and picking meat off bones.
Tseng says that he and colleagues plan to return to the area to search for more fossils that could help enlighten us on the evolutionary history of big cats. “The gap still isn’t completely filled yet,” he says. “We need to find older big cats to put the picture together.”