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Versuch einer vergleichenden Anatomie des Verdauungssystemes der Vögel

Smithsonian Libraries
"Separat-Abdruck aus der Jenaischen Zeitschrift für Naturwissenschaft. Bd. 13, N.F. 6."

Also available online.

Elecresource

Beiträge zur mikroskopischen Anatomie des Vogeldarmes / von M. Cloetta

Smithsonian Libraries
"Separat-Abdruck aus dem Archiv für mikroskopischen Anatomie, Band 41.

Thesis (doctoral)--Universität Zürich, 1893.

Also available online.

Elecresource

Recherches anatomiques, histologiques et embryologiques sur l'appareil gastrique des oiseaux

Smithsonian Libraries
Thèse--Faculté des sciences de Paris.

Also available online.

Elecresource

Bird Extinctions with Helen James

National Museum of Natural History
How can common birds such as the passenger pigeon go extinct? Find about more at: https://qrius.si.edu/ RECORDED LIVE Dec. 11, 2014 Join ornithologist Helen James to consider what factors make birds vulnerable to extinction. Follow Helen into Hawaiian lava tubes to look for fossil evidence of bird life on the islands. See which bird species survived and which did not after humans arrived on the scene. The Smithsonian Science How webcast features the research and personalities of the Smithsonian's National Museum of Natural History, providing your students with positive STEM role models, information about science careers and pathways, and more! The program delivers real-world science through free, live webcasts and teaching resources. Thanks for making Smithsonian Science How an award-winning program! We were recognized by EdTech Digest as the winner of the 2015 Cool Tool Award in the “E-learning Solution” category and by the American Alliance of Museums with a 2015 MUSE award for Education and Outreach. TEACHING RESOURCES https://qrius.si.edu/webcast-teaching-resources-bird-extinctions-recent-geologic-time STEM Subject: Bird Extinctions in Recent Geologic Time National Middle School Science Standards: Life Science, Earth Science Key Terms: ornithology, bird conservation, extinction, endangered species, island ecosystems, Holocene period Key Concepts: Human influences on bird populations Ecology of birds and vulnerability to extinction Impacts of human activities on ecology Conservation of endangered bird species Technology used by ornithologists NEXT GENERATION SCIENCE STANDARDS (NGSS) The Bird Extinctions - Time Travel through Lava Tubes Webcast Package supports students in meeting the following middle school NGSS Performance Expectations by offering a set of resources that integrate science concepts with science practice skills. MS-LS2 Ecosystems: Interactions, Energy, and Dynamics MS-LS2-1 Analyze and interpret data to provide evidence for the effects of resource availability on organisms and populations of organisms in an ecosystem. MS-LS2-2 Construct an explanation that predicts patterns of interactions among organisms across multiple ecosystems. MS-LS2-4 Construct an argument supported by empirical evidence that changes to physical or biological components of an ecosystem affect populations MS-ESS3 Earth and Human Activity MS-ESS3-4 Construct an argument supported by evidence for how increases in human population and per-capita consumption of natural resources impact Earth's systems.

The Scariest Zombies in Nature

Smithsonian Magazine

Once the fungus invades its victim’s body, it’s already too late. The invader spreads through the host in a matter of days. The victim, unaware of what is happening, becomes driven to climb to a high spot. Just before dying, the infected body—a zombie—grasps a perch as the mature fungal invader erupts from the back of the zombie’s head to rain down spores on unsuspecting victims below, starting the cycle again. This isn’t the latest gross-out moment from a George A. Romero horror film; it is part of a very real evolutionary arms race between a parasitic fungus and its victims, ants.

One zombie by itself is not necessarily very scary, but in B movies from, Night of the Living Dead to Zombieland, Hollywood’s animated corpses have a nasty habit of creating more of the walking dead. Controlled by some inexplicable force, perhaps an intensely virulent pathogen, the main preoccupation of a zombie is making other zombies. The story line is pure drive-in movie schlock, yet the popular mythology of zombies has lately been spattered with a coating of biological truth. There actually are organisms that have evolved to control the minds and bodies of other creatures, turning once normal individuals into dazed victims that fulfill the parasite’s need to reproduce itself.

Some of the most successful zombie-masters are fungi from the genus Ophiocordyceps. The parasites infest many kinds of arthropods—from butterflies to cockroaches—but it is among ants that the fungi’s ability to control other beings’ behavior is most apparent. One prototypical scenario is found in Costa Rica, where infected bullet ants (Paraponera clavata) climb to a great spore-sprinkling height before the fungus erupts.

In the jungles of Thailand, the fungus Ophiocordyceps unilaterius parasitizes Camponotus leonardi ants, which forage on the ground and nest in the canopy. When infected, these ants shamble toward “ant graveyards,” where they bite down on the undersides of leaves, anchoring their fungus-infested husks at a level of the forest with just the right humidity and temperature to allow the fungus to grow properly. When Sandra Andersen of the University of Copenhagen and colleagues placed the bodies of infected ants higher in the canopy, the parasites grew abnormally, and infested ants placed on the ground were eaten by other insects. “The fungus is sensitive to UV light, and the heavy rainfall in a tropical forest would most likely also be able to damage the fungus,” Andersen says. “The position of the ant on the underside of the leaf limits the exposure of the parasite.” The fungus drives the ants to seek out specific places to die that best benefit the growth of the fungus.

Ophiocordyceps-like parasites have been manipulating other organisms for millions of years—their disturbing behavior has been preserved in the fossil record. Forty-eight million years ago, during the global hothouse epoch of the Eocene, the place now known as Messel, Germany, was draped in a lush, semitropical forest. Archaic primates scrambled among the trees; cousins of early horses browsed; and an Ophiocordyceps-like fungus caused ants to put a death grip on leaves just before the infesting fungus fully overran their bodies. Exceptionally preserved fossil leaves from the Messel quarry show the same pattern of leaf scars made by some living ant species when they have become fungus-controlled zombies.

Image by Yanoviak et al., 2008. The nematode parasites inside this Cephalotes atratus ant have caused its gaster to turn red and mimic berries found in its habitat. This attracts birds which help spread the parasites to new ant colonies. (original image)

Image by David Hughes. Some of the most successful zombie-masters are fungi from the genus Ophiocordyceps. In the jungles of Thailand, their victims are Camponotus leonardi, or carpenter ants. (original image)

Image by Christian Ziegler. The nematode infestation thinned the exoskeleton of the ant's gaster, which, combined with the presence of nematode eggs, caused it to look red and to detach easily from the rest of the ant's body. (original image)

Image by Christian Ziegler. After the nematode eggs pass through the bird's digestive system, they are deposited back onto the forest floor in bird droppings. (original image)

Image by Christian Ziegler. As ants develop, the nematodes grow and reproduce inside the ant's body, leaving eggs in the gaster. (original image)

Image by Christian Ziegler. In the jungles of Thailand, the fungus Ophiocordyceps unilaterius parasitizes Camponotus leonardi ants, which forage on the ground and nest in the canopy. (original image)

Scientists are looking for these types of interactions even farther back in time. “Now that we know the behavior like this can fossilize, I would not be surprised if we find more,” says University of Exeter behavioral ecologist David Hughes. “I believe samples tens of millions of years older are likely.” The fungus is clearly ancient: in 2008, another team announced that a 105-million-year-old insect trapped in amber was shot through with an Ophiocordyceps-like fungus. It is possible that zombie-style parasitism between the fungus and its hosts goes back to the Cretaceous days of the dinosaurs (though evidence of zombie dinosaurs has not been forthcoming).

Fungi aren’t the only parasites to hijack ants. A different kind of parasite changes the appearance of giant gliding ants (Cephalotes atratus) from Central and South America. While studying this ant species in Panama, Stephen Yanoviak of the University of Arkansas and colleagues noticed that the gasters of many ants–the bulbous back end of the abdomen–were bright red, and the ants held them up high in a behavior called “gaster flagging.” When the scientists dissected the ants, they found hundreds of tiny, transparent eggs of a previously unknown species of nematode worm.

The nematode infestation thinned the exoskeleton of the ant’s gaster, which, combined with the presence of nematode eggs, caused it to look red and to detach easily from the rest of the ant’s body. The gasters of these infested ants are easy pickings for local birds that usually eat red berries. After the nematode eggs pass through the bird’s digestive system, they are deposited back onto the forest floor in bird droppings. Gliding ants regularly eat bird droppings, and when worker ants bring avian feces back to the nest, they inadvertently feed nematode eggs to ant larvae. As the ants develop, the nematodes grow and reproduce inside the ant’s body, leaving eggs in the gaster. The ants totter around until a bird picks them off, continuing the cycle.

Some parasites cause even more dramatic anatomical changes in their victims. The flatworm Leucochloridium paradoxum is the scourge of North American and European snails unfortunate enough to eat the droppings of birds containing the eggs of the parasite. Once inside the snail’s body, the worms infest the eye stalks, turning the tentacles into brightly colored, pulsating organs that attract birds. Once the bird eats this part of the infested snail, the parasites reproduce inside the bird and leave their eggs in its digestive system. Simple as they are, parasites have evolved to be masters of manipulation.

Scientists are just beginning to study how two species come to occupy the same body and vie for its control. It’s not yet clear what chemicals signals alter the behavior and appearance of parasitized ants and other victims. Somehow fungi and other parasites are manipulating brain chemicals, and one doesn’t have to be a mad scientist to want to understand more. Zombies have a long natural history, stretching back tens of millions of years, and nature is filled with creeping, oozing, blood sucking and otherwise ghastly creatures just as terrifying as anything Hollywood could concoct. Just don’t expect scientists to discover much about sparkling vampires or radioactive dinosaurs with a taste for Japanese cities.

Brian Switek is the author of Written in Stone: Evolution, the Fossil Record, and Our Place in Nature.

Why Seabirds Eat So Much Plastic

Smithsonian Magazine

Up to 90 percent of all seabirds eat plastic. In the 1960s that number was only about five percent, but by the 1980s it had risen to a staggering 80 percent. Researchers have found seabirds with all manner of plastics in their digestive tracts—bottle caps, plastic bags, broken-down rice-sized grains of plastic, synthetic clothing fibers and more, according to Laura Parker at National Geographic. It’s one of the factors contributing to a stomach-churning 70 percent drop in seabird numbers since the 1950s.

But bottle caps and Barbie doll heads don’t really look like the small fish and krill many seabirds favor for their meals. So why do so many species of birds actively hunt down these chunks of plastic? A new study in the journal Science Advances suggests that certain chemicals on the plastics mimic the smell of food, tricking the birds into thinking that these colorful bits are lunch, reports Chelsea Harvey at The Washington Post.

Ocean algae produces a chemical called dimethyl sulfide, or DMS—particularly when the algae is being digested by krill, tiny crustaceans that fill much of the worlds oceans. It’s believed that the chemical is part of the mutualistic relationship between birds and algae. The birds smell the DMS, which alerts them that krill are in the area. When they eat the krill, it reduces the number of krill chowing down on the algae.

But when plastic collects in the ocean it tends to also accumulate algae and other tiny bits of organic matter on its surface, writes Harvey, and these emit DMS, attracting the birds. “What we think is going on is that the plastic is emitting a cue that is getting [the birds] into moods to eat,” Gabrielle Nevitt of the University of California Davis, the study’s senior author, tells Harvey.

To arrive at this conclusion, the researchers filled mesh bags with beads of three different types of common plastics, high-density polyethylene, low-density polyethylene, and poly-propylene, according to a press release. They then tied the bags to a buoy and let them soak in the ocean for three weeks, after which they analyzed the plastics at UC Davis’s Robert Mondavi Institute for Wine and Food Science. This analysis showed that these beads were emitting a large amount of DMS. Yet plastic that had not soaked in the ocean did not give off any DMS.

The researchers also teased through 55 studies to figure out which birds are most likely to ingest plastic, reports Hannah Devlin at The Guardian. They found that procellariiform seabirds, which includes albatrosses, petrels and shearwaters, were almost six times as likely to snack on plastic compared to other seabirds—a finding that aligns with the chemistry. Those particular species strongly rely on their sense of smell to find food, which is weaker in other birds, making them more sensitive to DMS.

“This study shows that species that don't receive lot of attention, like petrels and some species of shearwaters, are likely to be impacted by plastic ingestion,” Nevitt says in the press release. “These species nest in underground burrows, which are hard to study, so they are often overlooked. Yet, based on their foraging strategy, this study shows they’re actually consuming a lot of plastic and are particularly vulnerable to marine debris.”

The hope is that materials scientists may be able to produce plastic that accumulates less algae. “[The study] provides a salient mechanism for how this group of birds might be detecting plastic and consuming it,” Nevitt tells Harvey. “And once you have a better idea of how a mechanism might work, you’re in a better position to potentially mediate that.”  

But engineering new types of plastic is a big stretch, say the authors. The best and easiest strategy is to keep the plastic out of the oceans in the first place.

How to Build a Giant Dinosaur

Smithsonian Magazine

They were the most gigantic animals ever to walk the earth. Sauropod dinosaurs—“thin at one end; much, much thicker in the middle; and then thin again at the far end,” as comedian John Cleese described them—were titans that thrived for more than 130 million years. The largest known species, such as Argentinosaurus and Futalognkosaurus from prehistoric South America, stretched more than 100 feet long and weighed in excess of 70 tons. Bones found in the 1870s (and since somehow lost) hint that an enigmatic species dubbed Amphicoelias may have been even bigger still.

No land mammal has ever come close to the size of these gargantuan dinosaurs. The prehistoric hornless rhino Paraceratherium—the largest land mammal ever—was a mere 40 feet long and weighed a paltry 17 tons, and today’s African bush elephants, at 5 tons, would look dainty next to the largest sauropod dinosaurs. (Blue whales, at 100 feet and 200 tons, are a bit more massive than sauropods, but it’s easier, physiologically, to be large in an aquatic environment.)

What was it about these dinosaurs that allowed them to become the biggest terrestrial animals of all time? Paleontologists have been puzzling over the question for more than a century. Even relatively modest-sized giants such as Apatosaurus and Diplodocus, early naturalists believed, were so huge that they must have been confined to rivers and lakes deep enough to support the dinosaurs’ bulk. On land, the argument went, these dinosaurs would collapse under their own weight. By the 1970s, skeletal evidence and preserved footprints in trackways confirmed that sauropods were land-dwellers. But it has only been recently that paleontologists have been able to start unlocking the secrets of how these seemingly improbable animals developed over their lifetimes and how they evolved in the first place.

Understanding the natural history of sauropods has been crucial to figuring out how they got so big. Though some of the earliest members of the sauropod lineage—such as the 230 million-year-old Panphagia from Argentina—were less than five feet long, even they possessed a unique combination of traits that eventually allowed the group to attain huge sizes.

The way sauropods reproduced may have been a key to their ability to grow to such prodigious sizes. Mother sauropods laid about 10 eggs at a time in small nests; scores of fossilized egg clutches have been found, as have thousands of eggs from sites all over the world. (Some even preserved embryos inside, allowing paleontologists to definitively identify sauropod eggs by their shape.) That means these dinosaurs grew outside of their mother’s bodies. According to Christine Janis of Brown University and Matthew Carrano of Smithsonian’s National Museum of Natural History, laying eggs opened up evolutionary possibilities for these dinosaurs.

For large mammals, carrying a fetus is a major investment. Developing African bush elephants gestate inside their mothers for a staggering 22 months, for example, and the larger mammal species get, the longer their offspring have to develop before birth. A lot can go wrong during a long gestation, including miscarriage, and nourishing such a large embryo for so long is a huge energy drain on an expectant mother (to say nothing of nursing the baby and providing care after birth). As mammals get larger, the risks and costs of carrying offspring increase, and so there might be some kind of size threshold that land mammals can’t cross.

Mother sauropods, on the other hand, did not have to carry their developing babies for nearly two years, and they could lay numerous eggs at relatively short intervals. Some species may have provided parental care after hatching: rare trackways show that some herds likely included sauropods of different ages. But fans of the animated movie The Land Before Time may be disappointed to know that others probably didn’t care for their young. Paleontologists have also found bone beds that contain only young sauropods of species such as Alamosaurus, indicating that these dinosaurs were on their own after leaving the nest.

Regardless of whether juvenile sauropods hung out in big herds or in smaller groups of dinosaurs their own age, though, the young dinosaurs were probably picky eaters. They had to be if they were to grow to adult size. Diplodocus is one of the most iconic sauropod dinosaurs, and adults of this Jurassic herbivore had broad, squared-off muzzles indicative of an indiscriminate diet. In addition to energy-rich ginkgo trees and conifers called monkey puzzles, they could have also survived on lower-quality food like cycads and the tough parts of conifers. The skull of a juvenile, described by John Whitlock, Jeffrey Wilson and Matthew Lamanna last year, hints that young Diplodocus had different tastes.

Paleontologists have recognized that the differences in menu choice between grazing and browsing herbivores can generally be seen in skull shape. While grazers have broad muzzles to scarf up a wide variety of food, selective browsers have narrower and rounded snouts that make it possible for them to pick specific plants or plant parts. (Some fanciful reconstructions gave Diplodocus and other sauropods elephant-like trunks with which to pluck food, but this idea has been thoroughly debunked.) Since the juvenile Diplodocus skull had a more rounded shape, Whitlock and colleagues proposed that it selected the juiciest browse – juvenile Diplodocus may have focused on foods like horsetails, ferns and high-energy evergreens, instead of sucking down whatever was available, as adults did.

From an energy perspective, it made sense for young sauropods to be choosy. Small dinosaurs required the most bang for their buck in terms of food; they were specialized to pick high-energy plants to fuel their rapid growth. Adults, which were already large and merely had to maintain—rather than grow—large bodies, could afford to hork down large amounts of lower-quality fuel. While they consumed more food in absolute terms, adult sauropods could eat lower-quality foods, whereas smaller sauropods required high-quality food. (This is a common pattern seen among animals even today: a tiny shrew has to eat nutritious insects almost constantly, but African elephants can subsist on a diet of lower-quality grass and other plant food.) The dietary difference may have allowed young and mature Diplodocus to live in the same area through a phenomenon ecologists call “niche partitioning.” The specialization of the juveniles and the more generalist diet of the adults kept them out of constant competition for food, meaning that the young and old Diplodocus fed almost as if they were two different species.

Image by © Julius T. Csotonyi, csotonyi.com. Early naturalists believed sauropods were so huge that they must have been confined to rivers and lakes deep enough to support their bulk. It wasn't until the 1970s when skeletal evidence and preserved footprints confirmed that sauropods were land-dwellers. (original image)

Image by © Julius T. Csotonyi, csotonyi.com. Argentinosaurus and Futalognkosaurus, pictured, from prehistoric South America, stretched more than 100 feet long and weighed in excess of 70 tons. (original image)

In order to consume all that food, though, sauropods had to reach it. Long necks were a critical, early adaptation that allowed sauropods to attain large body sizes, according to a recent review by Martin Sander and 15 other scientists. Think of an Apatosaurus standing at the edge of a prehistoric forest. The dinosaur’s long neck would allow it to reach a wide swath of vegetation—high and low, left and right—without moving its body at all. From early on in sauropod evolution, long necks made these dinosaurs efficient feeders able to reach resources that were inaccessible to other herbivores, and even with tiny heads, big sauropods would have easily been able to vacuum up huge quantities of food.

Just how these dinosaurs converted all this green food into energy and tissue is a trickier matter. Sauropods did not have robust batteries of molars to chew their food. Many had only a few pencil- or spoon-shaped teeth to pluck food before swallowing it whole. Given sauropods’ poor table manners, scientists used to think that the dinosaurs might have swallowed stones to grind up food still in the stomach the way some birds do. Paleontologists Oliver Wings and Martin Sander have argued that this probably wasn’t the case—so-called “stomach stones” found with some sauropod fossils do not show a pattern of wear consistent with what would be expected if they were being used this way. Instead, the dinosaurs extracted as much nutrition as possible from their food by retaining it for long periods in their digestive systems.

A few details of sauropod digestion were experimentally modeled by Jürgen Hummel and colleagues in 2008. The scientists placed modern-day samples of the most abundant sauropod chow from the Mesozoic—ferns, horsetails, ginkgoes and conifers—in simple artificial stomachs. They inoculated the fake guts with microbes taken from the part of sheeps’ digestive systems where plant food is initially broken down. As the plants fermented, the scientists tracked how much nutrition they released.

Contrary to what had been assumed, many of these plants degraded relatively easily in the crude stomach environments. Horsetails and monkey puzzles were especially nutritious. Actual dinosaur stomachs might have been even better equipped at breaking down these plants, and there was certainly enough available energy in the plants of the time for sauropods to grow large. Sauropods probably did not require extraordinary gut architecture to survive.

Another major feature allowed these titans to balloon in size. It is a trait they share with birds. Birds are the direct descendants of small theropod dinosaurs related to species like Velociraptor and Anchiornis, but they are not very closely related to sauropod dinosaurs; they last shared a common ancestor more than 230 million years ago. Even so, both the theropod and sauropod lineages shared a peculiar trait that was extremely important in their evolution—a network of internal air sacs connected to the lungs.

The soft air sacs haven’t been seen directly in the fossil record, but the structures left telltale pockets where they invaded bones. Naturalists recognized the indentations more than a century ago, but modern paleontologists are only just beginning to understand their significance. As in birds, the lungs of sauropods were probably connected to a series of air sacs, and attached to these organs was a network of smaller pockets—called diverticula—that infiltrated the bones in the neck, chest and abdomen of the dinosaurs. From a structural point of view, this network of air-filled structures lowered the density of the sauropod skeleton, and allowed these dinosaurs to have a relatively lightweight construction for their size. Rather than having extra-strength bones, as had once been suggested, sauropod skeletons were made lighter by a trait they share with birds, and the network of air sacs probably had other benefits, too.

In birds, air sacs are part of a flow-through breathing arrangement that is far more efficient at extracting oxygen than is the respiratory system of mammals. We don’t yet know if sauropods breathed the same way birds did—the degree to which their skeletons were modified by air sacs varied across species—but it is likely that the air sacs of the giant dinosaurs were better equipped at delivering oxygen to their bodies than the alternative seen in giant mammals. Birds have a high metabolic rate that requires a great deal of oxygen for sustained flying; similarly, the size and active lives of sauropods would have required a great deal of oxygen, and the air sac system would have provided them with essential breathing benefits.

Not all sauropod dinosaurs were giants. Some species—such as Magyarosaurus from the strata of Romania—were small descendants of much larger species. They shrunk in size because of their isolation on islands, though the exact reason why such island dwarfs evolve is debated by scientists. Still, sauropods weighing more than 40 tons evolved independently in at least four lineages during the long tenure of this dinosaur group, all thanks to a suite of characteristics that made large body size possible.

Paleontologists are still investigating the evolutionary pressures that made such large forms advantageous. Their size gave them some protection from predators, presumably, and their long necks let them reach food that smaller creatures looked at hungrily but couldn’t reach. What other advantages giant size might have provided remain unclear. Nevertheless, sauropods were astounding creatures that could only have existed thanks to a peculiar confluence of events. They were fantastic forms unlike anything that came before or has evolved since.

How Eating Poop Makes These Mole-Rats More Motherly

Smithsonian Magazine

In the animal kingdom, "it takes a village to raise a child" is often the norm. Rather than putting the burden on one pair of parents, often an entire social group of animals will care for newborns. Marmoset moms hand off their young to other males, who spend so much energy carrying around the babies that they lose weight. Subordinate wolves and wild hogs that have lost their own litters nurse other pups. Even ducks aren’t shy about letting someone else watch their ducklings for a bit while they grab a quick mouthful of algae.

This behavior, called alloparenting, likely has evolutionary advantages that we don't fully understand (it occurs in 9 percent of the known species of birds and around 3 percent of mammals). But we do know that those urges to lick and feed someone else’s baby are nurtured along by caregiving lessons learned early in life and a few squirts of affection-inducing hormones like prolactin, oxytocin and estrogens, though researchers haven’t figured out exactly how the system works. Add to the list of questions about alloparenting the behavior of the naked mole-rat. Members of naked mole-rat colonies take care of babies that aren't their own, despite not being able to produce their own estrogen. Now, new research published in PNAS suggests that they receive estrogen—and their motherly instincts—from a very unusual source: mole-rat feces.

The naked mole-rat, Heterocephalus glaber, is a rodent found in the Horn of Africa that lives in colonies like ants do. In the colony, only one mole-rat, the queen, is sexually mature, while subordinate handmaidens take care of her offspring, licking them, building nests, and keeping them warm. But that system baffled researchers at the veterinary school at Azabu University in Sagamihara, Japan.

Azabu researcher Kazutaka Mogi writes in an email that his team had studied alloparenting in mice, where non-moms babysit other pups. The babysitters' maternal instincts seem to be strengthened by estrogen, which the mice produce in their ovaries (just like human women). It's a virtuous cycle in which the more alloparenting a mouse does, the better she gets at it—and the more her hormones push her to do it. But naked mole rats engage in alloparenting despite having no mature sex organs. "We were surprised to hear this phenomenon and decided to investigate this subject,” he writes.

That's how the researchers stumbled onto the revolting discovery. Coprophagy—eating feces—is common among naked mole-rats. The team wondered if the subordinates could be receiving not just nutrients but hormones from eating the queen mole-rat's poop.

Researchers fed the naked mole-rats poop pellets from a pregnant queen. They then tested their estrogen levels and their response to the yipping sounds of naked mole-rat pups. The study showed that the estrogen levels in the would-be alloparents gradually rose throughout the queen’s pregnancy, peaking after the queen gave birth to her litter and was done feeding them, the time when the subordinate females more or less take over care of the young. The study showed that after eating the hormone-laced feces, the subordinates became super-responsive to the mewling pups. This poopy hormone transfer represents a previously unknown system of communication between the mole-rats.

Coprophagy is not uncommon in mammals, as many people with a dung-eating dog can attest. In many cases, especially among rabbits and rodents, it’s a normal part of digestion. There are certain nutrients that their guts can’t process in the first pass, so they ingest their own fecal pellets for a second go. Some baby animals, including elephants and hippos, also eat their parent’s caca soon after weaning to help seed their guts with the right intestinal bacteria.

It’s likely that naked mole-rats do both. In their extensive underground colonies, the animals maintain a toilet chamber where feces pellets are deposited. It also serves as a snack room, where they get a second chance to nom on the poo and digest the fibrous roots and tubers that they munch on. Mature mole rats have also been observed pooping directly into the mouths of young pups, which is probably to transfer gut bacteria and to help impart a “colony” smell to the younglings. Each naked mole-rat colony has its own specific odor, and if an intruder doesn’t have the right smell, it will be ripped to shreds.

Mogi says he and his team are unaware of any other mammal—or any creature for that matter—that transfers hormones in this manner. However, in a 2016 paper in eLife, researchers found that carpenter ants exchange food, pheromones and hormones via trophallaxis, which is essentially throwing up in one another’s mouths. It’s possible that other social insect species engage in similarly revolting forms of communication.

It’s possible that other mammals transfer hormones via feces, though it wouldn’t be surprising if naked mole-rats are the only ones: The strange animal that National Geographic describes as “bratwurst with teeth” is unique in almost every way. Besides having a society set up more like bees than mice (one of only two mammals to live in such a way), they live in underground colonies and are functionally blind. And they are indeed naked, with just a few hundred hard-to-see guide hairs and giant, sensitive buckteeth to help them navigate their dark labyrinths. While most rodents of a similar size live two to three years, naked mole-rats can live up to 30, and are thought to be almost completely immune to cancer, which has made them popular research animals. They can also survive up to 18 minutes without oxygen and are essentially cold-blooded, unusual for a mammal, and must cuddle together to regulate their body temperature in cold weather.

“I think it’s funny, on the surface they look different but you don’t think about all the cool things we know about them,” say Kenton Kerns, assistant curator of small mammals at the Smithsonian’s National Zoo, who deals with the mole-rats on a daily basis and is preparing to unveil a new colony. “And it seems like once a year if not more there’s cool new research about them. You know how grade school teachers tell children we shouldn’t cut down the rainforest because it might have the next new medicine or scientific breakthrough? Mole rats are like that, but people just slide by their exhibit saying ‘I don’t like rats or mice.’”

Diana Sarko has been studying naked mole-rats for years and currently maintains two colonies at Southern Illinois University ruled over by "Queen Cersei" and "Queen Daenerys." Her main research involves their giant teeth, which are essentially a sense organ—though her recent work has found they have the same bite strength as a lion. Sarko regularly sees alloparenting behavior taking place with subordinates moving pups around and snuggling them in the warm sleeping chambers. She isn’t surprised by the idea that hormones could be transferred via feces, though she hasn’t witnessed much poo-munching in her colonies since the food the lab animals get, like sweet potatoes, fruits and other vegetables, might be easier to digest than wild tubers.

In fact, hormones may regulate other activities within mole-rat colonies. Just last year one of Sarko’s queens was killed by a usurper.

Typically, a mole-rat queen can expect to sit on her throne into her twenties without an uprising, so the revolution in the lab colony was unexpected. “Once established, a queen usually stays put,” Sarko says. “She was overthrown after having a litter so she was somewhat weakened but otherwise she seemed healthy. I was shocked.”

Now, Sarko and her team are examining hormone levels, including the stress hormone cortisol, collected in their weekly poo samplings in the months leading up to the coup to see if hormonal changes were happening throughout the colony before the overthrow of their queen.

It doesn't end there when it comes to mole-rats and hormones. Mogi says the Azabu team has preliminary evidence that the queen has a way to influence the reproductive success of the tiny handful of sexually mature males allowed to breed with her. It’s not clear yet if it involves feces, urine, vomit, saliva or is just the naked mole-rat version of the come-hither look.

A new 24-hour webcam trained on the National Zoo's colony of naked mole rats goes live on August 31, 2018. Visitors can see the Zoo's new habit for its colony of 17 naked mole rats beginning September 1.

Behind the Scenes at a Tyrannosaurus Rex Dissection

Smithsonian Magazine

For centuries, students of medicine and even the public have flocked into specially designed theaters to witness dissections and autopsies of the human body. Now, the human body is less frequently treated as a source of spectacle, but in a recent TV special, another creature’s insides were exposed to many viewers. A team recently cut apart a (fake) Tyrannosaurus rex for National Geographic’s show "T. rex Autopsy."

But in order to dissect an animal that is extinct, you have to first have the animal to dissect. One of the dissectors, paleontologist Stephen Brusatte, explains how experts created a gloriously gross model of the long-extinct T. rex and then cut it up with chainsaws, at The Conversation (via Scientific American). 

The goal, he writes was to use "the pageantry of an autopsy to reveal how this most famous of dinosaurs actually functioned as a living, breathing, feeding, moving, growing animal." It’s not that different from the whale and other giant animal autopsies that have made it to television.

It took the Crawley Creatures workshop five and a half months to make the fake T. rex body out of five tons of clay, more than 20,000 feathers, 75 liters of latex, 130 liters of fax blood, and 200 liters of silicone. A time-lapse video from National Geographic’s YouTube channel gives some sense of the scale of this project:

Another video shows the autopsy team’s first sight of the new creation. "It was so beautifully made," says Tori Herridge, a paleobiologist. The reconstruction is 42 feet from nose tip to tail, explains the lead mold maker, Claire Green.

It may seem like an elaborate and expensive stunt, but Brusatte explains at The Conversation that the point was to make an ancient dinosaur more than just a concept. He writes:

If you thought dinosaurs were dim-witted, overgrown reptiles, think again. T.rex had a huge brain, its eyesight was keen, it had feathers and it grew really fast. It was essentially a huge fluffy bird from hell.

While organs and other soft tissues don’t fossilize easily, they can leave signatures in the bones. The team also looked to close living relatives — birds and crocodiles — to make their most informed guesses as to the size, shape and position of the T. rex innards.

The commitment to realism even extended to putting plenty of gross things inside the T. rex — the stomach contents smelled and the digestive tract held worms. 

Blood Clots, Liver Cells and Bird Flu Are Surprisingly Beautiful Under a Microscope

Smithsonian Magazine

Most people know about ear drums—but what about ear stones? In the inner ear, tiny calcium carbonate crystals clump together to form stones called otoliths, which rest atop tiny hairs. When a person's head moves, so do these stones and the hairs attached to them. The hairs send impulses to the brain, and the brain in turn uses these signals to keep the body balanced.

Colin Salter's new book Science is Beautiful: The Human Body Under the Microscope features a scanning electron micrograph of the bumpy surface of one of these stones, its many crystals artificially colored pink, purple and blue. It's among myriad examples of vivid micrographs and MRI scans the science writer has curated to show cells, blood vessels, organs and diseases from a unique and sometimes startling perspective. The collection highlights "images of elements within the body whose existence you may never have pondered but whose functions are vital and fascinating," says Salter.

For most of the images, biologists stained the samples or added colors digitally to highlight various parts for their research and for other viewers. A dendritic cell looks like a pale pink peony in an ion-abrasion scanning electron micrograph. And while H1N1, or bird flu, has nasty effects on those who contract it, the virus itself becomes a spectacular mosaic in a filtered transmission electron micrograph. Here's what Salter had to say about the project:

What inspired you to write this book?

I have often written about the ingenuity of mankind’s scientific mind, our capacity for technical invention and innovation. But the most extraordinary machine of all is the one we inhabit—the human body.

With this book, I wanted to convey some of the wonder I feel about the complex systems that operate inside us all; repair and regenerate us; move both deliberately and instinctively, with and without conscious thought; learn how to do things better; and defend us from viruses, bacteria and just about anything we can throw at our digestive system.

What do you personally find compelling about micrographs of the human body?

Even without knowing what you’re looking at, they are beautiful. I’m fascinated by that: the idea that beauty doesn’t depend on meaning. The same shapes and colors can be beautiful whether they’re in an artery or in an art gallery.

But when you add meaning to beauty, when you add understanding to that instinctive visual pleasure, it greatly enhances your sense of wonder. Looking at these vivid organic shapes and intense colors and knowing that they show what’s going on inside of me, I am in awe.

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What is your favorite image in the book, and why?

There’s a very pretty artificially colored image of hundreds of E. coli bacteria, which look like the sort of tasty candy you could scoop up and eat in handfuls! The picture of the cells that line the lungs is strikingly graceful. The structural skeletons of the cells appear as spun gossamer and make me think they are dancing some fantastic air ballet.

But I think my favorite is a rather stark black-and-white image of nerve cells in the cerebral cortex. They are responsible for conscious thought, memory and language, which is in itself a wonderful thought for a writer. But the picture looks like a forest of bare trees in a snowy landscape and speaks to my northern soul. I am Scottish, and we Scots are born and raised in wind and rain, in a land of short summers and dark winters. I can picture myself happily hiking through that forest.

What was the most interesting thing that you learned about the human body in the making of the book?

I had never heard of Henrietta Lacks, who suffered from cervical cancer and died in 1951. The cancer cells removed from her body proved to be particularly durable, and in a sustaining laboratory environment, they are still able to divide and multiply to this day. They are known as HeLa cells in Ms. Lacks’ honor. Although there are ethical questions about their continuing growth and use, it’s a kind of immortality, and this precious resource offers scientists a stable basis for decades of ongoing research into cancer treatments. There are two micrographs of HeLa cells in the book.

What do you hope readers take away from it?

Most of us don’t give much thought to what goes on inside us, which is probably just as well—not out of squeamishness, but because the complexity of it all is overwhelming. In Science Is Beautiful, I haven’t written a medical textbook, but I hope the book presents some strikingly beautiful images with enough simple explanation for readers to be able to say, “Wow! That’s amazing.” Because it is, it really is.

The World's Parasites Are Going Extinct. Here’s Why That’s a Bad Thing

Smithsonian Magazine

What if the world’s parasites suddenly went extinct? Given how much work we’ve put into combating malaria-carrying mosquitoes and horrifying Guinea worms, it sounds like a reason for celebration. But think twice: Actually, losing these much-despised mooches, bloodsuckers and freeloaders could have disastrous consequences for the environment and human health.

A parasite, in essence, is any organism that makes its living off another organism (think bed bugs, leeches, vampire fish and even mistletoe). These freeloaders have been rather successful: up to half of Earth's 7.7 million known species are parasitic, and this lifestyle has evolved independently hundreds of times. But in a study published this week in the journal Science Advances, researchers warn that climate change could drive up to one-third of Earth's parasite species to extinction by the year 2070.

That kind of mass die-off could spell ecological disaster. "One thing we've learned about parasites in the past decade is that they're a huge and important part of ecosystems that we've really neglected for years," says Colin Carlson, a graduate student studying global change biology at the University of California at Berkeley and lead author on the study.

Carlson had experience researching how climate change is driving the current spate of species die-offs. But four years ago, he saw the potential to look into a lesser known group: parasites. "There has been a lot of work that's been done in the late couple of decades focused on understanding why big mammals go extinct, or how crops respond to climate change," Carlson says, "but there's a lot of types of animals and plants that we don't know a lot about."

He formed a team to find out more about how parasite species could feel the heat in the coming decades. The team based their predictions for this research on a "deceptively simple model" from a landmark 2004 study in the journal Nature, which connected species extinction rates to how much of their habitat they're expected to lose. "The problem is, we don't know very much about where parasites live," Carlson says.

The key to answering that question lay in the Smithsonian-run National Parasite Collection, a 125-year-old accumulation that contains more than 20 million parasite specimens from thousands of species dating back to the early 1800s—a massive yet still relatively small slice of global parasite diversity. Carlson knew that the collection, which has specimens primarily from North America but represents every continent, could serve as a historical database from which to figure out estimates of geographic ranges for specific parasites.

Specimens from the Smithsonian's National Parasite Collection (Paul Fetters / Smithsonian Institution)

So he reached out to the curator of the collection, research zoologist Anna Phillips, at the Smithsonian National Museum of Natural History. The first step was to sort through a lot of old paper records. "Since this is such an old collection, many of these still used a precise locality written out, such as 'this stream at this crossing of this highway, 10 miles down east of this town,'" Phillips says. "While that's very helpful, usually today we prefer to have GPS coordinates."

Her team of researchers digitzed tens of thousands of specimens and their locations in an online database, creating what Carlson calls the biggest parasite record of its kind. Using this immense resource, researchers could then use computer models to predict what would happen to more than 450 different parasite species when climate change altered their habitats, based on how their ranges have changed over the past two centuries.

Their conclusion: Even under the most optimistic scenarios, roughly 10 percent of parasite species will go extinct by 2070. In the most dire version of events, fully one-third of all parasites could vanish.

This kind of die-off would have myriad unfortunate consequences. Consider that parasites play an important role in regulating the populations of their hosts and the balance of the overall ecosystem. First, they kill off some organisms and make others vulnerable to predators. For example, when infected with nematode Trichostrongylus tenuis, the red grouse bird emits more scent that helps predators find and eat it more easily, thus serving to control the bird’s population.

Parasites can also have more indirect effects. Periwinkle snails infected with the trematode species Cryptocotyle lingua, for instance, eat significantly less algae along their Atlantic coast homes, because the parasite weakens their digestive tracts. Their small appetites make more algae available for other species to consume. And there are millions of undiscovered parasite species, whose ecological niches we can only guess at.

"It's hard to predict what their impact on the ecosystem will be if we don't know about it yet," says Phillips. "That's one of the things that's scariest about these model predictions ... it creates a much more urgent feeling about the recognizing the diversity that's out there."

In the future, she and Carlson hope to do further analysis using this new database at finer scales, to predict how certain parasites will fare in different regions under climate change. They expect that, like many organisms, parasite species that are better able to migrate and adapt to new habitats will do better than those that are more tied to certain places.

But even if the parasites emerge successful, those possible geographical shifts present troubling prospects for humans. Parasites can certainly be harmful to people, as in the case of mosquitoes that transmit Zika, malaria or dengue fever. But in this case, the devil you know may be better than the one you don't.

Parasites and their hosts have often evolved together over many years to maintain a delicate balance. After all, parasites usually have little interest in killing their hosts, Phillips explains, since that would mean losing their homes and sources of nutrients. That’s why tapeworms are rarely fatal to the people who get them; the worms have evolved to travel to your gut and feed on the food you ingest, but they rarely siphon off enough calories to actually kill you.

But when a known parasite goes extinct, it creates new open niches in an ecosystem for other invasive species of parasites to exploit. That can create opportunities for new encounters between parasites and hosts that aren't familiar with each other, and haven’t yet developed that non-lethal relationship. In 2014, for instance, a tapeworm species foreign to humans was found in a man’s brain in China, leading to seizures and inflammation of the brain.

"I find that to be equally terrifying to the idea of the extinctions [alone]," Phillips says.

Kevin Lafferty, an ecologist with the U.S. Geological Survey who has extensively studied parasites and biodiversity, says the study raises important questions about our attitudes toward parasites as they face increasing risks of being wiped out. "In many cases, we have an affinity for the species or can place a human value on it," Lafferty said by email. "This motivation is less likely for parasites."

"The field of conservation biology has moved to view species neutrally when considering the need for protection," Lafferty added, "and this view requires that parasites be protected alongside their hosts."

Captivating Long-Exposure Photos of New Zealand’s Glowworm Caves

Smithsonian Magazine

It's one of the world's most spellbinding sights: million-year-old limestone caves sparkling with thousands of blue-green lights, like the giant jewelry chest of some ancient sea princess. Photographer Joseph Michael recently spent several months exploring these caves, located on New Zealand’s North Island, to create long-exposure images that capture their sculptural interiors in all their luminous glory.

While the caves might appear to be dangling with precious gems, the truth is a little more down-to-earth. The cerulean glow is produced by the larvae stage of a carnivorous fungus gnat, Arachnocampa luminosa, which emits light from organs in its tail. The gnats also create sticky "fishing lines" covered in drops of mucus, which they use to ensnare prey. The bioluminescent blue light—created in part thanks to a chemical the gnats produce called luciferase—attracts the prey, which gets stuck in the mucus before being sucked up and devoured.

Arachnocampa luminosa is found only in New Zealand and thrives in the caves, which offer dark, protected spaces for their bewitching light as well as the horizontal surfaces necessary for dropping their sticky lines of death. The gnats spend about nine months as larvae before turning into pupa in a cocoon. They then emerge as flying insects that look like big mosquitoes. The adult insect lives only a few days—without a digestive system it can't eat, so its only purpose is to mate and die.

Michael, who is from New Zealand, says photographing insects was a new experience—his work usually focuses on landscapes. That informed this project's focus, he told Smithsonian.com: “[I looked] at it like a landscape, rather than individual insects. It's interesting when you view the images upside down, for example. They give the viewer a whole different perspective.” The glowworm series, which Michael calls “Luminosity,” is part of a larger multi-media installation planned around the theme of bioluminescence.

The photos were created in four caves on New Zealand’s North Island: Nikau Cave, Waipu CaveRuakuri Cave and Spellbound. Some of the exposures took only five minutes, Michael says, while others required hours of standing in cold water. The prolonged time in the caves was a memorable experience for the photographer: “The moving water echoes through the cave system which creates quite a loud ambient noise level. After a while the sound of the water becomes a constant hum … When you come out of the cave after a long night of photographing, the songs of insects and birds outside felt sharpened and intensified.”

The project also gave Michael a new appreciation for the wonders of New Zealand. “Growing up here, like most things in this spectacular country I thought [the glowworm] was just a regular thing to see,” he says. “As I’ve traveled to many interesting places around the world, I've begun to realize more and more how amazing and unique this little island in the South Pacific is.”

Bioluminescence isn't the only natural wonder Michael's been documenting—he's also been taking photographs of icebergs, which will be projection-mapped onto major buildings in a 2016 project. Michael calls it a “cinematic collision of nature and architecture.” “The bioluminescence work was a nice chance to take my mind off the icebergs for a little while,” he says.

Several of New Zealand’s glowworm caves are open for visitors, who can explore them by foot or by boat. And while a trip to New Zealand is necessary to see Arachnocampa luminosa, they're far from the world’s only species of glowworm. A similar species, the North American Orfelia fultoni, known more commonly as Dismalites, is found in Alabama's Dismal Canyon, among other places in Appalachia. Both species offer the chance to see just how beautiful a gnat can be.

(H/T This is Colossal)

The Key to Protecting Life on Earth May Be Barcoding It

Smithsonian Magazine

The herbivores that roam the African savannah are massive, and they eat a lot. Yet somehow, they all manage to live in roughly the same place, supported by the same sparsely vegetated environment. In 2013, ecologists wanted to know exactly how this worked. However, because elephants, zebra, buffalo, and impala roam many miles to feed and aren’t fond of nosy humans watching them eat, it was nearly impossible to figure out their diets.

The researchers were left, as they so often are, to scrutinize poop. But the digested plants were impossible to identify by human eyes alone. So for this puzzle, they turned to what was a relatively new genetic technique: DNA barcoding.

Ecologists took samples to the lab and scoured the DNA of the plant remains, looking for one specific gene known as Cytochrome c oxidase I. Due to its location in the cell’s mitochondria, the gene, known as COI for short, has a mutation rate roughly three times that of other forms of DNA. That means it will more distinctly show the genetic differences between even very closely related organisms, making it a useful way to tease apart species in groups from birds to butterflies—like the tag on the inside of your shirt, or a grocery store barcode.

For this ingenious method, aptly referred to as DNA barcoding, we can thank one geneticist who found himself fed up with the “stressful” and time-consuming methods of traditional taxonomy. Paul Hebert, a molecular biologist at the University of Guelph in Canada, recalls one wet, cloudy night that he spent spent collecting insects in a sheet as a postdoctoral researcher in New Guinea.

“When we sorted them morphologically the next day, we realized there were thousands of species that had come in,” Hebert says. Many, as far as he could tell, had never been described by science. “I realized on that one night I’d encountered enough specimens to keep me busy for the rest of my life," he says.

Hebert continues: “It was at that moment that I pretty much … realized that morphological taxonomy couldn’t be the way to register life on our planet." He gave away his specimen collections, and moved on to other research in Arctic evolutionarily biology—the “lowest species diversity habitats I could find,” in his words—but the topic of measuring the Earth’s biodiversity always lingered in the back of his mind.

Technology continued to advance in the mid-1990s, allowing researchers to isolate and analyze smaller and smaller bits of DNA. Hebert, who was working in Australia as a visiting researcher, decided to start “playing around” sequencing the DNA of different organisms and searching for a single sequence that could be easily isolated and used to quickly distinguish species. “I settled upon this one mitochondrial gene region as being effective in many cases,” he says. That was COI.

Hebert decided to test his method in his own backyard, by collecting scores of insects and barcoding them. He found that he could distinguish the bugs easily. “I thought ‘Hey, if it works on 200 species in my backyard why won’t it work on the planet?”

And, with some exceptions, it has.

Using this technique, the researchers in the 2013 savannah study were able to piece together the varied diets of these coexisting animals. "We could tell everything the animals were eating from barcoding their scats," says W. John Kress, botany curator at the Smithsonian's National Museum of Natural History, who collaborated on the study. By informing wildlife managers and scientists exactly what grasses each animal feeds on, these results “could have direct impact on designing new conservation areas for these animals,” Kress says.

It also gave ecologists a bigger picture of how the entire ecosystem works together. "Now you can see how these species are actually coexisting in the savannah," says Kress. Today the very idea of what makes a species is changing, thanks to DNA barcoding and other genetic techniques.

It may not look like much, greenery-wise. But somehow, the African savannah supports a variety of iconic herbivores. DNA barcoding helps show how. (Cultura RM / Alamy)

Since the days of Darwin, taxonomists have sifted out species based on what they could observe. I.e. if it looks like a duck, walks like a duck, and sounds like a duck—throw it in the duck pile. The advent of DNA sequencing in the 1980s changed the game. Now, by reading the genetic code that makes an organism what it is, scientists could glean new insights into species’ evolutionary history. However, comparing the millions or billions of base pairs that make up the genome can be an expensive and time-consuming proposition.

With a marker like Cytochrome c oxidase I, you can pinpoint these distinctions faster and more efficiently. Barcoding can tell you in a matter of hours—which is how long it takes to sequence a DNA barcode in a well-equipped molecular biology lab—that two species that look exactly the same on the surface are substantially different on a genetic level. Just last year, scientists in Chile used DNA barcoding to identify a new species of bee that insect researchers had missed for the past 160 years.

Working with Hebert, experts like National Museum of Natural History entomology curator John Burns have been able to distinguish many organisms that were once thought to be the same species. Advances in the technique are now allowing researchers to barcode museum specimens from the 1800s, Burns says, opening the possibility of reclassifying long-settled species definitions. A year after Hebert outlined DNA barcoding, Burns used it himself to identify one such case–a species of butterfly identified in the 1700s that turned out to actually be 10 separate species.

Pinning down murky species definitions has ramifications outside of academia. It can give scientists and lawmakers a better sense of a species' numbers and health, crucial information for protecting them, says Craig Hilton-Taylor, who manages of the International Union for the Conservation of Nature's "Red List." While the organization relies on different groups of experts who can work from different perspectives on how best to define a species, DNA barcoding has helped many of these groups more precisely discriminate between different species.

"We ask them to think about all the new genetic evidence that's coming forward now," Hilton-Taylor says of the IUCN’s procedures today.

While innovative, the original barcoding technique had limitations. For instance, it only worked on animals, not plants because the COI gene didn’t mutate fast enough in plants. In 2007, Kress helped expand Hebert's technique by identifying other genes that mutate similarly rapidly in plants, allowing studies like the savannah one to take place.

Kress recalls how, starting in 2008, he and a former colleague of his, University of Connecticut ecologist Carlos García-Robledo, used DNA barcoding to compare the various plants that different insect species fed on in the Costa Rican rainforest. They were able to collect insects, grind them up, and quickly sequence the DNA from their guts to determine what they were eating.

Previously, García-Robledo and other scientists would have had to tediously follow insects around and document their diets. “It can take years for a researcher to fully understand the diets of a community of insect herbivores in a tropical rain forest without the help of DNA barcodes,” Garcá-Robledo told Smithsonian Insider in a 2013 interview.

They've since been able to extend that research by looking at how the number of species and their diets differ at different elevations, and how rising temperatures from climate change could impact this as species are forced to move higher and higher. "We've developed a whole, complex network of how insects and plants are interacting, which was impossible to do before," Kress says. 

"Suddenly, in a much simpler way, using DNA, we could actually track, quantify and repeat these experiments and understand these things in a much more detailed fashion," he adds. Kress and other researchers are now are also using barcoding to analyze soil samples for the communities of organisms that inhabit them, he says. Barcoding also holds promise for helping to identify remnants of genetic material found in the environment.

"For ecologists," Kress says, "DNA barcoding is really opening up a whole different way of tracking things in habitats where we couldn't track them before.”

By allowing scientists to scrutinize one specific gene instead of having to sequence entire genomes and compare them, Hebert had hoped his method would allow genetic analysis and identification to be performed much more rapidly and cheaply than full sequencing. "The past 14 years have shown that it works much more effectively and it's much simpler to implement than I anticipated," he says now.

But he still sees room for progress. "We're really grappling with inadequate data in terms of species abundance and distribution," Hebert says of conservationists now. Rapidly improving technology to analyze DNA samples faster and with less material required paired with DNA barcoding offers a way out, Hebert says, with modern scanners already able to read hundreds of millions of base pairs in hours, compared to the thousands of base pairs that could be read in that same time by earlier technology.

Hebert envisions a future where DNA is collected and sequenced automatically from sensors around the world, allowing conservationists and taxonomists to access vast amounts of data on the health and distribution of various species. He’s working now to organize a worldwide library of DNA barcodes that scientists can use to quickly identify an unknown specimen—something like a real-life Pokedex.

“How would you predict climate change if you were reading temperature at one point on the planet or one day a year?” Hebert points out. “If we're going to get serious about biodiversity conservation we just have to completely shift our views about the amount of monitoring that's going to be required.”

The Great Chinese Dinosaur Boom

Smithsonian Magazine

Not long ago in northeastern China, I found myself being driven in a Mercedes-Benz SUV down a winding country road, trailed by a small motorcade of local dignitaries, past flat-roofed brick farmhouses and fields full of stubbled cornstalks. Abruptly, we arrived at our destination, and my guide, Fangfang, slipped out of her high heels into fieldwork gear: pink sneakers with bright blue pompoms on the Velcro straps.

We were visiting a dinosaur dig, but there was also a museum under construction—steel beams riveted together to form layers, stacked one atop another, climbing a hillside in two parallel rows. The two wings connected by a central pavilion looked like a bird about to take off. The new museum—its name roughly translates as Liaoning Beipiao Sihetun Ancient Fossils Museum—is due to open sometime in 2019. It was unmistakably huge. It was also expensive (Fangfang estimated $28 million for construction alone). And it was in the middle of nowhere.

We were in a rural village called Sihetun, about 250 miles northeast of Beijing. In the exuberant fashion of a lot of modern development in China, the new structure is going up in anticipation of visitors arriving by speed train from the capital, except that the speed train network hasn’t been built yet. The new museum is located at an epicenter of modern paleontological discovery, an area that is at least as rich in fossils, and in some ways as wild, as the American West during the great era of dinosaur discovery in the late 19th century.

In the mid-1990s, on that hillside in Sihetun, a farmer stumbled onto the world’s first known feathered dinosaur, a creature now named Sinosauropteryx (“the China dragon bird”). Actually, the farmer found two halves of a slab, each preserving a mirror image of this dinosaur. In the freewheeling spirit that has characterized the fossil trade in the area ever since, he sold one half to one unwitting museum, and one half to another. It was the start of a fossil gold rush.The region has yielded more than 40 dinosaur species to date.

Image by Stefen Chow. Liang Shi Kuan, a farmer, is credited with some of the earliest fossil discoveries in Liaoning. He stands in one of the excavation sites. (original image)

Image by Map by LaTigre. (original image)

Image by Stefen Chow. The site of the Beipiao Sihetun museum is surrounded by farmland on all sides. Visitors can access the area only in off-road vehicles. (original image)

Image by Stefen Chow. A slab with several chostracans (an aquatic arthropod) found at a dig site near Bei Piao, and a sign at the site saying “Danger, Keep Out.” (original image)

Image by Stefen Chow. The construction site of the Sihetun Museum in Liaoning province (original image)

Standing on a slope a few minutes’ walk from the museum site, my guide pointed out the hills of a nearby farm where Yutyrannus, a 3,100-pound feathered dinosaur, turned up a few years ago. (Think Tyrannosaurus rex, but plumed like a Mardi Gras Indian.) This was also the former home range of Anchiornis huxleyi, a chicken-size creature with enough preserved detail to become the first dinosaur ever described feather by feather in its authentic colors—an event one paleontologist likened to “the birth of color TV.”

What has emerged from beneath the fields of Liaoning province (and parts of neighboring provinces) is, however, bigger than dinosaurs: A couple of decades of digging have uncovered two miraculously well-preserved ancient worlds. The first, called the Yanliao Biota, is from the middle-late Jurassic period, 166 million years ago. The second, the Jehol Biota, is Cretaceous, from 131 million to 120 million years ago. The Jehol is more famous among paleontologists, and far more diverse. Among the ancient biota—or plant and animal life—found so far: four turtle species, eight amphibian species, 15 fishes, 17 mammals, 24 of the winged reptiles called pterosaurs and no fewer than 53 ancient bird species. Taken together, these finds tell dramatic new stories about the dinosaur origin of birds and the evolution of feathers and flight. That’s in addition to some of the earliest flowering plants, plus assorted pine, cypress and gingko trees, algae, mosses and ferns, snails, clams, crustaceans, insects, spiders and almost endlessly onward. It’s a measure of this diversity that, in addition to its other displays, the museum in Sihetun will house 26 different specimens—from fish to a parrot-faced dinosaur called Psittacosaurus—all partly excavated but still embedded in the hillside where they were discovered.

Here’s another measure of that diversity: Liaoning already has at least ten other fossil museums, some with important collections, others mainly products of local boosterism or bureaucratic career-building. There’s typically lots of money for constructing new buildings, less for acquiring collections, and none at all, at least in the provinces, for scientific staff to make sense of them. Many of the best specimens also turn up in Beijing, or at the Shandong Tianyu Nature Museum seven hours south of the capital, which one paleontologist described as “the best place to see Liaoning fossils.”

**********

One chilly December morning, a week into my trip, I looked out a hotel window in Chaoyang, a city of three million about 45 miles west of Sihetun. The mist rose off a bend in the Daling River and the sunrise lit up the mountains. Some say Chaoyang gets its name from an old poem about a mythological bird singing to the rising sun. It’s known today as a city for fossils, and some of its most celebrated inhabitants are extinct birds.

Image by Stefen Chow. The Nanyuan Hotel in Chaoyang serves a dish named after the Sinosauropteryx, made from raw fish, shellfish and vegetables. (original image)

Image by Stefen Chow. A fossil shop on an ancient street in Chaoyang, Liaoning province (original image)

Image by Stefen Chow. Fossils on display inside a shop in Chaoyang (original image)

These fossils might not wow visitors whose idea of paleontology is limited to massive dinosaur reconstructions at other natural history museums. What Liaoning province typically produces are articulated skeletons in slabs of stone. I first saw one lying flat in a glass display case at the Beijing Museum of Natural History, too high off the ground for children to see, and often obscured for adults by lighting ingeniously positioned in precisely the wrong spots. Then I looked more closely. The backgrounds of the slabs, in mottled shades of beige, brown and ocher, were like old monochrome watercolors, or like a landscape scroll painted in the Tang dynasty. The fossils stood out against this background like bold strokes of calligraphy, and they were stunningly intact. “It looks like somebody’s chicken dinner,” a friend remarked when I showed him a photo of one such fossilized bird.

It looked, in truth, as if something had swatted the bird out of the sky and instantly entombed it in rock, which is more or less what happened, over and over, to vast numbers of such creatures, across tens of millions of years. In the early Cretaceous era, northeastern China was mostly forest and lake country, with a temperate climate. But it was prone to ferocious volcanic eruptions. Lake-bed mud and volcanic ash quickly entombed victims without the oxygen necessary for decomposition, and these fine-grained sediments preserved not just bones, but also feathers, hair, skin tissue, organs and even stomach contents.

The Chaoyang native Microraptor, for instance, is a small, four-winged dinosaur, a tree-dweller built for short predatory plunges from branch to branch. Researchers examining one specimen recently found evidence in its abdomen that its last meal was a bird swallowed nearly whole. (They also identified the bird.) A mammal called Repenomamus, resembling a modern bulldog, turned out to have eaten a small dinosaur.

For paleontologists, the value of Liaoning fossils lies not just in the extraordinarily preserved details but also in the timing: They’ve opened a window on the moment when birds broke away from other dinosaurs and evolved new forms of flight and ways of feeding. They reveal details about most of the digestive, respiratory, skeletal and plumage adaptations that transformed the creatures from big, scary meat-eating dinosaurs to something like a modern pigeon or hummingbird.

“When I was a kid, we didn’t understand those transitions,” says Matthew Carrano, the curator of dinosauria at Smithsonian’s National Museum of Natural History. “It was like having a book with the first chapter, the fifth chapter and the last ten chapters. How you got from the beginning to the end was poorly understood. Through the Liaoning fossils, we now know there was a lot more variety and nuance to the story than we would have predicted.”

These transitions have never been detailed in such abundance. The 150-million-year-old Archaeopteryx has been revered since 1861 as critical evidence for the evolution of birds from reptiles. But it’s known from just a dozen fossils found in Germany. By contrast, Liaoning has produced so many specimens of some species that paleontologists study them not just microscopically but statistically.

“That’s what’s great about Liaoning,” says Jingmai O’Connor, an American paleontologist at Beijing’s Institute of Vertebrate Paleontology and Paleoanthropology (IVPP). “When you have such huge collections, you can study variation between species and within species. You can look at male-female variation. You can confirm the absence or presence of anatomical structures. It opens up a really exciting range of research topics not normally available to paleontologists.”

Image by Stefen Chow. This cluster of dinosaur egg fossils, on display at the Tianyu Museum, dates back 70 million years to the late Cretaceous era. (original image)

Image by Stefen Chow. Jingmai O’Connor, an American paleontologist in Beijing, has a tattoo of an enantiornithine, a prehistoric avian that was the subject of her PhD thesis. (original image)

Image by Stefen Chow. At the Institute of Vertebrate Paleontology and Paleoanthropology, a specimen is studied and prepared for exhibit at a Chinese museum. (original image)

Image by Stefen Chow. A 125 million-year-old fossil of a Psittacosaura, found in China’s Liaoning province and on display at the Tianyu Museum in Shangdong. (original image)

Image by Stefen Chow. The Tianyu Museum opened in 2004, and at roughly 300,000 square feet, is the largest dinosaur museum in the world. (original image)

Image by Stefen Chow. A fossil of an Ichthyosauria (or “fish dragon”) at the Tianyu Museum. The fossil, discovered in Guizhou province, dates to the Triassic era. (original image)

Image by Stefen Chow. Paleontologist Jingmai O’Connor stands on the grounds of Beijing’s Institute of Vertebrate Paleontology and Paleoanthropology (IVPP). (original image)

Image by Stefen Chow. The skull of a 50 million- to 60 million-year-old mouse being prepared at the workshop at IVPP in Beijing. (original image)

Image by Stefen Chow. Researchers prepare fossils at the workshop at IVPP. (original image)

But the way fossils get collected in Liaoning also jeopardizes research possibilities. O’Connor says it’s because it has become too difficult to deal with provincial bureaucrats, who may be hoping to capitalize on the fossil trade themselves. Instead, an army of untrained farmers does much of the digging. In the process, the farmers typically destroy the excavation site, without recording such basic data as the exact location of a dig and the depth, or stratigraphic layer, at which they found a specimen. Unspectacular invertebrate fossils, which provide clues to a specimen’s date, get cast aside as worthless.

As a result, professional paleontologists may be able to measure and describe hundreds of different Confuciusornis, a crow-sized bird from the Early Cretaceous. But they have no way to determine whether individual specimens lived side by side or millions of years apart, says Luis Chiappe, who directs the Dinosaur Institute at the Natural History Museum of Los Angeles County. That makes it impossible to track the evolution of different traits—for instance, Confuciusornis’ toothless modern bird beak—over time.

**********

In Chaoyang, late one afternoon, I visited a darkened, minimally heated apartment to find precious fossils stacked on every available surface. On the coffee table, next to some vitamin pills and a water bottle, was a 160-million-year-old Anchiornis, its dinosaur tail and its plumy smudge of feathers preserved in exquisite detail. Nearby, the twin halves of a split fossil lay side by side, displaying a fish that now seemed to be perpetually swimming toward itself. A child’s sparkle-painted pink bicycle stood on the balcony, and it occurred to me that the only way its owner could get it to the front door would be by wheeling it through a treasure house of perfectly preserved life-forms from scores of million of years in the past.

The apartment belonged to the child’s father, a museum director, who was holding the specimens for the new museum at Sihetun. Lu Juchang, a paleontologist visiting from the Chinese Academy of Geological Sciences, picked up a specimen from the floor and, pointing to different parts of the anatomy, said, “This part is real, this part is not.” To me, the difference was indiscernible, but to Lu’s eye, it leapt out: “I think someone went to find another specimen, cut a groove,” and cemented in a suitable-looking wing bone. The museum, he said, would have a preparator remove the fake parts and preserve what’s authentic.

This kind of forgery is routine, and only a handful of Chinese experts can spot it with the naked eye. Other researchers rely on ultraviolet light, which reflects the light differently from fake and authentic sections of the same slab.

“It’s just a fact,” adds O’Connor, “that most of the people buying these specimens are not scientists, or they are ‘scientists’ with quotation marks. I’m constantly being shown a specimen by someone who says, ‘You have to describe this. This is a Jeholornis with a weird furcula’”—that is, a wishbone. She tells them it’s actually a Jeholornis with a furcula manually added. In the early days, she says, forgers actually painted feathers on some specimens. “You’d do the water test and the feathers would come right off. Now they don’t use water-soluble inks.”

Nonetheless, there’s genuine fossil wealth being revealed in Liaoning. Many of the slabs have been transferred to Beijing, where preparators are getting them ready for display. One morning in the basement of the IVPP, I watched a young man stare through the dual lenses of a microscope as he worked an air-pressure tool along the length of a wing bone. The needle-pointed tip whined and flecks of stone flew out to the sides, gradually freeing bone from matrix. Nearby a woman used an old credit card to apply a tiny drop of 502 Super Glue to a break in a fossil, then went back to work with a needlelike pick in one hand and an air pump in the other. Eight preparators were working at that moment at different fossils. It was an assembly line, dedicated to opening old tombs and bringing whole empires of unimaginably strange and beautiful creatures almost back to life.

How a Tiny Worm is Irritating the Most Majestic of Giraffes

Smithsonian Magazine

What is a fly to a giraffe?

It’s difficult to imagine a single insect even coming to the attention of these peculiar animals, which weigh in at thousands of pounds and routinely stretch their necks to heights of more than 14 feet. In Uganda’s Murchison Falls National Park, however, Michael B. Brown, a wildlife conservation researcher, has noticed something that might be harder to ignore: Whole clouds of insects swarming around the necks of these quadrupedal giants.

Under ordinary circumstances, such irritants might be unexceptional. But a growing body of evidence suggests that those flies might be linked to a more serious problem, a skin disease that seems to be spreading through giraffe populations across the continent. It sometimes takes the shape of holes in the animals’ flesh, circles of dead tissue, altogether distinct from the animals’ distinctive spots.

For giraffes, it’s just one problem among many—and it’s likely far less serious than the effects of climate change, poaching and habitat loss. But a better understanding of this ugly disease’s causes might help us make sense of the many other threats to these long-necked animals that have led wild giraffe populations to a precipitous decline—nearly 40 percent in the past 15 years.

According to a recent paper from the journal Biological Conservation, the giraffe skin disease “was first described in the mid-1990s in Uganda.” The Smithsonian National Zoo’s partners have identified similar lesions on giraffes in Tanzania and elsewhere. Since 1990, other possible evidence of the disease has been spotted in numerous other countries, including Namibia, Zimbabwe and Botswana. As the Biological Conservation paper’s authors note, however, it’s unclear whether the disease is becoming more common or whether we’re just getting better at spotting it as our ability to study giraffes improves.

One way to clear up that uncertainty would be to identify the disease’s etiology—the underlying cause of the problem, assuming there’s just one.

Image by Michael B. Brown. The skin disease sometimes takes the shape of holes in the animals’ flesh, circles of dead tissue, altogether distinct from the animals’ distinctive spots. (original image)

Image by Michael B. Brown. Even if the skin lesion doesn’t expose giraffes to other diseases, the mere presence of it could have other effects, including irritating them in a way that limits their willingness to socialize—and hence their capacity to reproduce. (original image)

Kali Holder, an infectious disease researcher and veterinary pathologist at the National Zoo's Global Health Program, whose efforts has been supported by the Morris Animal Foundation, is working on a likely possibility: A tiny parasitic nematode that another Zoo pathologist spotted in samples of diseased tissue. The nematode, Holder suspects, could be carried by flies like those Brown has reported.

Studied through a microscope, the problem doesn’t look like much, especially to the untrained eye: on the slide that Holder showed me, a bright pink flush crept down the magnified chasm of a giraffe’s hair follicle. That discoloration, Holder said, is probably evidence of the hyperkeratotic areas—unusually thickened skin under attack by the giraffe’s own immune system—that Brown and others in the field have spotted on the edges of skin lesions.

Though evidence of the disease is clearly visible in photographs of giraffes, the problem’s source is harder to spot back on the slide. Curled up against itself, and seen in cross section, the worm is barely recognizable as a worm. But, as Holder told me, it is still recognizably alien from its surrounding tissue, thanks in part to the shimmering outer layer that surrounds it. Resembling nothing so much as a cracked, but still intact, window, that region is, Holder says, “kind of like the cuticle. It’s a specialized protein that helps protect these guys from the hostile environments of a host body.” Surveilling the terrain within, she points out other landmarks, most notably the worm’s digestive tract and its reproductive organs.

“The skin is one of the most important defensive organs, both against the elements and infections,” Holder said, who is studying a likely possibility—a tiny parasitic nematode. (National Zoo)

If you were to study it with the naked eye, this tiny worm would be visible, but only just. That doesn’t mean that the worms are harmless. “The skin is one of the most important defensive organs, both against the elements and infections,” Holder said.

Accordingly, those lesions may be opening the giraffes to other pathogens. But she’s also concerned about other possibilities: “Maybe lower reproductive success because they’re spending more time grooming. Or maybe they aren’t as mobile, because they’re in pain, so they aren’t eating as much,” she says. Coupled with other stressors, including habitat loss, the nematode could have dire consequences for giraffe populations more generally.

Some are thinner than a “strike from a mechanical pencil,” they’re small, sure, Holder says. “Their longest dimension might be two or three millimeters, and they’re fractions of a millimeter in diameter.” But there’s something on the slide that’s smaller still: the parasite’s young.

These nematodes, she explained, “don’t lay eggs. They lay live embryos called microfilariae, which just means ‘tiny threads.’” Though the slide Holder shows me is static, it’s hard not to imagine what it must have been like for the giraffe from which it was taken—flesh wriggling with tiny creatures, alive with a microscopic life not its own. In other words, this hungry invader is there to make more of its own.

That sounds horrifying, and it is, but only up to a point. Apart from those grotesque lesions, the nematode that Holder is studying doesn’t appear to be as terrible as some related parasites. In humans, other nematode species that reproduce by microfilariae are the causative agents of river blindness—a debilitating eye disease caused by black fly bites—and a handful of other tropical illnesses, but these ones aren’t quite so troubling, as far as we know.

Even if the skin lesion doesn’t expose giraffes to other diseases, the mere presence of it could have other effects, including irritating them in a way that limits their willingness to socialize—and hence their capacity to reproduce. As Holder puts it, “For any given animal, [this nematode] may not be the cause of a specific problem or death. But on a population level, you may start to have lower reproductive success. There are cascading potential effects.”

For now, such fears are partially speculative, since scientists aren’t even sure what the worm is. That makes it hard to say how far it has spread, which makes it harder still to evaluate how much harm it’s doing. This is where Holder’s work becomes so important: She and her colleagues—including Chris Whittier, a veterinary global health researcher at Tufts University—suspect that the nematode infecting giraffes belongs to a genus called Stephanofilaria, which is best known for a species that parasitizes domestic cattle. To better confirm that, though, they’d need to acquire a fully intact sample of an adult parasite, in order to establish a full description of it.

That proves easier said than done: For a while, Holder couldn’t even figure out how to get a whole worm out of a host, partly because there’s so little work done on Stephanofilaria. (Relatively easy to kill off with anti-worm drugs in cattle, the parasite has long been considered economically unimportant.)

Holder eventually found what looked to be a protocol in a veterinary journal, but there was a catch—it was written in Portuguese. Fortunately, she claims, “I speak pathology. So I can read most romance languages, as long as they’re talking about pathology.” After some careful study—and with the help of her “Romance language background, Google magic, and citing references”—she was able to puzzle out the method, which involves finely chopping up the infected flesh and then soaking it in a saline solution, at which point the worms should abandon ship of their own accord.

With a worm to examine, the Zoo and its partners in the field will be better positioned to make sense of the parasite’s genetics.

As Robert C. Fleischer, head of the Zoo’s Center for Conservation Genomics, tells me, they’ve already been able to examine the nematode’s DNA, but they can’t find a match for it in GenBank, a major database of genetic information for tens of thousands of organisms. That means in part that they can’t yet confirm whether the giraffe parasite is actually Stephanofilaria—or how it might be related to similar-seeming organisms in domestic cattle. More clearly identifying physical specimens—from both giraffe and cattle—would go a long way toward overcoming that uncertainty.

Once they do, they’ll have much more information about the scope of the problem. As is the case with cattle, treating such parasites should be relatively simple—Holder suggests a regimen of Ivermectin, which is sometimes administered to giraffes in zoo settings, would do the trick—but understanding its origins and the risks it presents is more difficult. Once they’ve genetically sequenced the nematode, it will be far easier for their partners in the field to confirm whether the same parasite is infecting different giraffes in discrete locations.

This matters in part because, as Brown says, they’ve noticed that the lesions seem to be far more common among some Ugandan giraffe populations, but is largely absent in other regions. That, in its own turn, would make it easier to target the infection vectors. They might also be able to determine if this is a new parasite species or just one that’s on the rise due to other factors.

“Maybe this parasite is not that important, but knowing if the vector is new to this area may offer an insight into other vector-borne diseases that may be more relevant,” Holder says.

Brown, for one, says that he hasn’t identified declining birthrates among populations with the skin diseases—though he also notes that it can be difficult to definitively confirm such observations in an animal with a 14-month gestation period. It’s entirely possible, then, that the parasites don’t present a real risk, at least not in and of themselves. But that exposed necrotic tissue could lead to other problems. It might, for example, attract ox peckers, birds that can both expand lesions as they feed on them, and potentially spread the infection to other animals. The only way to know for sure would be to study the nematodes more fully.

Suzan Murray, director of the Smithsonian’s Global Health Program, suggests that climate change may play a role: Insects such as horn flies that could be transmitting parasites could be thriving in generally warmer and wetter conditions. Such information could benefit wildlife conservation more generally, since it could help us anticipate and respond to emerging crises before they reach epidemic levels. Given that a similar skin disease has been identified in Kenyan rhinos, better understanding the underlying environmental roots of the problem might contribute to our understanding of the broader ecosystem, even if it doesn’t have an immediate effect on the well-being of giraffes.

In other words, the inquiries of scientists such as Holder and the field researchers whose efforts intersect with them have potentially enormous, practical consequences, even when their actual objects of study are minute.

Field work supporting the Smithsonian's Global Health Program's research into the skin parasite has proceeded in large part through the work of the Uganda Wildlife Authority and the Uganda Conservation Foundation. They have collaborated on the Rothschild Giraffe Conservation Project, an effort funded by SeaWorld and Busch Gardens Conservation Fund.

Five Things The Gulf Oil Spill Has Taught Us About the Ocean

Smithsonian Magazine

The 2010 Deepwater Horizon oil spill is considered the largest accidental marine spill in U.S. history and a disaster for human and non-human communities along the coast of the Gulf of Mexico. But the spill created an opportunity to rigorously study the effects of oil spills on the environment and public health, and to develop new technologies to fight future spills.

BP set aside $500 million to fund spill-related research, and for the past five years the independent Gulf of Mexico Research Initiative (GoMRI) has used that funding to support the research of more than 1,200 scientists.

Along the way, these researchers have made fundamental ocean science discoveries that otherwise may never have been known. Here are five of the most interesting ocean findings that have come out of Gulf oil spill research:

Never-Before-Seen Ocean Currents

Researchers launched plastic drifters into the Gulf of Mexico in 2012. (CARTHE)

Our understanding of ocean currents is limited by our tools, says Tamay Özgökmen, a physical oceanographer at the University of Miami. Our eyes can pick out small currents off the side of a boat, and satellites can identify large ones that are tens to hundreds of miles wide. But we don't have good tools for seeing currents that lie somewhere in the middle—around 300 feet to 6 miles wide—and they remain largely invisible.

Led by Özgökmen, the CARTHE team of oceanographers and engineers found a new tool during the Gulf spill: the oil slick itself. By some estimates, the slick covered almost 4,000 square miles by the end of April 2010. They carefully watched the slick spread across the ocean's surface, and they noticed that it didn't move in the way they suspected based on known currents. "We looked at many images of the oil spill, and it became clear to us that flows at the small scale were very influential on how this thing spread," Özgökmen says.

CARTHE researchers developed a suite of small, GPS-enabled ocean drifters that could be dropped into the Gulf and tracked by location. Their data confirmed the existence of these small currents, called sub-mesoscale currents. "This was a discovery, the first time that these currents have been measured," Özgökmen says. "People always suspected them, but they could never measure them because they required a huge number of drifters." The CARTHE team continues to develop cheap, compact, easy-to-build and biodegradable drifters that researchers can use to identify other small, local currents throughout the world.

A Tally of Gulf Critters

A scanning electron micrograph of the mud dragon Echinoderes skipperae. (Martin Sørensen)

After the spill, one of the first questions asked was how it would affect animal populations in the Gulf and along the coast. People immediately worried about large charismatic animals like dolphins, pelicans and bluefin tuna, as we can easily see and empathize with their suffering. However, many of the abundant but less traditionally appealing animals, like insects and zooplankton, are just as crucial to these ecosystems, if not more so.

The spill gave researchers an opportunity to count and identify these tiny critters in the Gulf region, some for the very first time. Linda Hooper-Bui, an entomologist at Louisiana State University, studies insects and spiders, which play often unnoticed but important roles in coastal habitats, such as aerating and altering nutrients in soil, competing with crabs and other arthropods for food, transporting plant seeds and serving as food for songbirds and other animals. In the wake of the spill, Hooper-Bui studied the effects of stressors on insects and spiders in the marshes and coastal dunes fringing the Gulf of Mexico. One of those stressors is oil—but she has also been looking at flooding and storm surges, which will be increasingly common as sea level rises along the Gulf coast. "We now have excellent data on diversity of insects and spiders, those taxa that are resistant to stressors, those that are resilient in the face of extreme stress and those that take a longer time to recover," she says.

Meanwhile, Troy University biologist Stephen Landers is digging around in the sand for meiofauna, microscopic animals that live between grains of sand. Before the spill, he and his colleagues collected sediment off the Gulf coast and counted more than 33,300 animals, including nematodes, copepods and small marine worms called polychaetes. As he continues the sampling work post-spill and puts names to the meiofaunal faces, he's "found about 15 species that appear to be new to science," he says. For instance, he and University of Copenhagen's Martin Sørensen have described two new mud dragon species. "Only through an understanding of what is out there now will we be able to look at the effects of changes in the future," Landers says.

Energy and Life Surround Deep-Sea Seeps

Methane ice worms gather on a lump of methane hydrate in the Gulf. (NOAA Okeanos Explorer Program, Gulf of Mexico 2012 Expedition)

Every year, natural oil seeps leak up to 1.4 million barrels of oil into the Gulf of Mexico. Bubble by bubble, oil and gas escape from reservoirs beneath the seafloor—the same reservoirs that oil and gas companies tap into when they drill in the deep sea.

Unique communities of animals surround these seeps, feeding on microbes that can digest the hydrocarbon-rich oil and gas. "The presence and movement of oil and gas is essential for these organisms to flourish," wrote Caroline Johansen, a graduate student at Florida State University, in a blog post at the Smithsonian Ocean Portal. As part of a deep-sea GoMRI project, she films the seeps to precisely measure how much oil and gas emerges and to identify factors that control bubble release.

These seeps are also a formation site for methane hydrates, a crystalline form of methane that is considered both a potential new source of natural gas and a potentially dangerous contributor to future climate change. Methane hydrates are a major hazard at deep-sea drilling sites, and even prevented BP from stopping the Deepwater Horizon spill in early May 2010 when they grew inside the containment dome.

There's still a lot to be learned about how and why they form, their stability at different temperatures and pressures and what role they play at seep sites. The spill has given researchers an opportunity to spend dedicated time at these inaccessible sites and better understand their physics, chemistry and biology. "This all relates to the 'big picture', in that we generate a better understanding of the workings of these seep sites that are energy-producing areas for many of the organisms in these benthic ecosystems," Johansen says. Perhaps more urgently, the Gulf of Mexico is considered the best spot in the U.S. to drill for methane hydrates—if scientists can figure out how to safely extract them. The more that researchers can learn about Gulf hydrates before that day, the better.

How Hidden Sharks of the Deep Migrate

A bluntnose sixgill shark in Hawaii. (Dean Gubbs)

We fear and delight in sharks when they swim at the surface. But the majority of sharks stay in the ocean depths, remaining invisible to us. "Most people don't realize that more than half of all shark species in the world live their whole lives below 700 feet deep," says shark scientist Dean Grubbs of Florida State University.

While sampling deep-sea fish for oil exposure after the spill, Grubbs used the opportunity to learn more about one of the most common large deep-water sharks: the bluntnose sixgill shark. Reaching lengths of 17 feet, they are found throughout the world in water up to 6,000 feet deep. With his team, he attached satellite tags to 20 of these sharks around the world, including seven in the Gulf of Mexico, to track their movements. They were surprised to find that Gulf sixgill sharks swim towards the ocean's surface at sunset and back to the depths at sunrise, following a strict schedule. This follows the same pattern of daily vertical migration used by billions of small fishes, squids and shrimp. Grubbs thinks that sixgilll sharks may be following this migration to feed on the predators of these smaller organisms.

Additionally, his team sampled deep-sea fish populations, including sharks, throughout the eastern Gulf. They were surprised to find that deep-sea fish communities vary significantly across the region. This is relevant to understanding the impacts of the spill, since as many as 10 million gallons of oil may have settled on the seafloor where these fish live and forage. But it also provides fundamental information to researchers trying to understand what forces shape these deep-sea communities.

Invasion of the Lionfish

In the summer after the spill, Will Patterson of the University of South Alabama and Dauphin Island Sea Lab surveyed artificial and natural reefs across the north central Gulf shelf to see if oil affected the reef fish living there. Taking video with small remote-controlled cameras, he and his graduate student Kristen Dahl made a surprising observation: invasive lionfish perched all over the artificial reefs.

These fish are voracious predators, reproduce quickly and are hard to catch and kill. This was the first time that the troublesome fish had been seen in such high numbers around artificial reef communities the northern Gulf of Mexico, so Patterson started tracking them. By late 2013, lionfish populations in the region had grown exponentially, and they've increased even more since then. He found higher lionfish densities on artificial reefs than natural reefs, densities that are among the highest in the western Atlantic.

As they continue to study the oil spill's impacts, they'll also follow the lionfish. "What we're interested in documenting are lionfish population trends, potential mechanisms to control lionfish and what impact they are having on native reef fish populations," says Patterson. 

How Driftwood Reshapes Ecosystems

Smithsonian Magazine

Logs the size of telephone poles drift along the shore of the Salish Sea. Erik Hammond turns the wheel of his aluminum skiff and closes in. He grabs his ax and towlines, then leaps atop the floating wood, much as his father did, and his father did before him. With the butt of his ax he drives anchor pegs into the choicest three and ties them to the stern. When he turns his boat, the lines go taut—the logs startle, then come to heel. Satisfied, he unties the lines and tosses them over before circling back to the beach. But the logs sail on, toward his partner, George Moore, who adds them to the growing haul already tied behind his skiff.

Hammond and Moore are beachcombers, or log salvors, based in Gibsons, British Columbia, a small coastal community less than 50 kilometers north of Vancouver. They are practitioners of an occupation once common on the Pacific Northwest coast. Moore, 72, has been chasing logs since he was a kid. Hammond, 41, was still in diapers when he started tagging along with his father. It’s a demanding and sometimes dangerous pursuit that calls for strength, balance, finesse, and a command of mechanics and physics. In return, it offers uncertainty and little pay.

“I love it,” Hammond declares. “It’s all I know how to do.”

On this calm summer afternoon, Hammond and Moore gather merchantable timber that has escaped log booms owned by logging companies. Once wood is floating free, it’s a hazard to navigation—and fair game for licensed log salvors. Today’s catch, mostly fir and cedar, will be sold through a cooperative that returns a share of the total value back to the logging companies. What’s left for Hammond and Moore averages CAN $25 per log—which they split. They’re also on the lookout for pristine, uncut trees that have ended up in the water through wind, erosion, or flood. With no logging company to lay a claim, this wood can fetch far more. They say the best time for beachcombing is during the fall and winter months, when high tides coincide with the arrival of powerful storms, which upset log booms and topple trees into swollen rivers and streams.

Be it clean sawlogs, twisted branches, or stumps with the rootball still attached—whether the result of industry or flood—driftwood is the remains of any tree that ends up washed ashore or floating in the sea. Beyond a dwindling number of beachcombers hoping to make a buck, and mariners wishing to avoid striking deadheads, why should anyone care?

Driftwood makes an enormous if underappreciated contribution to the food web connecting the forests and the sea. From streams to estuaries to the deep ocean floor, driftwood shapes every environment it passes through. While there’s an awareness that temperate rainforests are enriched with nitrogen from the marine environment, delivered by decomposing salmon, less well known is the fact that dead trees from those same forests travel to the sea and become a vital source of food and habitat. Driftwood is in need of a PR campaign, celebrity spokesperson, or publicist at the very least. Driftwood, it turns out, is also rapidly disappearing.

Dead trees were sailing the seas long before our ancestors conceived of the ax or skiff, long before the continents split and went their separate ways. And yet, when a tree falls in a river or stream today, it can set out on a journey that remains little studied and poorly understood.

A tree undergoes reincarnation when it lands in flowing water. Branches, bark, and heartwood—what appears to be nothing more than floating debris—become either home to or sustenance for a range of plants and animals. In old-growth forests, up to 70 percent of the organic matter from fallen trees remains in streams long enough to nurture the organisms living there, passing through the digestive tracts of bacteria, fungi, and insects. Caddis flies and mayflies undergo their metamorphosis into adults while anchored to floating wood. When they emerge, they in turn become food for salmon fry, salamanders, bats, and birds. Larger logs control the very shape and flow of streams, creating pools and back eddies where returning salmon rest and spawn. These pools provide critical shelter for young salmon as they hatch, feed, and hide from predators before they make a break for the open sea.

As wood passes through the floodplain, it collides with and remakes the shore. Some becomes anchored there, trapping silt and seeds. As new vegetation takes root, deer mice, voles, shrews, and chipmunks move in for the harvest. Weasels, minks, and hawks make meals of them and fertilize the soil. Wood that drifts into estuaries becomes perches for hungry bald eagles and herons; rafts for weary cormorants, pelicans, and seals; and nurseries for herring eggs.

The estuaries of the Pacific Northwest are young, between 15,000 and 10,000 years old. Shaped by ice, they have remained dynamic environments due largely to the transformative power of driftwood. Here, trees still arrive after falling into rivers the old-fashioned way, but since the advent of stream clearing for navigation, industrial logging, riverside development, and hydroelectric dams, humanity has taken the lead in shaping waterways—just as it has the world over.

In Oregon, Washington, and British Columbia, logging companies continue to float timber down rivers for processing at lumber mills. As recently as the 1990s, an annual 10 billion board feet of lumber was rafted or stored as logs along rivers in the Pacific Northwest. If only one percent of those logs escaped and somehow eluded beachcombers, that means 100 million board feet of merchantable timber became driftwood each year. But these days, only a fraction of that enters the marine environment. Whether cut logs or whole trees, less wood completes the journey from the forests to the sea.

When Hammond is ready to tow a week’s worth of logs to his booming grounds, he trades up to the bigger boat he keeps tied to the government dock in Gibsons, which sits at the western entrance of Howe Sound, a body of water that was once clogged with tugboats pulling log booms. In fact, the words “Gibsons” and “beachcombing” will be forever intertwined for Canadians of a certain age. The Beachcombers was the immensely popular CBC television show that ran from 1972 to 1990, and was syndicated around the world. While Hammond appreciates what the dramedy did for his hometown’s reputation, he rolls his eyes when asked how accurately it portrayed the job. And yet with gumboots, a beard, suspenders, and belt, he looks as if he just arrived from central casting. Brush off the actual bark and sand, and he’d also fit right in among the young, plaid-wearing lumbersexuals found slouched in hipster coffee shops from Brooklyn to Seattle.

Hammond is in perpetual motion—moving between his boats and wood with remarkable ease. With three dozen logs already trailing behind, he scans the water for more. “Peelers,” Hammond calls them, logs suitable for making into plywood. Currently, cedar is the most valuable. At one time, salvaged fir was worthy of being milled into lumber. Nowadays, most logs he brings in end up being pulped for paper products.

There are fewer logs in Howe Sound than when Hammond’s father and grandfather were around. Across the Pacific Northwest, the volume of timber harvested is down and logging companies are taking greater care in securing their booms and bundling their logs.

“At one time,” Moore declares, “Howe Sound was the largest [log] sorting grounds in the world. There was wood everywhere. A blind man could pick up wood.”

Natalie Kramer has spent years researching driftwood on the Slave River in Canada’s Northwest Territories. (Photo by Jesika Reimer)

Though beachcombing’s a sunset industry, for Hammond and Moore, it remains worth doing; worth putting to use the hard-won knowledge and skills, feeling the connections to this place and their past. Both men are obliged to take other part-time work, but find their greatest source of professional satisfaction—and identity—out here, on the water, finding and rounding up logs.

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The beachcombers of British Columbia are not alone in their attraction to driftwood. Natalie Kramer has spent the past seven summers paddling among the remains of fallen and floating trees in Canada’s Northwest Territories, 1,400 kilometers north of Gibsons. Kramer is a 32-year-old fluvial geomorphologist, a scientist who studies rivers. And, with an impressive list of epic river descents and elite competitions behind her, she also happens to be one of the top pro female kayakers in the world

Kramer’s PhD in wood transport dynamics focused on the Slave River, which flows north into Great Slave Lake, which in turn flows into the Mackenzie River, which in turn flows into the Arctic Ocean. In North America, only the Mississippi drainage basin is larger. Relatively undisturbed by large-scale industrial development, the Mackenzie River system functions much as it has for millennia, making it a natural laboratory for studying the long-term effects of driftwood and its relationship with marine and riverine ecosystems.

To Kramer, rivers are the lifeblood of the planet, and driftwood the nutrients in that blood, an analogy that came to life for her in 2011, when she watched a huge, continuous mass of logs go floating past her base on the bank of the Slave River for three consecutive days.

“That’s when I was like, oh, this is a lot of material!” she exclaims. “It’s a major component of the landscape many people take for granted.”

One day, Kramer happened upon a massive logjam on the river—the same logjam described in explorer Alexander Mackenzie’s journal in 1789. She cored a tree growing out of the jam itself and found it was over 50 years old.

Immense logjams and floating rafts of naturally occurring wood were once common and well-documented features in rivers and estuaries before they were cleared for navigation. The Great Raft on Louisiana’s Red River, perhaps the most famous, existed for an estimated 375 years before its removal in 1830. The raft and associated jams blocked 227 kilometers of the main channel and stretched approximately twice as far.

Kramer’s research shows that driftwood serves as building blocks for stable sand dunes and spits in estuaries, providing an important buffer from rising tides and waves. But shorelines around the world—especially in developed, temperate zones—are now severely wood impoverished compared to their condition before human settlement. As rivers lose driftwood, water travels through faster and there is less time for nutrient cycling. Excess nitrogen, mostly from agriculture, is one contributor to algal blooms in the marine environment. In wood-starved rivers, there is less opportunity for nitrogen to get reprocessed before being flushed out to sea.

Kramer identified the same driftwood raft on the Slave River noted by explorer Alexander Mackenzie in his journal about his 1789 quest to find a route to Canada’s west coast. (Photo by Natalie Kramer)

“With the wood gone, our rivers are simpler, less complex, and offer a lot less buffering capacity against contamination and sea level rise,” she says. “The simpler they are, the less resilient they are to change.”

Although her PhD project is now complete, Kramer still paddles the rivers of the Northwest Territories and still has unanswered questions. Like, how much longer will the Slave River run free?

“This river is under threat from hydropower development, and when you build hydropower you block your wood.” She points out that the threat comes not just from proposed development on the Slave itself, but also from the approved Site C dam farther upstream on the Peace River. “If that wood is no longer being delivered to the delta, what do we stand to lose?”

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The Mackenzie River system exports large volumes of driftwood into the Arctic Ocean, where it gets frozen into or rafted on sea ice. The sea ice can become caught in the Beaufort Gyre (a clockwise current) before it melts or otherwise shrugs off its cargo. Driftwood then finds its way to distant shores far beyond the tree line. By studying the amount and distribution of driftwood in the Arctic, researchers have learned more about changing ocean currents, sea ice extent, and climate over the past 12,000 years.

Long before driftwood caught the eye of environmental scientists, Arctic people had a primordial relationship with the wood arriving from a forested world they could scarcely imagine. They transformed this precious resource into everything from shelter and weapons to carved, tactile maps that could be read by hand. So valuable was this gift from the sea, archaeologists have speculated that when Inuit ancestors migrated from Alaska to the east over 1,000 years ago, they carried driftwood with them.

(Illustration by Mark Garrison)

The Inuit are not the only Indigenous people who relied on the bounty of distant forests. The wood flowing from the rivers of the Pacific Northwest also shows up in some surprisingly far-off places. Driftwood that escapes inshore tidal currents can get caught in the North Pacific Gyre, which pulls it far to the west. In the subarctic tundra of southwest Alaska, where the vegetation runs from moss to stunted willow, the Yupik have chants, songs, and stories about the importance of driftwood. Driftwood sheltered them in their qasgiq and ena(men’s and women’s houses), warmed and illuminated their nights, and helped invoke the spirit world through its transformation into exquisitely carved shamanic masks. On the treeless Aleutian Islands, between the Alaskan mainland and Siberia, the Unangan people carved and bent yellow cedar from the Pacific Northwest into incomparable baidarkas—precursors of the modern kayaks Kramer uses in her research and competition today.

Far to the south, logs from the Pacific Northwest once made up the majority of wood washing ashore in the Hawai‘ian Islands. Wood from tropical forests in the Philippines, Malaysia, and Japan also arrived, but the Hawai‘ian people chose Douglas fir and coastal red cedar from over 4,000 kilometers away to integrate into the customs and rituals of their culture. They prized the wood from temperate coastal rainforests for building their large double canoes—symbols of wealth, prestige, and power.

Most driftwood, of course, goes untouched by human hands. The afterlife of these dead trees can be just as surprising.

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The fate of most driftwood ultimately awaits at the bottom of the sea. But as researchers like Kramer work to advance our understanding of the dynamic force of logs careening down rivers and streams, less is being added to our knowledge about the role it plays in the marine food web. Pioneering research was conducted on that part of the story by Ruth Dixon Turner during the 1970s–1990s, and later compiled by James Sedell, a leading US Forest Service research scientist and director of fish conservation at the National Fish and Wildlife Foundation. Sedell was intrigued by the disappearance of driftwood from the beaches of the Oregon coast, where he roamed as a boy.

Massive amounts of wood flow from rivers into the ocean. (Photo by Natalie Kramer)

Driftwood can remain afloat in the open ocean, depending on species, for up to 17 months. During that time, these unrooted trees transmute into floating reefs, drifting habitat for a wide range of marine species, including the wingless ocean strider, the only insect known to live in the open ocean. Ocean striders attach their eggs to driftwood even as gribbles (a kind of crustacean) and shipworms (a bivalve mollusk)—the bane of early explorers—consume it from within.

In From the Forest to the Sea: The Ecology of Wood in Streams, Rivers, Estuaries, and Oceans, Sedell and his coauthor Chris Maser explain that over 100 species of invertebrates and 130 species of fish are known to congregate on and around floating objects like driftwood. They do so because of Langmuir currents, pairs of counterrotating convection currents generated by surface winds, which sweep floating logs and organic debris into long, parallel rows often called “slicks.” This in turn attracts plankton and small fish, which in turn draws larger, predatory fish such as dorado, tuna, and sharks. Shade, abundance of food, a place to lay eggs, and protection from waves are among the reasons scientists suspect these temporary environments are so attractive to marine life. It is estimated that, in the habitat associated with a single large piece of oceangoing driftwood, the combined weight of the associated tuna alone can add up to as much as 100 tonnes—or the equivalent of well over half a million cans of tuna.

Tuna are known to time their migration to the continental shelf for spawning with the beginning of the monsoon season. In the eastern Pacific, driftwood carried by the resulting floods arrives just as young yellowfin tuna are emerging from their eggs. Juvenile yellowfin associate with large driftwood and researchers suspect this relationship is important in determining whether or not they’ll reach reproductive age. In the western and tropical Pacific, the tuna fishery went from minuscule to the world’s largest (in terms of total catch) within a decade of recognizing that tuna school around large collections of driftwood—and then seeking out this bait. In the late 1990s, Spanish fishers in the eastern Atlantic even began to enhance natural driftwood with artificial logs to attract more tuna.

For ocean-going driftwood, the journey ends far from where it all began. After a life lived rooted to the land, turning sunshine into energy among insects and birds, after enriching and reshaping rivers and streams, after sheltering and feeding plankton and fish along the surface of the sea, the remains of trees that do not wash ashore sink to the bottom. This submerged wood is most abundant off the estuaries and shores of forested coastlines, but dredging frequently digs up logs in the deep ocean floor and even in deep-sea trenches.

Deep-sea wood borers (Xylophaga, a genus of bivalve mollusks) take over where shallow water gribbles and shipworms left off. These creatures depend on driftwood for survival. They rapidly convert wood into fecal pellets, which in turn support more than 40 species of other deep-sea invertebrates, creating a temporary but productive habitat on the ocean floor, what Sedell called “an island of biodiversity.” Twenty-three years ago, he worried about the decreasing amount of driftwood and the increasing amount of plastic taking its place in the world’s oceans.

The Slave River’s outer delta shows the importance of driftwood. For example, the formation of a driftwood barrier protects the mainland from waves. (Photo by Natalie Kramer)

Studies off the coast of Washington State in the late 1990s suggest a rich and vital relationship between the forest and marine environments. Researchers found the amount of organic terrestrial carbon (wood debris and soil from forested rivers and streams) was high, and that dead trees are a significant source of energy in the ecosystem of the ocean floor. How much? Upward of 60 percent of the total organic carbon in shallow coastal waters and about a third in waters up to a kilometer deep. Even at depths beyond that of the Grand Canyon—far off shore—as much as 15 percent of the total organic carbon was byproducts of driftwood.

On the coast of British Columbia, Hammond and Moore recall the late 1990s as being the heyday for log salvaging. Although today’s pickings and profit are comparably slim, Moore says he’ll keep beachcombing as long as he’s able. Will Hammond be the last beachcomber on this stretch of the coast? He shrugs, but points to the half-dozen logs tied to a float in front of his house—all hauled in by his seven-year-old son.

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Almost 150 kilometers south of the Hammond family float, a series of explosions between 2011 and 2014 released the Elwha River on its course to the Salish Sea. The US National Park Service destroyed a pair of old hydroelectric dams on Washington State’s Olympic Peninsula, initiating the largest dam removal project in US history. While many people are aware that removing a dam can help clear the way for returning salmon, few realize it frees wood to reach the sea.

The dams were in place for just over a century. During that time, the river was not fully alive, according to Robert Elofson, former director of the river restoration project for the Lower Elwha Klallam Tribe and current fisheries harvest manager.

“You had higher water temperatures in the summer. No woody debris transport, no sediment transport. Now the wood is doing exactly as predicted,” he says, providing food and habitat for insect nymphs and larvae that in turn become food for salmon.

The removal of the Elwha Dam and Glines Canyon Dam restored over 70 kilometers of spawning habitat—habitat once again shaped in part by floating wood. The river is producing salmon again: sockeye, pink, chum, steelhead, coho, and chinook. Birds perch on beached logs and fertilize the soil at the water’s edge. Seeds get trapped and new shoots sprout as other creatures move in. Young fish hide and adult fish rest in the new back eddies and shadows along the shore. The river system, far more complex and diverse, is free to flow along its original course for the first time in living memory.

The rapid rebirth of the Elwha is precisely why Kramer worries about any plans to dam the Slave: it would be a shock felt far beyond the river system. Like Sedell before her, Kramer hopes to wake people up to the need to better understand the vital role of waterborne wood before it’s gone—like the immense log jams and floating rafts of centuries past. Part of that work lies in reimagining the boundaries between words like river, tree, and sea.

Related Stories from Hakai Magazine:

Top Nine Ocean Stories That Had Us Talking in 2015

Smithsonian Magazine

It’s been a year of extremes for Earth's oceans, and many were not good. But there are stories that balance the bad news with reasons for #OceanOptimism about the year ahead.

Here in no particular order are the top ocean stories from 2015, curated by the National Museum of Natural History's Ocean Portal team:
Senses in the Sea
(amanaimages/Corbis)

We learned a lot this year about how animals use their senses under the water. Mantis shrimp, which have built-in polarized lenses, are able to send each other messages with twisted light that only other mantis shrimp can see. Salmon moving upstream can flip a biological switch that allows them to see infrared light. Chitons, which don’t look like much more than a bump on an ocean rock, build thousands of eyes into their hard shells, while octopuses can sense light levels with their skin. And the Navy is interested in a discovery that explains how some fish manage the ultimate sensory trick of making themselves nearly invisible.

When it comes to the sea, sound travels much farther than light. The skulls of baleen whales actually channel the frequencies of the whale songs they hear underwater, sending them right to their ear bones

Small Plastics Are a Big Problem

(MPCA Photos)

We know the ocean is full of plastic, most famously in the eastern Pacific garbage patch and in the stomachs of birds. But what about the plastic we can’t see?

This year we learned that our synthetic clothes and sportswear are leaching their plastic threads into water systems every time we run a wash cycle. Tiny plastic microbeads—used as exfoliators in facewash, toothpaste and other personal products that help keep our skin soft and our teeth clean—are also making their way to our water. Both the strings and beads are too small to be filtered out by water treatment systems. Found in rivers, streams, lakes and the ocean, these incredibly tiny pieces of plastic are now an unintended staple in the diets of mammals, fish and plankton. They can clog up corals and leach chemicals into the fish.

In response to the problem, several states have passed legislation that would phase out microbead use in the coming years. Now a bill approved by Congress and sent to the president would speed up that process nationwide. You can support the overarching cause by donning a shoe made of recycled ocean plastic—a step in the right direction for sure.

Poop to the Rescue

(Frizi/iStock)

Poop can be more than just a byproduct of digestion. Unsurprisingly, the largest animal on earth—the blue whale—produces a significant amount of excrement that is typically released at the ocean’s surface and helps stimulate plankton growth. But the loss of blue whales and other large whale species over the past century, due mostly to hunting, means that the oceans have lost a significant pathway for recycling nutrients. Will “Save the Whale Poop to Save the Oceans,” as suggested by Maddie Stone at Gizmodo, be the next conservation slogan?

The plankton populations that bloom from whale poop at the ocean surface of course poop themselves. This poop makes up a portion of what scientists call marine snow—a general term that encompasses dead organisms, feces and other organic matter. Scientists are now learning how much carbon sinks to the bottom of the sea thanks to marine snow, effectively removing it from the climate change equation.

Back on land, penguins need rocky locations free of ice to lay their eggs, and this year citizen scientists poring over hours of mundane video footage helped discover a key ingredient to their success. That’s right, their poop! Scientists think groups of pooping penguins speed up the melting of ice, allowing them to start laying eggs earlier.

Which Fish Am I Eating?

(hlphoto/iStock)

We don’t really know what types of fish we are eating—that’s what study after study has found. This is true for many species, including salmon, where mislabeling of farm-raised versus wild-caught fish can leave us pulling out our hair. Now, we’ll have a third choice—the FDA this year approved commercial sales of genetically engineered salmon.

What does that really mean? The fish are engineered to grow fast and get big when raised in their indoor environment. The approval process took two decades, and genetically altered salmon seem to be safe to eat, but negative effects on the environment are harder to rule out.

Hot, Hot, Hot

(NASA/JPL)

It’s official: This year’s El Niño is the strongest on record—meaning that water in the Pacific Ocean is the hottest we’ve ever seen, bringing with it deadly heat waves, floods and droughts. Blooms of algae grow in these warm conditions, and ocean mixing is disturbed, leaving many animals without their usual food sources and poisoning others. The El Niño, plus generally warmer waters from climate change, has also spurred the third global coral bleaching event ever recorded.

Global warming means that glaciers are surrounded: warm air from above, warm water below, and small rivulets of water going right through them. All of this means that Greenland’s glaciers are melting at record speeds. As Arctic ice is seeing all-time lows due to the warming, Antarctic ice is increasing. But there is a net loss for global sea ice. Not to mention, it’s only a matter of time until the unstable West Antarctic ice sheet moves into the sea.

Rapid melting can threaten sea life and also seed the growth of certain plankton species, putting ecosystems out of whack. While it’s no surprise some of the tiniest things in the ocean would be impacted by all this melt, such large-scale changes can even alter the rotation of the Earth.

Animals (and Plants) On the Move

(semet/iStock)

Despite strict fishing limits on cod in New England waters in place since 2013, the fish are just not coming back. The restrictions may have come too late, as 2015 brought news that the U.S. fishery is not rebounding. The problem? The warming waters mentioned previously are not only causing sea level rise and coral bleaching, but are also triggering species to move outside of their typical ranges and making it hard for juvenile fish to survive—even causing adult cod to die.

The increased water temperatures are not just impacting cod stocks—pink sea slugs in the Pacific are moving north, blob-like creatures called sea hares are taking over California beaches, walruses are crowding Alaskan shores, king crabs are invading Antarctica and there are increasing instances of large species, like whales, seen on the other side of the world from where they are usually found.

Massive influxes of sargassum, a brown seaweed, have been taking over the shorelines of the Caribbean. The unprecedented amount of sometimes-stinky seaweed turned away some tourists and in some instances reached heights of ten feet.

The good news? The cod stocks in Canada seem to be doing well, which means if we manage species properly, there is hope.

Skeletons in the Closet

(A. Boersma/SI)

Among the fossil findings of 2015, this one was a seriously amazing tale. A mostly forgotten skull long thought to be from an extinct group of walruses is actually from a new group in the sperm whale family. Smithsonian scientists scanned and digitized the hefty 300-pound fossil 90 years after it was first described, piqued by the shapes of the teeth that just didn’t add up.

Elsewhere, a newfound sea urchin fossil was shown to be the oldest of its kind—moving its branch in the family tree of invertebrates back a full 10 million years.

For some groups there are no fossils, but that doesn’t mean we can’t reconstruct their history. An entirely new microbe was discovered from DNA in Arctic sea floor sediment. The new microbial phylum may be the closest living relative to an ancestral cell that swallowed a bacterium and began the journey to a more complicated cellular world—including us!

Species We Barely Know

(Video still courtesy the NOAA Office of Ocean Exploration and Research, 2015 Hohonu Moana)

New ocean species get discovered on a regular basis and it’s hard to know just how many species there are still waiting in the depths. No wonder, when even old friends can be hard to find. A rare squid mugged for the camera, and for the first time since its discovery 30 years ago, we caught a glimpse of the enigmatic fuzzy nautilus. Some creatures help us by lighting the way—fluorescent animals were everywhere in the news this year. A glowing sea turtle wowed us, followed by brightly lit eels and deep-sea sharks.

And that’s just the tip of the iceberg. Some species are so new to science they don’t even have names yet: What might be the world’s cutest octopus laid nine eggs for scientists and just might wind up being called Opisthoteuthis adorabilis.

A New Hope

(Reinhard Dirscherl/Corbis)

Last, but certainly not least, there was some major movement forward this year in the realization that we must work together to preserve our planet and its seas.

Pope Francis raised the environmental alarm with his encyclical in June that urged individuals and governments to take action. The document specifically called out melting sea ice, ocean acidification and coral reef biodiversity, among other ocean issues. His call to action may be the push needed.

The Pope continued this call as the United Nations’ Climate Change Conference—or COP21—occurred in Paris this December. The negotiations were successful, and the groundbreaking document that resulted calls for keeping the increase in global average temperature “well below 2 degrees Celsius [3.6 degrees Fahrenheit]” through reductions in fossil fuel emissions. Even better, despite being initially ignored, the oceans are now included in the agreement by name.

And it’s not just the climate front that is seeing progress. Chile, Palau, New Zealand and the U.K. all expanded the ranges of their surrounding oceans that are fully protected. In Palau, this amounts to a whopping 80 percent of its territorial waters. The U.S. is also expanding its marine sanctuaries, approving the first new sites to be designated in 15 years. 

(GIF by Smithsonian Ocean Portal)