While it seems that we can find just about anything on the Internet, it doesn’t mean we know everything yet. Every year, Smithsonian scientists discover many new species around the globe and even in their own backyards.

Let’s take a look at some of this year’s interesting newcomers from the animal kingdom, found by our very own Smithsonian scientists. Scroll through to meet them.

1. Poison dart frog from Panama

If you had the chance to name a poisonous species, would you name it after your wife? That’s what Smithsonian Tropical Research Institute researcher Marcos Ponce did when he and his team discovered a bright orange poison dart frog in Donoso, Panama. His wife, Geminis Vargas, was the inspiration for the new species, Andinobates geminisae, “for her unconditional support of his studies of Panamanian herpetology.” Read more…

Andinobates geminisae (Photo: Brian Gratwicke)

2. Dragon-like mite

This new species has a face only a mother could love. But when you aren’t looking for a mate it doesn’t matter if you are attractive. Osperalycus tenerphagus, less than a millimeter long, has evolved an all-female lineage. No males and no mating. They lay eggs that don’t need to be fertilized, making little clones of themselves. The species was discovered in Ohio by Samuel Bolton, an entomologist and fellow at the Smithsonian’s National Museum of Natural History and researcher at Ohio State. Read more…

The front end of Osperalycus tenerphagus showing three of its legs and the unusual structure of its skin. (Photo courtesy Samuel Bolton)

3. Bolivia’s golden bat

Whether or not you like bats,, you can’t deny this new species is golden. Myotis midastactus, is just one of more than six species described by Ricardo Moratelli, a scientist at the Oswaldo Cruz Foundation (Brazil) and post-doctoral fellow at Smithsonian’s National Museum of Natural History. Read more…

Adult female of “Myotis midastactus” captured at Noel Kempff Mercado National Park, Department of Santa Cruz, Bolivia. Ricardo Moratelli and Don Wilson, mammalogist at the Smithsonian’s National Museum of Natural History recently named this bat as a new species. (Photo courtesy Marco Tschapka)

4. Armored catfish from Colombia

Farlowella yarigui is a new species of stick catfish from South America, so called because the thin, elongated bodies of these fish mimic sticks. About 5 inches long, it lives on the bottom of clear-running streams among partially submerged vegetation and sticks. This discovery by Gustavo Ballen from the Smithsonian Tropical Research Institute represents the first and only species of its genus found living in the Magdalena River basin, west of the Andes Mountains in South America. Read more…

“F. yarigui” belongs to a subfamily of armored catfish and is covered in bony plates that protect it from predators, such as birds and predator fishes.

5. Poppy pollinating fly

The new fly, named Sericomyia khamensis, mimics the bumble bee to fool predators into leaving it alone. Found in the highlands of southern China by Christian Thompson, an entomologist at the Smithsonian’s National Museum of Natural History, these flies are pollinators of the yellow poppy (Meconopsis integrifolia). Like bees, the female flies visit yellow poppies to drink nectar, but unlike their fellow pollinators they also eat the poppy pollen on the spot. Read more…

“Sericomyia khamensis,” a newly discovered flower fly from China

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Ornate Fruit-Dove (Photo: Bruce Beehler)

The genomes of modern birds tell a story of how they emerged and evolved after the mass extinction that wiped out dinosaurs 66 million years ago. But the family tree of modern birds has confused biologists for centuries and the molecular details of how they arrived at more than 10,000 species is barely known.

Now that story is coming to light, thanks to an ambitious international collaboration underway for four years that has sequenced, assembled and compared full genomes of 48 bird species. The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 23 papers — eight papers today, Dec. 12, in a special issue of Science and 15 more in Genome Biology, GigaScience and other journals. The full set of papers in Science and other journals can be accessed by clicking this link www.sciencemag.org/content/346/6215/1308.full

Led by Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, Erich D. Jarvis of Duke University and the Howard Hughes Medical Institute and M. Thomas P. Gilbert of the Natural History Museum of Denmark, the consortium focused on species representing all major branches of modern birds including the crow, duck, falcon, parakeet, crane, ibis, woodpecker and eagle.

Red bellied woodpecker (Photo by Ken Thomas)

The Avian Phylogenomics Consortium has so far involved more than 200 scientists from 80 institutions in 20 countries, including the BGI in China, the University of Copenhagen, Duke University, the University of Texas at Austin, the Smithsonian Institution, the Chinese Academy of Sciences, Louisiana State University and many others.

This first round of analyses suggests some remarkable new ideas about bird evolution. The first flagship paper published in Science presents a well-resolved new family tree for birds, based on whole-genome data. The second flagship paper describes the big picture of genome evolution in birds.

Six other papers in the special issue of Science describe how vocal learning may have independently evolved in a few bird groups and in the human brain’s speech regions; how the sex chromosomes of birds came to be; how birds lost their teeth; how crocodile genomes evolved; ways in which singing behavior regulates genes in the brain; and a new method for phylogenic analysis with large-scale genomic data.

The new family tree resolves the early branches of Neoaves (new birds) and supports conclusions about some relationships that have been long-debated. For example, the findings support three independent origins of waterbirds. They also indicate that the common ancestor of core landbirds, which include songbirds, parrots, woodpeckers, owls, eagles and falcons, was an apex predator, which also gave rise to the giant terror birds that once roamed the Americas.

The whole-genome analysis dates the evolutionary expansion of Neoaves to the time of the mass extinction event 66 million years ago that killed off all dinosaurs except some birds. This contradicts the idea that Neoaves blossomed 10 to 80 million years earlier, as some recent studies suggested.

Based on this new genomic data, only a few bird lineages survived the mass extinction. They gave rise to the more than 10,000 Neoaves species that comprise 95 percent of all bird species living with us today. The freed-up ecological niches caused by the extinction event likely allowed rapid species radiation of birds in less than 15 million years, which explains much of modern bird biodiversity.

(Visit Science to learn more.)

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Bright orange with a distinctive call the Panamanian poison dart frog Andinobates geminisae lives in only a small area of the Caribbean Coast of Panama. It was discovered and named just a few months ago yet scientists already fear for its future from habitat loss, pet-trade collectors and chytrid fungus—a deadly disease that is decimating frog populations across the globe.

“Andinobates geminisae” (Photo: Brian Gratwicke)

At the Smithsonian’s National Zoo Brian Gratwicke leads the Panamanian Amphibian Rescue and Conservation Project, a modern-day Noah’s Ark that is attempting to save endangered frog species from chytrid by raising and breeding captive populations. Gratwicke answers a few questions about the Amphibian Rescue Project and if A. geminisae might become its newest member.

Q: How do you decide to add a new species to the Amphibian Ark?

Gratwicke: We have about 12 different species now in the Amphibian Rescue and Conservation Project and our goal is to grow that to about 20. To add a new species like A. geminisae we’d need to collect at least 10 males and 10 females to be represented in its first captive generation. For species that are difficult to breed we might need to collect more animals than that to ensure that we can maintain a genetically healthy captive population.

So that’s one big unknown; A. geminisae is a fairly rare frog and we don’t know if we will be able to find more. Maybe they have already declined from chytrid, which can happen rapidly. We’ve run into a situation before where we found three frogs of a species that is highly sensitive to chytridiomycosis on our first trip, and after going back numerous times, never saw any ever again.

Limosa harlequin frogs are among the 12 frog species currently in the Amphibian Rescue Project. (Photo by Brian Gratwicke)

But before we add a species to the Amphibian Rescue Project and devote the resources and staff necessary to care for it, we also need to be in a position to make a really informed decision about adding it. So, we first try to make as many natural history observations about a potential candidate as we can. With A. geminisae we are not sure what its susceptibility is to chytrid. It seems to be a fairly terrestrial frog [chytrid is a water-borne fungus] and we are not even sure if chytrid will kill them.

We also need to figure out what environmental cues a frog needs to reproduce, where it reproduces and what habitat might be limiting for reproduction. For some species we may also turn to people who keep similar species as pets to learn about successful husbandry practices and what they have done to rear them successfully. There are a fair number of Andinobates in the pet trade because they are really attractive little frogs.

So, right now our real priority is to learn a little more about this species and whether we can breed it in captivity.

Q. Are pet-trade collectors a problem for frogs?

Gratwicke: Because of its color A. geminisae might be attractive animal to collectors. Once people know where it is some will certainly go looking for it. Panama has few collectors but they could have an impact when they harvest frogs from a very small population. For example, Panamanian golden frogs were once found in Cerro Campana National Park in Panama, but they were totally collected out of that locality, even before chytrid became an issue.

Brian Gratwicke swabs a frog in the field to test it for the deadly chytrid fungus. (Photo courtesy Brian Gratwicke)

Q. If chytrid is here to stay, what is the ultimate plan for the frogs in the ark?

Gratwicke: The ultimate plan for our existing collection is to develop some tools that we might use to help these frogs resist chytrid infection, and then reintroduce frogs that are less susceptible to the disease back into the wild. We’ve been actively researching the frog’s skin microbiome, with the hope that we could treat susceptible frogs with beneficial skin bacteria that might protect them from fungal infections, but it has proven much more difficult to manipulate the frog skin microbiome than we anticipated.

We also have been looking at the immune response of frogs to chytrid fungus and we’ve found that some frogs have very strong immune response as measured through their transcriptomes. Basically each cell has a nucleus full of DNA that is converted to RNA before making the proteins that govern cell function. So when we do a transcriptome analysis we are reading the RNA that is actually giving orders to all of the organelles to make various different kinds of proteins and ultimately get a glimpse of the genes being expressed at a single moment in time in any particular tissue.

So let’s say we actually find a frog that manages to resist a chytrid infection. We’d look to see if this group has a different genetic signature than the non-chytrid resistant group. Our ultimate aim would be to understand the frog’s immune response to chytrid infection so that we could help give them a leg up in the battle against chytrid.

“Atelopus certus,” lives Cerro Sapo (or Toad Mountain) in the Darien Region of eastern Panama, and is one of the most strikingly colored or all harlequin frogs. This species is in the Amphibian Rescue Project. (Photo by Brian Gratwicke)

Q. How long do these frogs live and are they breeding well?

Gratwicke: A frog’s lifespan depends on the species. Some species like the La Loma tree frog seems to be really short lived. The oldest frog of this species we’ve had in captivity has lived about 5 years, but on the other hand Panamanian golden frogs can live for more than 15 years!

All the frogs in our Amphibian Rescue Project pods are wild-collected founding members or their first generation offspring. Our goal is to breed all of the founders as quickly as possible. We don’t want to begin breeding a second generation until we have as many of the founders bred as we can. This way we capture as much of the genetic diversity of our founders before those animals die. If they die without being bred, they’re gone forever, so we are really racing against the clock.

Q: Are there things you can do to get captive frogs in the mood to mate?

Gratwicke: Yes, there are a lot of different potential cues to get a frog, male and female, into breeding condition. For certain species we’ve tried making it rain, we tried a simulating misting system, we tried making waterfalls, we played calls back to them at night, we tried giving them a little bit of light, we tried giving them no light, we tried giving them all different kinds of food.

Nutrition is important; you’ve got to have an animal in a really positive nutritional space before they can expend energy on reproduction. For our harlequin frogs, we breed them a special kind of moth larva that has a high fat content and we give them to the females to get them to start producing eggs.

Q: What other measures are being taken to save these frogs?

Gratwicke: We’re also doing some research to see if we can freeze frog sperm and we have pretty good results coming out of that program right now. So hopefully we could actually freeze frog sperm of all of our male founders that are not yet represented in captivity, so that if they do die before they are actually breed we can still have a plan B. Frozen sperm is kind of an insurance policy. Researchers have been trying to do this for many years and have largely failed, because frog sperm is activated in a frog’s urine and once activated it is really hard to cryopreserve, and then thaw.

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Newly hatched Cuban crocodile (Photo by Barbara Watkins, Smithsonian’s National Zoo)

The challenges of conceiving only get greater as we get older. But if you have some of the most prized genes within your entire species, then the pressure is really on.

The Smithsonian’s National Zoo is home to one of the oldest female Cuban crocodiles in captivity. For most of her life she has been a rather reluctant member of the North American breeding program tasked with ensuring the survival of her critically endangered species. However biologist Matthew Evans from the Smithsonian’s National Zoo’s Reptile Discovery Center is not about to give up on her just yet.

“She has not successfully mated or shown an interest in nest building while at the National Zoo. As she approached her mid-50s we almost gave up on her as an animal we would ever get to breed. This would have been really disappointing as she is very important genetically to the species,” explains Evans.

Cuban crocodile (Photo Credit: Smithsonian’s National Zoo)

But in 2012 Evans and the Zoo team saw a remarkable change in her behavior when they altered her diet and increased her activity.

“After we began introducing some basic training and enrichment into her normal routine she became interested in the male in mating season and began fighting with a rival female. Crocodiles are highly intelligent creatures and it seems the increased interaction we had with her got her a little more energized and active. We ended up with two male offspring from her that season and we are hoping to try again this breeding season.”

The value in this reluctant mother’s genes lies within their lack of representation in the species studbook — a giant list of who is breeding with whom among Cuban crocodiles held in captivity at zoos and parks across North America. With only two offspring to represent her genes into the future, the team of geneticists tasked with maintaining genetic diversity in the population are keen to get more babies from the National Zoo’s sexagenarian mother.

At approximately 60 years of age however, Evans concedes that the crocodile’s best reproductive years are probably over.

“Last year we got a clutch of eggs from her but a lot of the eggs she produced were not fertile. It could be an issue with the male, as he is also older, or it could be an issue with her age. Out of a clutch of 30 we would only get three or four eggs that might be fertile. Even then a lot of things can go wrong during incubation. Some embryos just stop developing for unknown reasons,” explains Evans.

With crocodilian species living up to 75 years in captivity, Evans and his team may have a few more years for breeding success. While zoos and crocodile farms are breeding Cuban crocodiles with the aim that someday they might join their wild relatives, that dream is still out of reach.

Habitat for this species is dwindling, with the 3,000 to 6,000 Cuban crocodiles left in the wild restricted to only two swamp habitats in Cuba. Widespread destruction of wetlands for agriculture, heavy hunting pressure, and the introduction of the common caiman (Caiman crocodilus), which compete for food and space, have all contributed to the Cuban crocodile’s decline. So for now, until there is more habitat in their homeland, the captive Cuban crocodiles will continue to find romance with a little human help.

Video provided by Smithsonian National Zoo

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Yellowstone National Park is one of the world’s most protected ecosystems. But that’s still not enough to keep its grizzly bears completely safe. Click here for show times of Smithsonian Channel’s “Mass Extinction: Life at the Brink.”

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Black vultures (Flickr photo by e_monk)

A new study of microorganisms living on the skin and in the intestines of North America vultures (black and turkey vultures) has turned up a remarkable find. The large intestines of these birds are dominated by two groups of flesh-digesting bacteria toxic enough to kill a human and most other birds and animals.

The discovery suggests that millions of years of eating decaying, contaminated flesh have not only given vultures a strong tolerance to bacterial toxins, but that these birds have perhaps harnessed the decaying power of pathogenic bacteria, allowing vultures to absorb more nutrients from the food they eat.

Such a mutualistic, co-evolutionary relationship between vultures and bacteria probably evolved over millions of years, says Gary Graves, a Smithsonian ornithologist who is a co-author of the study published today in the journal Nature Communications.

Turkey vulture (Flickr photo by George Lamson)

“In birds, scavenging is an old profession. From an evolutionary perspective vultures branched off from hawks and eagles millions of years ago,” Graves says.

The benefit the bacteria receive from this arrangement, the scientists theorize, is that it gives them “a uniform, stable environment in which to live,” Graves adds. “Vulture chicks are fed by regurgitation. Whatever the adult has on its face and in its crop is transferred to the baby. This chain has likely been perpetuated for millions of years.”

Conducted by scientists at the University of Copenhagen, the Copenhagen Zoo, the Technical University of Denmark, the Smithsonian’s National Museum of Natural History and Aarhus University, the study’s aim was to document all of the bacteria and other organisms that live on the face and in the guts of both black and turkey vultures in North America. In particular, the scientists wanted to investigate how vultures survive eating carrion. The team took swabs from the faces and throats and extracted samples from the hind guts of 25 turkey vultures and 25 black vultures in Nashville, Tenn.

Turkey vulture, left; Black vulture, right. (Flickr photo by Dave Govoni)

A second discovery made during this study is that the vulture stomach is an extremely harsh chemical environment that acts as a strong bacterial filter, killing a majority of the bacteria the vultures consume. On average, the scientists found 528 different types of microorganisms living on the vultures’ faces, yet only 76 of these made it through to the large intestine. It appears that only bacteria species that have adapted to survive the harsh conditions of the vulture’s stomach acid are able to colonize and thrive in their lower intestines.

Clostridia and Fusobacteria, the anerobic bacteria that dominate the vulture’s guts, most likely originate from physical contact with food sources or from soil clinging to the carcasses, the scientists say. To eat, a vulture will frequently place its head inside a carcass and often eats meat contaminated with feces.

“It looks like some sort of competition is going on between Clostridia and Fusobacteria in the vulture gut,” Graves observes. “Both occur in high abundances so they tolerate one another and dominate all other bacteria in the gut.”

A black vulture. On average, the scientists found 528 different types of microorganisms living on the faces of vultures in the study. (Flickr photo by Phil)

“Vultures are nature’s disposal unit. They are cleaning up the environment. They are an unpaid sanitation service that cleans up almost all of the small and mid-sized carcasses in the United States,” Graves adds.

DNA from a majority of large-bodied mammalian families found in the vicinity of Nashville was found on the vulture’s faces including rabbit, dog, deer, opossum, skunk and raccoon. One vulture had human DNA on its face and hindgut sample, the result of lab contamination or eating sewage, the scientists speculate. DNA detected on the facial samples however was absent from the majority of the vulture gut samples, further indication of the harsh chemical environment inside the vulture stomach.

“This study is a kind of first scratch at the surface of a larger mystery,” Graves says. “The next step is we need to do more work on identifying and documenting exactly what pathogenic strains of bacteria are in these intestines and to find out how virulent these things are. We also need to find out if they are biologically active when the vultures expel them. It’s one thing to have these bacteria in the vulture’s intestine but are they active in the environment after they leave the birds, and how?”

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Bleached coral off the coast of Panama.

A new study by Florida State University and Smithsonian Institution biologists shows that bleaching events brought on by rising sea temperatures are having a detrimental long-term impact on coral.

Bleaching—a process where high water temperatures or UV light stresses the coral to the point where it loses its symbiotic algal partners that provides the coral with color—is also affecting the long-term fertility of the coral the scientists reveal in the latest issue of Marine Ecology Progress Series.

Don Levitan and William Boudreau of Florida State University; Javier Jara from the Smithsonian Tropical Research Institute in Panama, and Nancy Knowlton from the Smithsonian’s National Museum of Natural History are co-authors of the study.

Most corals reproduce by releasing sperm and eggs into the ocean during brief annual spawning events. The chance of sperm finding and fertilizing an egg depends on corals spawning in close proximity and in synchrony with each other.

In a study of the corals that build the major framework of Caribbean coral reefs, the team found that the species living in shallower water experienced near total reproductive failure, while the species living in deeper water were about half as likely to spawn.

“The remarkable finding from this study was that the reduction in spawning persisted for three additional years, long after the corals had regained their symbiotic partners and regained their normal appearance,” says Levitan, chair of the Department of Biological Sciences at Florida State. “Even corals that didn’t bleach aren’t reproducing at the levels they should.”

The worldwide decrease in coral abundance in combination with long-term reductions in spawning and reproduction following bleaching events put reef- building corals in a difficult situation. Eggs might be released, but never fertilized. And that could have a major impact on the ecosystem at large.

Levitan and other researchers been studying coral just off the coast of Panama since 1996. Since then, those corals have been exposed to two bleaching events. On average, it takes coral three to four years to recover from bleaching.

“Even if we can fix what’s killing these corals, it’s going to be hard for coral populations to recover, because the surviving corals might not successfully produce enough offspring to repopulate reefs,” Levitan said.

Coral reefs provide protection and shelter for many different species of fish. Without the reefs, certain fish are left homeless and without an area to reproduce. They also protect coastlines from large waves and flooding, a major issue in areas that are prone to tropical storms or hurricanes.

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When two red panda babies are born in critical condition at Smithsonian’s National Zoo, caretakers make the crucial decision to raise them by hand.

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“Sericomyia khamensis,” a newly discovered flower fly from China

Scientists studying pollinators of the yellow poppy (Meconopsis integrifolia) in the highlands of southern China have discovered a striking new species of flower fly that mimics the bumble bee. The new fly, named Sericomyia khamensis, has evolved to resemble a bumble bee as a way to fool predators into leaving them alone.

Like the bees, the female flies visit yellow poppies to drink nectar, explains Christian Thompson, an entomologist at the Smithsonian’s National Museum of Natural History. Unlike the bees they also eat the poppy pollen on the spot. Protein in the pollen is used for egg production in the female fly. Bees take flower pollen back to their nest where it is used to feed their larvae.

A yellow poppy, “Meconopsis integrifolia,” growing on Balang Mountain, Shihuan, China (Flickr photo by Autan)

Male flies visit the flowers to drink nectar and mate with the females. “The nectar gives them a sugar boost similar to what we get from Coca-Cola or other sugary drinks,” says Thompson, co-author of a paper describing the new fly in the journal Zootaxa. The new species is one of a number of Sericomyiine flower flies known to live in China that belong to a group of bee-mimicking flies.

Female flies lay their eggs in small pools of standing water where they hatch into aquatic maggots with long tails, known commonly as rat-tailed maggots. “These larvae are very common in tree holes that fill up with water and/or in plants like pitcher plants, where water collects,” Thompson says.

A respiratory apparatus located at the end of the maggot’s long tail sticks above the surface of the water and allows the maggot to graze on the bottom of a pool and breathe at the same time.

It is not known if this newly discovered fly pollinates other species of flowers, Thompson says. “We do know of a related species in North America–another flower fly–that only visits blueberries. This fly is very important to the pollination of wild blueberries.”

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Map of known dead zones (white dots) and predicted changes in annual air temperature for 2080-2099 versus 1980-1999. The air temperature predictions are based on a “middle-of-the-road” scenario of fossil fuel use. (Credit: Keryn Gedan and Andrew Altieri)

A full 94 percent of the dead zones in the world’s oceans lie in regions expected to warm at least 2 degrees Celsius by the century’s end according to a new report from the Smithsonian Tropical Research Institute and the Smithsonian Environmental Research Center published Nov. 10 in Global Change Biology. The paper states that warmer waters—mixed with other climate change factors—make for a dangerous cocktail that can expand dead zones.

Dead zones form in waters where oxygen plummets to levels too low for fish, crabs or other animals to survive. In deeper waters, dead zones may last for months, as with the annual summer dead zone in the Chesapeake Bay. Temporary dead zones may occur in shallow waters at night. The largest dead zones in the Gulf of Mexico and Baltic Sea can cover more than 20,000 square miles of the sea floor. The number of dead zones across the world is growing exponentially, doubling each decade since the 1960s.

“They’re having a big impact on life in the coastal zone worldwide,” said Keryn Gedan, a co-author and marine ecologist at the Smithsonian Environmental Research Center and the University of Maryland. “A lot of people live on the coast, and they’re experiencing more fish kills and more harmful algal blooms. These are effects of dead zones that have an impact on our lives.”

Dead juvenile menhaden fish (Brevoortia tyrannus) float to the surface during a dead zone event in Narragansett Bay, Rhode Island. (Credit: Andrew Altieri/Smithsonian Tropical Research Institute)

The main culprit is massive algal blooms, which pull oxygen from the water when they respire or decompose. Algal blooms form from excess runoff of nutrients like nitrogen and phosphorus. But climate change could exacerbate the problem.

Warmer waters hold less oxygen, the authors explain in the paper, enabling dead zones to form more easily. When temperatures rise, animals like crabs, fish and oysters need even more oxygen, which the ocean is less able to provide.

“Our study is the first to consider more than a dozen direct and indirect effects of climate change on dead zones, and suggests that we’ve underestimated its contribution to the growing dead zone problem and impacts on marine life,” said Andrew Altieri, the study’s lead author and ecologist at the Smithsonian Tropical Research Institute.

Altieri and Gedan looked at a database of more than 400 dead zones around the world and then overlaid them on a map of the annual temperature anomalies expected to occur in each region. Under a middle-of-the-road scenario, 94 percent of dead zones are in areas expected to warm by 2 degrees C or more by 2099. Then they did a thorough literature review, synthesizing information from many fields to predict how the various effects of climate change could work together to impact dead zones.

Piles of mussels (“Mytilus edulis”) washed onto a beach after a dead zone event in Narragansett Bay, Rhode Island. Besides providing food and habitat for other creatures, mussels can also filter water. When mussels die, the bay loses its ability to clear water of phytoplankton, increasing the risk of future dead zones. (Credit: Andrew Altieri/Smithsonian Tropical Research Institute)

Besides making it harder for water to hold oxygen, rising temperatures stifle ocean mixing that can keep dead zones in check. Dead zones near the bottom can dissipate if waters from the surface sink, injecting them with fresh oxygen from above. But since warmer waters float, this life-giving conveyor belt grinds to a halt.

Other factors besides temperature come into play. Sea-level rise leads to the expansion of bays and estuaries, raising the overall volume of water susceptible to low oxygen. The same rising waters also can destroy wetlands. Wetlands are one of the best defenses against dead zones because they filter out excess nutrient pollution that feeds massive algal blooms.

Shifting ocean currents could further expand dead zones by flooding them with more oxygen-starved waters. This is already happening in the St. Lawrence Estuary where cold, oxygen-rich waters from northern Canada have declined and are being replaced by warmer, oxygen-poor waters from the central North Atlantic.

Altieri and Gedan uncovered just one possible positive impact of rising temperatures: Since animal metabolism spikes under higher temperatures, tiny crustaceans, like copepods, and other zooplankton could eat up the algal blooms that create dead zones in the first place. “We do see some cases where algal blooms are smaller in warmer years, because the grazers are able to control algae better,” Gedan said. But, she added, it is unclear how that will interact with the other climate change impacts they have witnessed.

Altieri suggests there is an important lesson to learn from their study: “There is a lot of inertia when it comes to global climate change, but we can counteract climate effects on dead zones through local control of nutrient pollution.”

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Ever wonder why only male peacocks have such extravagant plumage? We ask caretaker Gwendolyn Cooper at Smithsonian’s National Zoo to explain.

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Swainson’s warbler (Gary Graves photo)

When Gary Graves cranks up his boom box and drives remote back roads through pine plantations in Texas, Louisiana and other southern states, a few locals often emerge just looking for a fight. “If they are in there, they’ll come out,” Graves observes. “When I turn it off they calm down a little bit. Then they start singing.”

Graves, an ornithologist at the Smithsonian’s National Museum of Natural History, is referring to one of North America’s rarest songbirds, the Swainson’s warbler (Limnothlypis swainsonii). Highly territorial, male warblers come out to defend their turf when they hear the song of another male on Graves’ boom box. This method of drawing them out is nearly the only way Graves, or anyone else, would ever see and hear these small, secretive, olive-colored migratory birds that live and breed in dense underbrush.

The global population of Swainson’s warblers is estimated at about 90,000, a low number attributed to the loss of breeding habitat in the U.S. and wintering habitat in Mexico, Cuba and Jamaica. After studying and surveying Swainson’s warblers across the South for more than two decades, Graves reports something remarkable today in the journal Bird Conservation International. Since the 1990s Swainson’s warblers have been establishing dozens of new breeding populations in industrial pine plantations across 10 different Southern states from Texas to Virginia.

Gary Graves examining the type specimen of the Swainson’s warbler in the collections of the Division of Birds in the  Smithsonian’s National Museum of Natural History. (Photo by Donald Hurlbert)

Unlike natural forests with many different tree species of many different ages, pine plantations are monocultures of one species, all the same age and size and planted in evenly spaced rows. They were once described as biological deserts.

“Pine plantation forests are a new ecosystem that didn’t really exist before the 1920s in the southeastern United States,” Graves explains. “They represent a fundamentally new wildlife habitat.”

Millions of acres of these industrial pine forests stretch from Texas to Virginia and are on a harvesting cycle of 25 to 35 years before they are cut. “They are the backbone of a $210 billion forest industry in the United States that keeps us in lumber for our houses, products from toilet paper to notebook paper and even woodchips to mulch your lawn,” Graves explains.

A surprising plasticity

Once thought to nest only in lowland canebrakes in North America, Swainson’s warblers are now known to also nest in a variety of broadleaf forest environments. The fact that this species is now establishing breeding populations in plantation pine forests reveals a surprising plasticity in its ability to select new habitats, Graves says. This behavioral trait is one not shared by the endangered Kirtland’s warbler (Setophaga kirtlandii) of Michigan’s jack pine forests which has rigid nesting requirements of small trees and open areas; or the Bachman’s warbler (Vermivora bachmanii), thought to be extinct, which was restricted to the swamps and lowland forests of the southeast United States.

A singing male Swainson’s warbler (Photo by Gary Graves)

“Behavioral plasticity in habitat selection may explain why Swainson’s warbler has survived two centuries of intense forest clearing and habitat alteration, while Bachman’s warbler has become extinct,” Graves says.

Swainson’s warblers find pine plantations attractive for nesting only during a specific stage in the forest’s development, when the pines mimic the early successional broadleaf habit these birds have traditionally used for breeding. Once the plantation pines reach about 20 feet high, the understory achieves a high-stem density and screening at about desk height that the Swainson’s warblers prefer. This condition persists for about 7 to 8 years, until the trees reach about 40 feet high and 15 years old. After that, the understory density thins out and the warblers disappear.

Learning to like a new place

There may be some type of behavioral learning, in the warblers’ transition to the pine plantations, Graves observes. “But its only been happening for the last 25 years and it appears to be accelerating. Sometimes we see these behavioral shifts in animals but we don’t know the mechanisms of why. These birds are just learning to like a new place. Sometimes these changes can evolve quite rapidly within a dozen generations, and the generation time of these birds is just one year.”

Most plantations occupied by Swainson’s warblers have a certain weediness, namely broadleaf saplings, vines and shrubs growing along the edges of roads and streams crossing the forests. (Photo by Gary Graves)

Swainson’s warbler breeding pairs require large territories of between 10 to 20 acres, which the pine plantations provide. Most warbler territories observed by Graves occurred in plantations planted on sandy loam soil, with normally low water tables, he says. “These pine forests may be creating a microhabitat at ground level where the birds feed on insects in the leaf litter, maintaining humidity and allowing them to live on dryer soils then they have traditionally.” Also, Graves observed, most plantations occupied by Swainson’s warblers had a certain “weediness,” associated with them: namely broadleaf saplings, vines and shrubs growing along the edges of roads and streams crossing the forests.

Covering some 40 million acres in the U.S. today, southern pine plantations are projected to increase to 66 million acres by 2060, Graves points out in his paper. “Given the 25 to 35 year rotation cycles commonly prescribed for private and commercial plantations, and a 7 to 8 year window of habitat suitability for Swainson’s warblers in a typical stand,” roughly one quarter of these pine plantations will be suitable habitat for these birds at any given time, provided that other requirements such as deciduous weediness and soil moisture are met, Graves concludes. “If current distributional trends continue, forestry lands managed for short rotation pine plantations will soon support a majority of the global Swainson’s warbler breeding population.”

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Mammal survey field assistant Megan Banner holds a dusky rice rat, “Melanomys caliginosus,” that was caught in a live trap in Costa Rica. It was later released. (Photo by Christopher Russell)

Scientists have long known that in the tropics shade-grown coffee plantations provide critical habitat for migratory and resident birds. Now a new survey conducted in Costa Rica reveals that shade coffee farms also harbor small mammals in greater species diversity and in greater numbers.

During a seven month study researchers used live traps and camera traps to survey a variety of small mammals living in three different habitats in the mountains of Costa Rica: forests, shade coffee plantations and sun coffee plantations.

A coffee farm in the mountains of Costa Rica where the survey was conducted. (Photo by S. Amanda Caudill)

“We found that both forests and shade coffee plantations had significantly more species of small mammals and in a higher abundance than sun coffee plantations,” says S. Amanda Caudill, an ecologist at the Smithsonian Migratory Bird Center of the Smithsonian Conservation Biology Institute, who led the study. One of the reasons is that shade trees may provide more food—fruit and seeds—for small mammals, Caudill explains.

“Prior diversity research on coffee plantations has been dominated by bird and insect studies,” Caudill adds. “This is one of the few studies to focus on small- to medium-sized mammals in coffee plantations.”

The study was published in a recent edition of the journal Agriculture, Ecosystems and the Environment.

This photograph snapped by an infrared camera trap shows a northern raccoon, “Procyon lotor.” (Photo by S. Amanda Caudill)

The dusky rice rat, Alfaro’s rice rat, northern raccoon, nine-banded armadillo, Mexican deer mouse, rabbits, mouse opossums, grey 4-eyed opossum and the northern tamandua were all among the 17 different species of small mammals recorded by the researchers during the survey.

Mammals clearly benefit from the increased canopy cover and vegetation complexity that shade coffee provides, Caudill says. In fact, some of the study sites showed no significant difference between forest and shade coffee for small mammals diversity.

A Robinson’s mouse opossum, “Marmosa robinsoni,” leaps from one coffee branch to the next in a plantation in Costa Rica. (Photo by S. Amanda Caudill)

On shade coffee plantations coffee shrubs are grown and nurtured beneath a canopy of tree cover. These farms are basically artificial forests devoted to coffee production and require less maintenance, pesticides and fertilizer. On sun coffee plantations the coffee shrubs are planted in the direct sun.

“Coffee is grown in what is called the ‘bean belt’ and it overlaps areas of high biodiversity which makes it a very interesting system to study, especially for biodiversity conservation,” Caudill says.

A group of field assistants gather to talk after an outing checking live traps for mammals during the rainy season in Costa Rica. (Photo by S. Amanda Caudill)

“The way coffee is managed and the way that it is grown can significantly influence the biodiversity that a farm and its surrounding landscape can support.

“On a broad scale, landscape perspective, when there was a lot of sun coffee in the landscape we saw a decrease in small mammal abundance and richness in the entire landscape.”

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Each year, a mysterious group of night herons flock to Smithsonian’s National Zoo. Then, they vanish. In episode three of our series, we go behind the scenes with the zoo’s caretakers as they investigate why.

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The shell of this nautilus at the Smithsonian’s National Zoo clearly shows the deformity–area characterized by black bands–that started after it began living in an aquarium. (Photo by Mehgan Murphy)

In the wild, wide milk chocolate-brown stripes adorn the beautiful smooth, white shells of the chambered nautilus, a deep-diving mollusk from the Indo-Pacific Ocean. But when placed in an aquarium, the new surfaces of shell these animals produce become thick, rough and stripped with a black substance. Why this ugly deformity occurs is a mystery that aquarists have puzzled over since the 1970s.

“We wondered if they are not getting something in their diet in aquaria or if something in the water is not available to them,” explains Alan Peters, a curator at the Smithsonian’s National Zoo in Washington, D.C.  “Aquarists have long known that in an aquarium the normal pattern of the nautilus’ shell never fully returns.”

This scanning electron microscope image (top) shows the orderly crystalline structure in a wild formed Nautilus. The disorderly crystalline structure of the aquarium-formed shell is at bottom.

Calling upon a variety of scientific techniques, including stable isotope mass spectronomy, scanning electron microscopy, micro X-ray fluorescence and X-ray diffraction, a team of researchers including Peters recently took a close look at this shell deformity. Using the shells of nautiluses that had first lived in the ocean and then been placed in an aquarium they carefully examined and compared the chemical and physical structure of portions of both the old and new shell.

What they first found under a scanning electron microscope was that the crystalline structure of aquarium-formed shell was less ordered, poorly defined and without a clearly defined shape or form.

Next, chemical analysis revealed that the black deposits in aquarium-produced shell contain excess amounts of copper, zinc and bromide and decreased amounts of calcium and magnesium.

High amounts of copper, zinc and bromide “point to the role that proteins play in the construction of the shell,” and do not appear related to diet or tank-water chemistry, Peters and colleagues write in a recent paper in the journal Zoo Biology.

When a nautilus is removed from its natural environment and placed in an aquarium, it experiences “environmental stress such as changed pressure, temperature and ultraviolet light patterns.” That may trigger an attempt to reinforce their aquarium-formed shell, compensating for a weakened crystalline structure.

The shell of this aquarium-living nautilus clearly shows the difference between its wild-produced and captive-produced shell. (Flickr photo by Michael Bentley)

In the end, the scientists were unable to reach a conclusion as to just what what causes a nautilus shell to deform in an aquarium. “We have all kinds of theories,” Peters says “but so far we are unable to confirm any of them.” The researchers next plan to conduct experiments measuring the impact of temperature and light on the production of black areas of shell, as well as the function of proteins in wild vs. captive  shell production.

Nautiluses appeared on earth about 500 million years ago during the Cambrian Explosion—they were jet-propelling themselves through ancient seas 265 million years before dinosaurs inhabited the Earth. They have remained mostly unchanged for millions of years.

Today the animals are characterized by experts as being on the “knife-edge” of extinction, overfished across their range because of their beautiful shells. A recent survey by the U.S. Fish and Wildlife Service disclosed that the U.S. imports some 100,000 nautilus shells each year. Their numbers in the Philippines have dropped by 80 percent since the 1980s. International trade sanctions against the capture and trade of the nautilus are virtually nonexistent.

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