A Blog by

Why It’s Crucial the New Superbug Was in a Urinary Tract Infection

Escherichia coli bacteria live in the intestines of humans and are a common cause of urinary tract infections.
Escherichia coli bacteria live in the intestines of humans and are a common cause of urinary tract infections.
Janice Haney Carr, Centers for Disease Control and Prevention

The alarm over the arrival of a grave new superbug in the United States is obscuring part of the story that is crucial to understanding what might happen next. Here it is: The woman who was carrying an E. coli containing resistance to the last-resort antibiotic colistin went for medical care because she had what felt like a routine urinary tract infection, a UTI for short.

The discovery of colistin-resistant bacteria is worrisome: Researchers have been watching for the arrival of this new superbug  for several months. But that it was found in  urine sample puts the discovery into a larger context. Highly drug resistant urinary tract infections happen potentially hundreds of thousands of times a year just in the United States. A small, dedicated corps of researchers has been trying for years to emphasize that these infections represent a serious danger, an unexamined conduit of bacterial resistance from agriculture and meat into the human population, and have mostly been dismissed.

Now that the new-new superbug has thrown light on the problem, will someone listen?

The Centers for Disease Control and Prevention weighed in Tuesday with a statement and a press briefing with health officials from Pennsylvania, where, last week, military researchers said they found the mcr-1 gene in an E. coli bacterium carried by a woman living there.

There are up to 8 million urinary-tract infections in the U.S. each year, and probably at least 10 percent, or 800,000, are antibiotic-resistant.

The MCR gene is important because it represents a breach in the last line of antibiotic defense: It confers protection against colistin, one of the oldest antibiotics out there, and one of the few that continues to work even against bacteria that resist multiple other drugs. Colistin was seldom used in people until recently because it is toxic, but agriculture has been using it enthusiastically for decades, which has seeded resistance through the bacterial world.

And those highly drug-resistant bacteria are turning up in urinary-tract infections. Why UTIs? Because E. coli bacteria are carried in feces, which can easily spread to the urethra and cause urinary-tract infections, especially in women. I’ve written about this several times; the long version in MORE magazine, and, even longer, in a collaborative investigation between the Food and Environment Reporting Network, the Atlantic, and ABC News.

The short version is this: Up to 8 million urinary-tract infections occur in the United States each year, and each year, a growing and significant proportion—hard to measure, but probably at least 10 percent, or 800,000—are antibiotic-resistant.

This has been happening with such frequency that it has actually changed medical practice. Medical specialty societies have been advising doctors for several years now that they should always do a test to determine which antibiotic will work for a UTI, rather than prescribing based on a standard checklist.

But only a few researchers have investigated why that tide of resistance is rising. What they have found is that these resistant UTIs infections are not random and singular, but instead constitute a focused epidemic, caused by particular sets of E. coli that bear the same resistance signatures as ones found in meat animals given antibiotics.

This idea has had difficulty gaining traction, because UTIs are usually dismissed as a minor problem, something that causes a few days of annoyance and requires a few days of antibiotics to fix. (And, not coincidentally, because they overwhelmingly happen to women.) But when UTIs go untreated—which is effectively what happens when the antibiotic administered for them doesn’t work —they climb up the urinary system from the bladder, into the kidneys, and thence into the bloodstream.

At that point, the minor problem becomes literally life-threatening. And resistant UTIs are not only a problem for the individual sufferer: They also pose the possibility of infecting others, if the original victim goes into a hospital for treatment and carries the resistant organism unrecognized in their system.

One reason it has taken so long to recognize this problem is that there is no single surveillance network that could capture all the resistance patterns in all those UTI sufferers, and compare them. There is also the problem of belief: It’s just difficult to imagine that something as minor as a UTI could be the signal of something as grave as a widespread epidemic.

Because of that, the MCR finding in Pennsylvania could end up being fortunate—no only for detecting a grave development early, but also for shining a light on a danger that has been growing, unrecognized, for a while.

A Blog by

Mapping the Creatures Living Beneath Our Feet

The ground beneath us is alive, very alive. A single gram of soil (about a fifth of a teaspoon) can contain thousands of species of bacteria, and millions of individual cells. It might also be packed with fungi, microscopic worms, and other strange creatures like tardigrades and rotifers.

A new atlas, released Wednesday at the United Nations Environment Assembly in Nairobi, attempts to map this biodiversity around the world.

“When we think about biodiversity, we usually think about plants and animals,” says Alberto Orgiazzi, a soil biologist with the European Commission’s Joint Research Centre and one of the principal authors. “But there’s a huge world of organisms under our feet.” Those organisms play important, but largely unappreciated roles in agriculture and natural ecosystems, Oriazzi says. The goal of the atlas was to drum up a little love and respect for these mostly invisible life forms among policy makers and the general public—and to convince people that they’re worth protecting.

Tardigrades are among the strangest creatures on earth. They can survive extreme temperatures and radiation, and live for 200 years.
Tardigrades are among the strangest creatures on earth. They can survive extreme temperatures and radiation, and live for 200 years.
N. Carrera, Global Soil Biodiversity Atlas

Reading it just might turn you into a soil geek. The book is an encyclopedia as much as it is an atlas, with hundreds of beautiful photographs and photomicrographs of soil-dwelling organisms, like the myriapod above (which belongs to the same taxonomic group as centipedes and millipedes).

It’s also brimming with fascinating tidbits of soil science. You know that earthy smell after a good rain? It comes from a compound called geosmin that’s made by Streptomyces bacteria and released when they die. The human nose is extremely sensitive to it. It’s the same compound that gives beets their earthy flavor.

The deepest known plant roots—223 feet (68 meters)—were discovered in the Kalahari Desert. But that’s nothing compared to nematodes: The tiny roundworms have been found 2.2 miles (3.6 kilometers) below the surface.

This map shows estimated soil biodiversity around the world, with green representing more biodiversity.
This map shows estimated soil biodiversity around the world, with green representing more biodiversity.
European Commission, Joint Research Centre

The map above is just a first attempt at mapping soil biodiversity, Orgiazzi says. DNA testing is the modern method for studying soil biodiversity, but scientists haven’t had the money or time to test every point on the globe (or anywhere close to that). So, they used statistical models that consider things like the climate and soil type and acidity to estimate biodiversity. In general, Orgiazzi says, the tropical regions richest in plant and animal life are also richest in soil biodiversity.

The researchers also tried to estimate the threats to soil biodiversity around the world, based on the best available data. You can see large swaths of red in the map below, but the reasons vary by region. In India, overgrazing is a major threat, Orgiazzi says.

Our Good Earth: Why Soil Matters Photographs by Jim Richardson, National Geographic Creative

This slideshow requires JavaScript.

In large parts of Europe, North America, and China the main threat is agriculture, especially the heavy-handed use of fertilizer and pesticides. In sub-Saharan Africa, it’s wind erosion and the threat of reduced rainfall with climate change.

The new atlas contains guidelines for protecting soil biodiversity, from less intensive farming methods to limiting erosion and controlling invasive species. The first step, though, will be getting people to pay more attention to the living world right beneath their feet.

Red regions of this map indicated the parts of the world where soil biodiversity faces the greatest threats, according to a new analysis.
Red regions of this map indicated the parts of the world where soil biodiversity faces the greatest threats, according to a new analysis.

The atlas, published by the Joint Research Centre, contains contributions from more than 120 soil experts. The digital version is freely available to download.

—Greg Miller

A Blog by

As Zika Advances, Can the U.S. Cope?

The Dallas County Mosquito Lab traps and searches through mosquitos looking for any that carry the Zika virus.
The Dallas County Mosquito Lab traps and searches through mosquitoes looking for any that carry the Zika virus.
Photograph by LM Otero, AP Images

The Zika virus that is advancing on the United States is unlike any other outbreak the country has faced, and countering it will require an effort unlike anything the U.S. and its public health infrastructure has done before.

More than 300 delegates to an emergency summit held at the Centers for Disease Control and Prevention in Atlanta—state, local and tribal officials, members of nonprofits and representatives of private companies—heard that message over and over again Friday. Scientists, political appointees, and public health experts urged them to find a way to pull together groups who seldom have a reason to communicate: health departments, academic physicians, community well-baby clinics, birth-defect surveillance programs, mosquito-control workers, even garbagemen and gardeners.

All of that expertise, they said, will be needed to prevent a disease that is carried by mosquitoes that elude spraying, infects most of its victims silently, damages fetuses in ways that are still not understood, and may not be detected until well after it has arrived.

“Nothing about Zika is going to be easy or quick,” Dr. Thomas R. Frieden, the CDC’s director, said at a press conference halfway through the all-day meeting. “The control of this particular mosquito is hard, and though we are learning a lot quickly, there is still a lot we don’t know. There is an urgent need to learn more.”

CDC Director Dr. Thomas R. Frieden addresses media during the Zika Action Plan Summit in Atlanta, April 1, 2016.
CDC Director Dr. Thomas R. Frieden addresses media during the Zika Action Plan Summit in Atlanta, April 1, 2016.
Photograph by Maryn McKenna.

The meeting, which was standing-room-only in its main sessions and watched by 2,000 people online, revealed a simmering anger over Congress refusing to authorize money to combat the disease. The Obama Administration requested an emergency appropriation of $1.9 billion in February, but no funds have been  approved; Congress recommended the White House use money from last year’s Ebola response instead.

“I understand the polarization of politics in this country; I don’t understand why children are being made the center of it,” Dr. Edward McCabe, the chief medical officer of the March of Dimes, who spoke at the summit, said in a side interview. “We know what needs to be done, and it’s not stealing fron Ebola to fix this disorder. Congress needs to do the right thing.”

The financial stress of anticipating Zika is already hitting some jurisdictions. Daniel Kass, New York City’s deputy commissioner for environmental health services, told the meeting the city has already spent $3 million preparing for Zika, without ever having a case, and expects to spend $5-6 million more. Dr. Umair Shah, executive director of public health and environmental services for Harris County, Texas, which encompasses Houston, said his county expects to spend about half that much but added: “The real challenge is a lot of our daily work has been moved to the side.”

Dr. Georges Benjamin, executive director of the American Public Health Association, said during a break that health departments may struggle because financial support for public health has been so erratic: high just after the World Trade Center attacks and the first advent of West Nile virus, then sliding, only to rise during the 2009 H1N1 flu and then fall again until Ebola arrived. “When the money goes away, the jobs go away, and you’re left without the people you need,” he said. “It’s yo-yo funding, when what we need is to build a consistent approach.”

Zika has barely touched the U.S., compared to the devastation it has wrought in South America. (See “Here’s What we Know Now About Zika and Birth Defects.”) So far, according to the CDC’s most recent numbers, 312 U.S. residents have been infected while traveling in the Zika zone, including 27 pregnant women. No one has contracted Zika from a mosquito in the mainland U.S., but 6 people have caught sexually transmitted Zika from travelers, including two pregnant women, and one person has developed Guillain-Barré paralysis. In US territories—Puerto Rico, American Samoa and the U.S. Virgin Islands—349 people have been infected by local mosquitoes and three while traveling, including 37 pregnant women.

Where Zika cases have been diagnosed in the United States as of March 30, 2016.
Where Zika cases have been diagnosed in the United States as of March 30, 2016.
Map courtesy of the CDC; original here.

Puerto Rico “could have hundreds of thousands of infections and tens of thousands of pregnant women infected,” Frieden said, but he declined to provide projections for the U.S. mainland. “We don’t want to  speculate what may happen,” he said. “We want to maximize our preparedness for what we can prevent.”

Without a vaccine, a disease-specific treatment or even a rapid diagnostic test, preventing Zika will fall on the expertise of mosquito control agencies, and summit attendees were clearly worried about the strain. (See “Disorganized Mosquito Control will Make U.S. Vulnerable to Zika.”) In some jurisdictions, mosquito control is a well-funded part of the health department. In others, personnel are so scarce that “it might be a guy who does water sampling during the day, and at night, it’s Chuck in a truck” spraying for nuisance mosquitoes, Stanton E. Cope, PhD, director of entomology and regulatory services for Terminix and president of the American Mosquito Control Association, told me.

A particular challenge, Cope added, is that existing mosquito control programs were built either to banish nuisance mosquitoes that interfere with tourism or to quell the night-biting mosquitoes that spread West Nile virus—but the Aedes species that transmit Zika bite during the day, breed in minuscule pools of water, lurk inside houses, and require different spraying equipment to dispel them and different traps to catch them so they can be tested to see whether they are carrying virus.

In a piece of irony, the CDC originated from a 1940s agency called the “Office of Malaria Control in War Areas,” and during the summit’s opening session, organizers showed a 70-year-old short movie about its work targeting Aedes aegypti, the mosquito that now spreads Zika. In the intervening decades, that insect slipped off the list of public health priorities, said Dr. Lyle Petersen, director of the CDC’s division of vector-borne diseases.

“It’s an important vector worldwide,” he told me. “It spreads dengue; there are several hundred milion cases of dengue every year. It spreads yellow fever, and right now we are having the first large urban yellow fever outbreak we have had in decades. It also spreads chikungunya. So it’s a bad actor.

“But what happened was, there’s a vaccine for yellow fever. And dengue was confined to the tropical world, and Zika wasn’t even on the horizon yet. So it became a very neglected mosquito, and now we are dealing with it again.”

A Blog by

Disorganized Mosquito Control Will Make US Vulnerable to Zika

As Zika virus advances in Central and South America, and more US residents (almost 150 so far) return from the area with infections, public health officials are braced for the next likely step: the moment when Zika passes from a traveler bearing the virus in his or her blood, to a local mosquito, and then to another person. That viral traffic has the potential to ignite Zika outbreaks in the United States in the areas where the mosquito species which carry it already flourish, across the South, in the Mid-Atlantic states and as far north as Des Moines, Cleveland and New York.

And though no one is yet talking about it publicly, that presents an enormous problem. In the United States, mosquito control — the tracking, spraying and surveillance that, in the absence of a vaccine, provides the best defense — is conducted by a crazy quilt of local districts that are dependent on cities and counties for funding and personnel. Some belong to local health departments, and others to departments of agriculture, transportation, or parks and recreation; almost none of them answer to the Centers for Disease Control and Prevention, the federal agency that directs US response to new disease threats.

When Zika arrives, that unorganized patchwork could leave the United States vulnerable to a rapidly expanding epidemic. The time that it would take to reorganize mosquito control into a coordinated system may already be running out.

CDC maps of the ranges of two mosquito species that could transmit Zika virus.
CDC maps of the ranges of two mosquito species that could transmit Zika virus.
Graphic from CDC.gov, original here.

“There are more than 700 mosquito-abatement districts in the United States, and it can be very difficult to figure out where they fit into public health,” says Joseph Conlon, a former US Navy entomologist who serves as a spokesman for the American Mosquito Control Association. “Chesapeake, Va. has its own taxing district, nothing to do with the health department. Massachusetts has seven mosquito-control districts, run by the state; so does Delaware. Florida has a government body that establishes policy, but mosquito control is done at the county level; I think they’ve got 66 local abatement districts.”

Some of those bodies, he cautioned, are as well-funded as if they were private industry: “Lee County, Fla., where Fort Myers is, has a budget of $24 million. They have 27 aircraft, more mosquito-control capability than anywhere else in the world. But other places don’t have the budget to do aerial spraying, or the capacity to do mosquito surveillance to drive their control programs. There’s not enough lab capacity, no funding for communication, which is critical.”

Al Hoffer, foreground, with Hoffer Pest Solutions, sprays for mosquitoes as homeowner Bryan Ballejo looks on in Boca Raton, Florida, February 2016. Photograph by Wilfredo Lee, AP
Al Hoffer, foreground, with Hoffer Pest Solutions, sprays for mosquitoes as homeowner Bryan Ballejo looks on in Boca Raton, Florida, February 2016. Photograph by Wilfredo Lee, AP

The uneven status of mosquito defenses is no secret among public health workers, who have been trying for several years to get policy-makers’ attention. Last year, the Association of State and Territorial Health Officials presciently wrote in a report, “Before the Swarm,” assessing vector (that is, not just mosquitoes, but ticks and other insects) control efforts:

The unpredictable nature and severity of vector-borne disease outbreaks demonstrates the urgent need for careful preparation and the incorporation of vector-control emergency-management activities into overall public health preparedness efforts. Since climate change is altering temperature and precipitation patterns across the country, it is critical that public health professionals also prepare for a potential increase in the geographic spread of existing vectors, such as Aedes albopictus or Aedes aegypti, and potentially for new vector-borne diseases.

In 2014, the Council of State and Territorial Epidemiologists examined staffing and budgets for mosquito control in state and large city health departments, comparing levels in 2012 and in 2004, the year that West Nile virus spread to all of the lower 48 states. They found dismaying drops:

  • Overall federal funding down 60 percent, from $24 million to $10 million.
  • Number of staff working at least half-time on West Nile surveillance: down  41 percent.
  • Proportion of states conducting mosquito surveillance: down from 96 percent to 80 percent.
  • States that had reduced mosquito trapping: 58 percent; states that had reduced mosquito testing: 68 percent.
  • States that had reduced testing of human patients suspected of having West Nile: 46 percent.

The group warned that lab capacity in the states, crucial for detecting which of many mosquito- and tick-borne diseases have arrived, and where they are going next, had been deprived of enough money and expertise to be unrecoverable.

Although many state public health laboratories have the capability to test for St. Louis encephalitis (79%), Eastern equine encephalitis (59%), Western equine encephalitis (39%) or LaCrosse (42%) viruses, routine testing for these viruses by state laboratories in meningoencephalitis patient specimens actually occurs much less frequently than for West Nile virus (SLE 73%, EEE 27%, WEE 9%, LaCrosse 8%). In part, this disparity results from inadequate laboratory staffing. Further, only nine state laboratories perform testing for dengue, four for Powassan, and two each for Chikungunya and Colorado tick fever viruses.

“There’s a critical gap of efficiency,” says Dr. E. Oscar Alleyne, a senior advisor at the National Association of County and City Health Officials, who at the start of the West Nile epidemic was the director of epidemiology of Rockland County, NY. “Those that do it obviously try to do it as well as they can, but the reality is, the defunding of many of these vector-borne programs for the sake of other programs, or for the sake of something that’s a little bit more sexy, from a Congressional standpoint, has had an impact on the ability for folks to rapidly mobilize.”

Making things worse, he pointed out, is that whatever mosquito-control capacity still exists was built to respond to West Nile. But Zika is spread by different mosquito species that live in different environmental niches and bite at different times of day; existing lab tests and already-owned mosquito-catching equipment do not match those species. Alleyne said: “You have a defunded system, you have a lessened capacity, and now you have a new threat that, with the equipment that you have, doesn’t provide you with adequate mechanisms to know how to detect them and respond.”

An Aedes aegypti mosquito, the chief vector of Zika virus.
An Aedes aegypti mosquito, the chief vector of Zika virus.
Photograph by James Gathany, CDC

Detecting the Aedes mosquitoes that spread Zika is a particular challenge because those species can breed in very small pools of water: puddles in discarded tires, upturned bottle caps. Anywhere with poor garbage collection, reduced municipal services, or low-quality housing represents prime habitat, and wiping out that habitat requires having enough personnel to scour private properties and go door to door. Dr. Peter Jay Hotez, a noted tropical disease expert who is dean of the National School of Tropical Medicine at Baylor College of Medicine in Houston, sees those practically outside his door.

“The Gulf Coast has both species of mosquitoes, and has the second risk factor for Zika, which is extreme poverty,” he told me. “People who live in poverty don’t have access to window screens, don’t have garbage collection;  in many poor neighborhoods, you see plastic containers filled with water, cups discarded, tires lying on the side of the road.”

Without well-funded, well-staffed mosquito surveillance, he said, “We won’t know that Zika’s here until babies start showing up in delivery suites with microcephaly.”

The Obama Administration has asked Congress to authorize a $1.8 billion emergency fund to respond to Zika, with $828 million of that for the CDC. As welcome as that will be, if it is approved, public health experts worry it may not be enough, for two reasons. First, since many mosquito control bodies don’t belong to the public health pyramid—which has the Department of Health and Human Services at the top, then the CDC, then state health departments, then county or city ones—there is no existing mechanism by which money can be funneled to them quickly.

And second, the money—as abundant as it might be—is a one-time emergency appropriation. That means it is likely there will be specific things on which it can and can’t be spent. On the likely list: equipment, assays, physical goods. On the not-likely: ongoing salaries. But those working in the field say that what public health needs most is steady funding to prop up its depleted workforce—and in the past decade, it has been persistently deprived.

“On an annual basis, public health funding continues to be at best fairly flat, and emergency preparedness funding has declined since the bump-up after 9/11,” says Richard Hamburg, interim president and CEO of the nonprofit Trust for America’s Health, which studies public health capacity. “We should be learning that we can’t jump from one emergency funding vehicle to another. We need to maintain a constant higher level of funding to ensure foundational capabilities, no matter what emergency comes through.”

 Update: Via Twitter, Tyler Dukes of WRAL.com in Raleigh, NC points out his colleague Mark Binker’s discovery that North Carolina has already sacrificed its mosquito-control funding to budget cuts.

You Just Missed the Last Ground Sloths

When did the last of the ground sloths disappear? The standard answer is “about 10,000 years ago”. That’s the oft-repeated cutoff date for when much of the world’s Ice Age megafauna – from mastodons to Megatherium – faded away. It’s nice and neat, falling just after the close of the last Ice Age and during a time when humans were spreading to new continents. In fact, it’s too clean a cutoff. The shaggy, ground-dwelling sloths that inhabited almost the entire span of the New World didn’t all topple over at once. They very last of their kind, both protected and made vulnerable by life on islands, were still shuffling 4,200 years ago.

Calling the time of death for any species or lineage is always complicated by definitions and details. Should a species be considered extinct when its very last member perishes, or when the population sinks below a level from which they can recover? And in these fading families, should the explanation for extinction be the cause of death of the last individual, or do we assemble a more complex picture that considers factors that made the population vulnerable in the first place? Both science and storytelling influence our answers to these questions, but one thing is abundantly clear. Extinction is a process, not a single fell swoop.

Consider the times when the giant ground sloths disappeared. They were one of the great success stories of the Ice Age – with 19 genera ranging through South, Central, and North America, as well as Caribbean islands at the end of the Pleistocene – but, as reported by paleontologist David Steadman and colleagues in a 2005 study, 90% of the existing Ice Age sloths disappeared within the last 11,000 years.

Megalonyx and other giants from North America were some of the first to go. While Steadman and colleagues stressed that the dates represent “last appearance dates” rather than actual time of species death, the youngest known sloth remains from North America date to about 11,000 years ago. South America’s ground sloths, such the enormous Eremotherium, soon followed – the youngest dung and tissue samples found on the continent date between 10,600 and 10,200 years ago.

But for another 5,000 years, ground sloths survived. They weren’t on the continents, but scattered through the islands of the Caribbean. I had not even heard about these sloths until paleo geneticist Ross Barnett told me about them in a Twitter exchange long ago, and, as reviewed in the paper by Steadman and colleagues, there were at least five genera and thirteen species of large ground sloths that were unique to these islands.

Cuba's extinct ground sloth Megalocnus rodens. Photo by Ghedoghedo.
Cuba’s extinct ground sloth Megalocnus rodens. Photo by Ghedoghedo.

The largest of all was Megalocnus. This sloth hasn’t received nearly as much attention as the other “mega”-prefixed sloths, but, as you can see from the bones on display at the American Museum of Natural History’s fossil mammal hall, this 200-pound sloth was still an impressive beast. Based on remains found in a limestone cave on Cuba, Steadman and colleagues determined that Megalocnus lived until at least 6,250 years ago.

Other smaller sloths persisted even longer. Parocnus, also found on Cuba, lived until about 4,960 years ago, and the small ground sloth Neocnus trundled over Hispaniola until about 4,500 years ago. There’s no direct evidence that people were hunting or eating the sloths, but, based on tentative evidence for human occupation of Caribbean islands around 5,000 years ago, Steadman suggest that the arrival of Homo sapiens tipped the sloth into extinction.

Of course, last appearance dates are often revised with new finds and updated techniques. Two years after the Steadman study, Ross MacPhee and coauthors published a new, youngest date for Cuba’s Megalocnus. From a tooth found on the island, the researchers estimated that the ground sloth survived to at least 4,200 years ago.

Through the lens of geologic time – wherein millions of years are thrown around because the numbers are too big to truly comprehend – extending the lifetime of a ground sloth another 2,000 years might not sound like much. But MacPhee and colleagues underscore the importance of getting good dates for when Ice Age creatures vanished. If people really showed up on Cuba and other sloth-bearing islands around 5,500 years ago, then humans and ground sloths coexisted for over a thousand years and the “blitzkrieg” model of extinction starts to crumble. Humans may have still been responsible for the extinction of the sloths and other species, but the record doesn’t show the pattern of rapid die-off that has sometimes been used to pin our species as the chief cause of megafaunal extinctions.

In time, we may get a clearer picture of why such a diverse and widespread ground of mammals disappeared. Assuming that humans, climate change, or any of the other traditional suspects without more detailed evidence masks the complexity of how extinction happens. But even if paleontologists eventually puzzle together what happened to these great beasts, I’ll still be saddened by the fact that I just missed the ground sloths. Especially because there are habitats – such as vast stretches of desert in the basin and range I call home – that could still host them. Sometimes, when hours of rolling over the interstate starts to addle my brain, I start to imagine them out among the Joshua trees – reminders that we still live in the shadow of the Ice Age world.


MacPhee, R., Iturralde-Vinent, M., Vázquez, O. 2007. Prehistoric sloth extinctions in Cuba: Implications of a new “last” appearance date. Caribbean Journal of Science. 43, 1: 94-98.

Martin, F., San Román, M., Morello, F., Todisco, D., Prevosti, F., Borrero, L. 2013. Land of the ground sloths: Recent research at Cueva Chica, Ultima Esperanza, Chile. Quaternary International. 305: 56-66. doi: 10.1016/j.quaint.2012.11.003

Steadman, D., Martin, P., MacPhee, R., Jull, A., McDonald, H., Woods, C., Iturralde-Vinent, M., Hodgins, G. 2005. Asynchronous extinction of late Quaternary sloths on continents and islands. PNAS. 102, 33: 11763-11768. doi: 10.1073/pnas.0502777102

A Blog by

Gold-Mining In Peru Is Much Worse Than Anyone Thought

I flew over the Peruvian Amazon two years ago, in a small propeller plane. An aerial perspective gives you a true sense of the rainforest’s scale, as treetops stretch from one horizon to another like an infinite and unbroken array of broccoli florets.

But from the air, the damage to the jungle also becomes more obvious. We flew over charred hectares of burnt trees, huge piles of felled logs and, most memorably of all, vast (and mostly illegal) gold mines.

Before the flight, I might have pictured a gold mine as a surreptitious doorway carved into a mountainside. The largest of the ones I saw, known as Guacamayo, was more like a pustulent wound—a gash of festering yellows and whites amid the lush greens of the jungle. It even seeped into the nearby river and jaundiced its water. It was a nauseating sight, and one utterly disconnected from the glistening metal that gets fashioned into jewellery and ornaments.

The Madre de Dios region of southern Peru is rich with both life and gold, and the latter threatens the former. A recent gold rush, prompted by skyrocketing prices and enabled by a new highway, have brought tens of thousands of hopeful miners to the region. Back in 2009, scientists showed that the three big mines—Huepetuhe, Guacamayo and Delta-1—had already claimed 15,500 hectares of forest, and were growing at a rate of 1,900 more every year.

But Greg Asner from the Carnegie Institution for Science—the same scientist who flew me over the Amazon—has found that the situation is even worse. The big mines like Guacamayo are an obvious problem, but thousands of smaller ones have sprung up in the last few years. They’re extremely hard to find or control, and Asner found that they collectively account for more than half the gold-mining in the region.

“The Ministry of Evnironment estimates that there are 50,000 to 70,000 of these miners in the region,” says Asner. “They’re working on groups of three to ten, so that’s a lot of mining.” Everyone was focusing on the big, gaping wounds, and ignoring the subtler infections creeping through the Amazon’s skin.

The small mines look like deep pits in forest clearings, up to 10 metres deep with debris and mud at the bottom. The miners cut down a small stand of trees, dig away the top layers of soil and blast away at what remains with high-pressured water. They transfer the resulting slurry into an oil drum and add mercury. “Someone stands in the drum and starts jumping up and down. It’s like squishing grapes,” says Asner.

The mercury binds to any gold in the mud, which the miners filter out with a pan. The nuggets are dried and heated, releasing even more mercury into the air as a vapour. It’s no surprise that the miners often suffer from mercury poisoning, as do people who live in nearby towns or settlements, or downstream of polluted rivers. And yet, they get gold. “Five days ago, I ran into an old Peruvian student on the river, and he told me that in some places, there’s half a kilo of gold per hectare, deep down below the forest floor,” he says.

The miners are getting craftier. They’re setting their mines back further and further from the edges of roads and rivers, and clearing away only small patches of trees. “As you go up and down the river, you don’t see anything,” says Asner, “and the methods that are used to map mines from satellite imagery are insensitive to small clearings.”

So, Asner turned to CLASlite—a piece of software he built to detect the signs of logging on satellite images. He trained the system to identify the signatures of small gold mines, and applied it to images that had been collected since 1999.

This CLASlite map shows the areas along the Madre De Dios river damaged by small, clandestine gold miners between 1999 and 2012. Credit: CLASlite Team
This CLASlite map shows the areas along the Madre De Dios river damaged by small, clandestine gold miners between 1999 and 2012. Credit: CLASlite Team

The images showed that gold mines in Madre de Dios have quintupled in coverage since 1999, from 10,000 hectares to more than 50,000 now. The three big mines are a problem, but the smaller ones have multiplied so quickly that they now account for 51 percent of mining in the area.

The mines are also expanding faster than anyone had thought—from a rate of 2,166 hectares per year before the gold price boom of 2008, to a current rate of 6,145 hectares per year. Those estimates are around 40 percent higher than any previous ones for the region, and they mean that gold mining is now the biggest cause of deforestation in the region, beating out logging or farming. (And that’s ignoring the fact that mining increases the odds of ranching, farming, bushmeat hunting, and environmental damage in nearby areas.)

Worse still, the mines are encroaching into new habitats. The big mines like Guacamayo are most found in swampy regions near the main rivers, but the smaller operations are heading deeper into the forest, and higher up the foothills of the Andes. These regions host very different communities of plants and animals, which are now being threatened. The mines are also spreading further up-river, which threatens to pollute more of the waterways with mercury.

To verify the satellite results, Asner’s team started checking out some of the supposed mines on the ground. “It’s extremely stressful going into these places,” he says. When he visited Guacamayo, he did so at a quiet time of day, and wearing a hoodie. The smaller mines are even more treacherous. “There are reports of people shooting or machete-ing each other, which I cannot confirm. But it’s definitely not comfortable, and the miners are very quick to threaten.”

Since the field surveys were so dangerous and time-consuming, the team also took to the skies. That is, after all, where Asner does most of his research. His small plane—the Carnegie Airborne Observatory—is fitted with a trio of sensors that can map the shape of a forest’s trees down to their individual branches, measure the chemical composition of their leaves and trunks and soil, and even identify species from these chemical signatures. (I profiled him, and wrote about his work, for Wired UK last year.)

The surveys confirmed that the satellite images are capturing between 84 and 94 percent of the mines in the area, and just 7 to 18 percent of the ones they identified are false positives. For the most part, the technique is accurate and reliable.

“Asner’s study helps further raise awareness about continued illegal gold mining in this area,” says Jennifer Swenson from Duke University, who ran an earlier mapping study of the three big mines. “[We now need] to focus on how to develop policies or strategies to at least decrease the mining rate, as well as miner education and policies to reduce the use of mercury and subsequent contamination.”

“It gives us a clear idea about the scale of the challenge,” says Ernesto Ráez Luna, a scientist from Peru’s Ministry of the Environment (MINAM) and a co-author on the new study. “We knew that illegal mining was taking place, but not how fast it was moving into the forest. We now know the velocity.”

Doing something about it is another problem, but Luna says that MINAM is pursuing several avenues. For a start, they want to prosecute the bosses who control the large proportion of the illegal mining operations, and push for harder jail sentences. “What used to be small-scale mining has been infiltrated by crime,” he says. “We don’t want to go after the labourers, who include a large number of sincerely poor people. We want to focus on the few at the top of the pyramid.”

They also want to formalise the small-scale mines, and help people who want to work lawfully to create proposals for environmental management. And they want to help those who are trapped in their current situations. “We also need to do social restoration, as well as ecological restoration,” says Luna. “The illegal mining has brought with it a number of other crimes, including slave-labour and sexual exploitation of minors.”

Asner adds that three other moves might help. First, rein in mining permits; these are current the responsibility of regional governments and they are given out freely, perhaps even aggressively. Second, limit the amount of fuel that’s delivered to the Puerto Maldonado, the region’s capital. Currently, Madre de Dios actually consumes more fuel than the Lima, Peru’s capital city, because gold-mining is so big. Finally, stem the import of mercury, much of which comes in via the black market.

Reference: Asner, Llactayo, Tupayachi & Luna. 2013. Elevated rates of gold mining in the Amazon revealed through high-resolution monitoring. http://dx.doi.org/10.1073/pnas.1318271110

If you want to read more about gold-mining in Peru, do read these two excellent pieces:

And for more about Greg Asner’s work:

Don’t Panic – How Humanity Might Survive the Next Million Years

Our species is going to go extinct. We may have descendants – a new species, or some sort of post-human meld that we construct ourselves – but the long roll of lost creatures preserved in the fossil record leaves no doubt that extinction is inevitable. But just as the survival of the human lineage is only a vague possibility at this point, our eventual downfall also remains in the realm of the unknown. Our destruction could transpire in a blink of geologic time, or be at some future point millions of years hence. What will make all the difference is our ability to learn from the past and how we use that knowledge to construct the foundation of our future. In Scatter, Adapt, and Remember, io9 editor in chief Annalee Newitz considers just that in an optimistic exploration of how the key to our long-term survival can be forged from prehistoric clues and technological possibilities.

scatter-adapt-rememberSo far, there have been five absolutely devastating mass extinctions in the history of life on Earth (with a smattering of lesser, but still calamitous, events scattered through time). And if we’re not actually in a sixth mass extinction right now, we’re not very far off from the tipping point. The blame for this state of affairs rests with us.

We’ve drastically altered the Earth’s climate and seas through greenhouse gas emissions, we are spreading invasive species around the world, and we’ve taken a horrifyingly active role in directly destroying a variety of species and ecosystems. And given all this change, we’re not guaranteed a persistent place on the planet. As adaptable as we are, we’re still the last human species in existence and can only claim a relatively short tenure on this planet – our species has only been around for about 200,000 years. Whether we’re snuffed out in the next few millenia or extend the track record far into the future relies on our abilities to understand the risks that face us and responsibly use the best scientific tools at our disposal to mitigate against our self-imposed threats.

Learning from prehistory is one way to outline possibilities of what the future might hold. Paleontologists with an ecological bent have already begun to investigate these potentials, looking to how organisms have reacted to climate change and other familiar phenomena in the past for a view to what makes the difference between persistence, evolution, and extinction. To that end, Annalee* briefly surveys four of the Big Five mass extinctions, reiterating the point that there have always been survivors. If there had not, we wouldn’t exist. Our ancestors, as well as the ancestors of every other species in existence today, persisted through extinction’s worst and continued to change through the ages. And while what makes the difference between death and survival during global disasters is still being debated for all of these extinctions, some trends – such as being a widespread generalist capable of wandering far to rare resources in extinction’s aftermath – give some organisms an advantage over specialists restricted close to home.

Threats to our existence don’t always come in the form of asteroid impacts or intense volcanic activity, as they were during some mass extinctions. Disease and famine have horrifically ended human lives much closer in time. From the fall of South American civilizations to the Great Irish Famine, Annalee also surveys dangers that we create for each other, from the spread of disease and war to the mismanagement of arable land. But after cataloging all the dangers, including the blip in prehistoric time when our species almost went extinct prior to a dramatic rebound, Annalee begins to lay out possibilities for survival in a conversational style that would feel just as at home on io9 as in a book.

Some of these examples in the middle section don’t entirely fire. While the long-range migration routes gray whales employ are certainly important for their survival (the “Remember” example of the title), Annalee recognizes that human conservation efforts and future attempts not to disturb the whales are why the cetaceans still exist in the Pacific today. Still, Annalee sets up the general strategies of being able to wander far, shift with changing conditions, and recall what survival tricks worked in the past as hopes that mold more specific ways in which we might allow humanity to avoid extinction for a long time yet to come.

Lessons of death and survival can be drawn from a variety of examples, from organisms that withstood mass extinctions to people who succumbed to pandemics in recent history. And the point of this reflection, Annalee writes, is to ask “How will we convert our guardedly hopeful stories of a human future into a real-life plan for survival that avoids some of the worst failure modes?”

An initial step involves altering cities, especially as our global population continues to climb. Aside from relatively abstract goals that depend on those living in a particular place – such as an openness to innovation and created areas of shared green space – Annalee also investigates the technologies that may allow us to survive in the near and long term. Carefully-designed subterranean cities might be essential in the aftermath of nuclear war or a terrible asteroid strike, while buildings partly made of biological materials might reduce energy costs while providing us with a space to grow food right where we live. Likewise, a better understanding of the way earthquakes and disease work, paired with models that better predict the damage such phenomena cause, could allow us to make ourselves more resistant to such persistent challenges and respond more effectively. Tragically, as Annalee recognizes, the benefits of such innovations will be spread unequally. Those in affluent, developed nations are more likely to see the kind of safe, green cities that Annalee describes, while people elsewhere will suffer.

The promise of geoengineering raises the same dilemma. Scientists and engineers are trying to come up with solutions to global climate change, ocean acidification, and other problems that are global in scale. Given the experimental nature of programs – such as creating more cloud cover to partly block the sun while also trying to lessen the amount of carbon dioxide in the atmosphere – no one really knows what such endeavors would do in this country or that as weather and climate patterns changed. We do not live on a homogenous planet, and alterations that benefit one part of the globe might devastate another. If we’re going to modify the planet to best suit our needs and survival, as Annalee argues we should if we want to celebrate the millionth birthday of our species, who will decide what changes to implement and how?

Many of the possible solutions Annalee discusses are still in the realm of science fiction, or, at least, speculative science beyond the reach of what we can presently achieve. That’s not to say that tweaking Earth to better ensure our survival or even setting up shop on a distant planet are out of the question. Technology, politics, and culture will constrain our long-term efforts at survival, but given how much the human experience has changed during the past century – not to mention our cultural evolution over the relatively scant 200,000 years since our species originated – how strange our future might be is a tantalizing  mystery. Will we live in a Star Trek like existence, strange yet still familiar? Or will “human” mean something entirely different – people genetically altered to cope with life elsewhere in the solar system, or perhaps digital copies of minds that have an almost immortal life inside machines? More likely, humanity one million years hence – if we ever get that far – will be something far stranger than we can imagine today.

We won’t ever live in the glow of another star unless we ensure our survival on Earth, though. The challenge that faces us, Annalee demonstrates, is how to pair new ideas and innovations with what already exists. We can’t simply start from scratch. The world of tomorrow is going to be built on top of and around the world we know. And even if we can predict the forces that might drive us extinct, there’s no guarantee that we’ll have the time or tools to react to such threats. But there’s hope that we can.

In the end, survival will mean stretching our perceptions of what is natural. The idea of “hacking the planet” or altering ourselves to better match our surroundings might sound anathema to some, but the truth is that we are already doing so. The history of Earth is one of dramatic and constant change, and trying to recapture some romantic notion of Nature would be ignoring the reality of persistent planetary permutation and the way we’ve already made use of the Earth (for good and ill). Even restoring damaged habitats requires human intervention and stewardship – places of we think of as wild still bear our distinctive fingerprints. Maintaining the dichotomy of “human-made, bad; natural, good” will help no one. Instead, we need to recognize and come to terms with our capacity for both destruction and preservation – to use the best of our scientific knowledge and imagination to predict what tomorrow might hold and make careful decisions of what the future of Earth is going to be like for our species and all the others that dwell here. Annalee’s new book is a hopeful overview of such a possibility. We’ll never have total control of the planet nor our ultimate fate, but we have the ability to explore what we want the future of our species to be like.

*Since I know Annalee personally and have worked with her for some io9 posts, I decided to call her by her first name in this review.

Further reading: Annalee wrote a guest post for this blog about her favorite icon of long-term survival, Lystrosaurus.

A Blog by

Will we ever… lose all our corals?

Here’s the 14th piece from my BBC column

John Bruno remembers swimming through Florida’s coral reefs as a child in the 1970s. At the time, the reefs were dominated by elkhorn and staghorn corals, whose vivid, branching structures provided shelter for a smorgasbord of marine life. “It was like snorkelling over a wheatfield – vast, golden coral coverage as far as you could see,” says Bruno, now a marine biologist at the University of North Carolina.

Such days are gone. In just a few decades, the Caribbean’s reefs have collapsed. Golden beds of elkhorns and staghorns have disappeared and been replaced by thick mats of green algae. The proportion of the reef covered by live coral has plummeted from 50% in the 1970s to just 8% now, changing the fish communities dramatically. “Florida was a scary place to snorkel then, with hammerhead sharks, groupers and sailfish,” says Bruno. “Now, it’s like snorkelling in an aquarium.”

It’s not just the Caribbean. A third of reef-building corals are in danger of extinction, and reefs the world over are in serious decline. Even Australia’s Great Barrier Reef, long held as a shining testament to careful management, has lost the majority of its coral. “Ten years ago, we thought, ‘At least we have the [Great Barrier Reef]’, but even that’s starting to look pretty grim,” says Bruno. The question now is not whether things will get worse – they assuredly will – but whether we will lose our reefs entirely.

This is a chilling prospect. To lose the reefs would be to lose the planet’s most diverse ecosystems – habitats that make even tropical jungles seem impoverished. “I’m not dissing rainforests, but you could walk for kilometres and see a thousand beetles and a hundred birds, all variations on a theme,” says Rick MacPherson from the Coral Reef Alliance. “But in one square metre of a reef, you could get every animal phylum known.”

People would also suffer. More than 450 million people live close to coral reefs and rely on them as sources of tourism revenue and protein, and as buffers that dampen the energy of incoming storms. “There are humans that depend on them for a daily basis not just as a nice place to visit for a holiday,” says MacPherson.

One-two punch

Coral reefs are besieged on many fronts. “It’s not like trying to protect rhinos, where we know that the cause of the decline is poaching,” says Bruno. “There are so many things happening and at such big scales that local managers are largely powerless to do anything.”

Rampant overfishing removes herbivorous fish that keep competitors like seaweed and algae at bay. Cyclones and hurricanes physically batter the reefs, as do sticks of dynamite thrown by fishermen. Diseases, some of which are exacerbated by bacteria carried in human sewage, kill them off. The voracious crown-of-thorns starfish – an evil-looking sunburst of spikes – liquefies them with its extruded stomach. Agricultural run-offs flood the oceans with nutrients, spurring the growth of algae and plankton that choke the waters and block out sunlight. Coastal construction projects cut down trees that hold topsoil together, allowing rain to wash sediment into the reefs, smothering the corals.

But climate change is the “big bad”, according to McPherson. The greenhouse gases that we pump into the atmosphere create an insulating blanket that warms the seas along with the rest of the planet. In warmer water, corals expel the algae that live inside their tissues and produce nutrients by harnessing sunlight. Without these lodgers, the corals lose their energy supply and their bright colours, becoming bleached and weak. Meanwhile, carbon dioxide also dissolves in the oceans, making them more acidic and depleting the carbonate ions that the corals need to build their limestone fortresses. They dissolve faster than they can be rebuilt. Hit by the one-two punch of hotter and more acidic waters, the corals, homeless and starving, become more vulnerable to the other threats they face.

Last year, ecologist Roger Bradbury provided a bleak outcome in an opinion piece for the New York Times, saying: “There is no hope of saving the global coral reef ecosystem.” It was a controversial claim, and many other coral scientists see less doom and gloom. “The trajectory is one of decline across the board, but I see areas of incredible resilience in even the most severely hit ecosystems,” says McPherson. “There are so many places you can go where reefs, if not bouncing back, are at least holding their own in a suppressed state.”

Not all corals, or all reefs, are the same. Some, like those in American Samoa, have genetic advantages that allow them to thrive in shallower warmer waters, and some can recruit strains of algae that tolerate higher temperatures. Others grow in waters that are naturally acidic, where carbon dioxide seeps from the ocean floor. Corals can acclimatise to changing conditions, and there’s some evidence that reefs which bleach extensively for one year are better able to handle warmer waters a decade later. And reefs can change at the community level, shifting from sensitive species like the elkhorns to sturdy, robust ones like big boulder corals.

Buying time

Humans can help, particularly by setting up marine protected areas – underwater national parks – where fishing is verboten. Not only do they allow local reefs a chance to recover, but they can seed nearby areas with coral larvae. “That’s our best weapon in our arsenal right now for coral conservation,” says MacPherson, “but they need to be managed.” While a quarter of the world’s reefs already lie in marine protected areas, many are protected on paper only. Their restrictions have to be actively enforced, and they need strong support from local communities. All of this takes money, education, and expertise.

But in the end, the fate of coral reefs comes down to global warming. “We stop climate change, or that’s that,” says Bruno. “That’s a precondition for conserving almost everything.” Setting up marine reserves, fighting coral diseases, reducing pollution… all of these measures are about buying time.

And with enough time, corals prove to be remarkably resilient. They have lived through several climatic fluctuations, including waters that were far warmer and more acidic than those today. Over geological timescales, corals have endured at least five severe crises, but have never been entirely wiped out. Small populations survived in refuges to restart their rocky kingdoms during more hospitable climates.

The difference, of course, is that these ancient changes played out across millennia, whereas we are causing similar upheavals within the space of decades. Based on the latest report from the Intergovernmental Panel on Climate Change (IPCC), it is entirely plausible that the oceans might be three or four degrees Celsius warmer by the end of the century. “Honestly, if we got to that, most reefs would be toast,” says Bruno. “Usually, one degree of warming is enough to cook and kill most corals. There are very few species that could survive three or four.”

However, those figures are a global average. Not every patch of water will warm equally, and some cold areas may even become more conducive to corals. “We’d lose a lot of what we have,” says Bruno, “but we probably wouldn’t lose everything and we’d gain reefs in some places. We could get close to a world without corals… but reefs aren’t going to go extinct, probably under any global scenario.”

Corals, after all, live in a fine mosaic of salinity, temperature and light, where adjoining areas experience different conditions to their neighbours. It’s that patchiness that creates abundant niches for life, and has turned reefs into engines for evolution. And it’s that patchiness that might help to save them, even if we cannot. “That is my rationale for hope,” says MacPherson.

A Blog by

Turning corpse-eaters and blood-suckers into census-takers

An antelope falls in a forest and there’s no one around to hear it. But there are plenty of things that will eat it. Blowflies and flesh flies land upon the carcass and start to feed on it. They also lay eggs, which hatch into maggots that also start devouring the dead flesh. The antelope will eventually disappear, but fragments of its DNA still exist inside the guts of the insects that feasted upon it.

And that’s great news for conservationists who are trying to work out what lives in this particular forest. They don’t have to hack their way to undergrowth in search of a skittish and elusive antelope. They just have to catch the flies.

That’s exactly what Sebastien Calvignac-Spencer from the Robert Koch Institute did. He captured carrion flies at two tropical forests—the Tai National Park in Côte d’Ivoire and the Kirindy Forest in Madagascar—and used the DNA in their guts to get a snapshot of the mammals in each area. He found a surprising proportion of the local species, including many that are hard to track and some that are highly endangered.

It was census-taking via corpse-eating, and one of several quick and cheap alternatives to the hard slog of traditional monitoring schemes. Typically, large teams of experts, including taxonomists and indigenous trackers, have to work for long periods of time under difficult conditions just to work out which species live in an area, much less measure their numbers or density. Such work is especially hard in thick tropical forests, which hold the greatest diversity of animal life.

But in recent years, scientists have developed several new approaches for detecting the presence of animals through their DNA, without having to actually find them.

From anthrax to antelopes

As I reported for Nature News, Calvignac-Spencer’s fly technique began with sick chimpanzees. Around a decade ago, his boss, Fabian Leendertz, had discovered a type of rainforest anthrax that was killing chimps in the Tai National Park.

Where was this infection coming from? Leendertz knew that the bacteria behind the more familiar version of anthrax can grow in the guts of some flies, so he wondered if the rainforest insects were harbouring the chimp-killing infection. His team captured several flies that emerged from carcasses found in the forest, and that were lured to bottle traps baited with meat. That work is still going on, but in the process, the team realised that they could use mammal DNA inside the flies to measure the forest’s biodiversity.

Obviously, DNA breaks down in the guts of flies but not to the extent you’d imagine. Unlike us, these insects don’t churn their food in a highly acidic stomach, so large fragments of DNA still remain—up to 300 ‘letters’ in length and occasionally up to 700. It’s “not gorgeous, but still usable,” says Calvignac-Spencer.

If you mush up a fly, you get a soup that contains its own DNA and that of its mammalian meals. The team pulled out the sequences they were interested in using primers that recognise the signatures of mammalian or vertebrate DNA.

Diana's monkey, one of the 6 species that Calvignac-Spencer detected in the Tai National Park thanks to flies. Photo by Greg Hume.

Around 40 percent of the captured flies yielded mammalian DNA, and they had clearly fed on a broad menagerie. In the Tai National Park, the flies carried DNA from 16 species including six of the nine local primates, two bats, a porcupine, a hippo, and a shrew. They also revealed the presence of Jentink’s duiker, an extremely endangered antelope with fewer than 3,500 individuals left in the wild.

In Madagascar, the team found the DNA of two lemurs, a tenrec (a creature that looks like a hedgehog but isn’t one) and a meat-eater, probably a fossa. That’s four of Madagascar’s 31 mammal species, revealed through the guts of flies.

They now want to see if they can use the flies to get precise information about one species, rather than broad information about many of them. Could they work out a species’ distribution? Could they detect rapid population crashes, including those that traditional methods would never see? For example, Calvignac-Spencer mentions that between 2002 and 2003, thousands of gorillas were killed by the Ebola virus in the Republic of Congo. “But only 44 carcasses were found, in spite of active monitoring,” he says. “And these were gorillas! Just imagine how hard it might be to monitor die-offs of bats or rodents,” which are important reservoirs for infections that could jump into humans. “Flies could really be precious in this context.”

Leech, by Thejaswi

This technique sucks

Corpse-eaters aren’t the only indirect source of animal DNA—blood-suckers could also be a monitoring goldmine. Last year, a team led by Thomas Gilbert from the University of Copenhagen studied the mammals of a dense Vietnamese rainforest, by extracting their DNA from the bellies of leeches.

His team collected 25 leeches in Vietnam’s Central Annamite region, and found that 21 of them carried mammalian DNA. These included the Ammanite striped rabbit, which was only found in 1996, and the Truong Son muntjac, a small deer that was identified in 1997. Both are extremely rare. We know so little about them that the International Union for Conversation of Nature classifies them as “data deficient”. The rabbit had never been seen in that particular area, even though camera-traps had snapped photos of the forest’s residents for more than 2,000 nights. And the muntjac is still only known from its skull—a living specimen has never been seen by Western scientists.

And yet, just by collecting 25 leeches, Gilbert had uncovered clear evidence that both animals were alive, roaming the forests, and getting drained by parasites. His leeches had also recently sucked the secretive Chinese ferret-badger and the Chinese serow, a rare goat-like creature whose populations are falling. Perhaps other leeches will reveal the presence of the soala or ‘Asian unicorn’—an antelope that was described in 1992 but has rarely been seen alive.

Vietnamese animals detected through DNA in leeches include, from left to right, the Ammanite striped rabbit, the Chinese ferret-badger, the Troung San muntjac, and the serow. Inset shows stability of DNA in a leech

The mountainous forests of the Annamite region are a treasure trove of undiscovered life. Including the rabbit and muntjac, five new mammals have recently been discovered here. But once found, they are hard to find again. The terrain is dense, rugged and humid, and many of the remaining mammals are understandably wary of humans.

Leeches could provide and easy way to assess what’s living in these forests and others. They’re found in fewer parts of the world than Calvignac-Spencer’s flies, but they preserve DNA in their stomachs for a lot longer—at least four months, according to Gilbert. They’re also keen on human blood, which makes them extremely easy to collect—just walk through the forest and get ready to remove them from your limbs and clothes. As Gilbert says, “Unlike camera trapping and dung-searches, leech data collection is simple, inexpensive and can be conducted by untrained personnel.”

A world of genetic litter

These techniques are just the tip of the iceberg. Throughout their lives, animals spread genetic litter throughout their surroundings, and this so-called environmental DNA (eDNA) is a boon to scientists. So far, groups have used eDNA to discern the presence of: bullfrogs in French ponds; frogs and giant salamanders in fast-moving mountain streams, invasive carp in American canals and lakes; and fish, whales and dolphins in Danish seas.

They have identified whales from DNA in skin that gets sloughed off while diving; large mammals like elephants and antelopes from DNA in the earth beneath their feet; and earthworms from DNA in the soil that they burrow through.

So, if an antelope falls in a forest, it doesn’t matter if there’s no one around. Its DNA inches through the undergrowth in the body of an engorged leech. It falls to the ground in pats of faeces. It zooms through the air in the guts of a well-fed flesh fly.

Animals aren’t just localised sacks of skin-bound flesh. They also cast a vast genetic shadow upon their environment, one that scientists are learning how to spot.

References: Calvignac-Spencer, Merkel, Kutzner, Kuhl, Boesch, Kappeler, Metzger, Schubert & Leendertz. 2013. Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Molecular Ecology http://dx.doi.org/10.1111/mec.12183

Schnell, Thomsen, Wilkinson, Rasmussen, Jensen, Willerslev, Bertelsen & Gilbert. 2012. Screening mammal biodiversity using DNA from leeches. Current Biology http://dx.doi.org/10.1016/j.cub.2012.02.058

Taberlet, Coissac, Hajibabaei & Rieseberg. 2012. Environmental DNA. Molecular Ecology http://dx.doi.org/10.1111/j.1365-294X.2012.05542.x

When Food Webs Flip: My New Story in Scientific American

New England’s fisheries are in such bad shape that the Department of Commerce has now declared them a disaster. It’s not merely the sheer volume of fish we’re catching that explains the woeful state of these fish stocks. Even in places where governments have established strict limits on fishing, some fisheries have been unexpectedly slow to recover. That’s because fish don’t exist in isolation. They’re part of ecological networks. And when we hammer these networks, they can suddenly flip into a new state. Getting them back to their old state can be surprisingly hard.

In the new issue of Scientific American, I’ve written a feature on recent research into how ecological networks flip, along with attempts to detect warning signs of food webs on the brink (subscription required).

P.S. A needless snarky commenter objected to having to pay for the article. As I pointed out to him or her, if you want to read two lengthy scientific reviews on the subject for free, here is a pdf and here’s another one.

[Image: Lake Michigan food web/NOAA]

A Blog by

Weapons made from shark teeth are completely badass, and hint at lost shark diversity

I was at the Ecological Society of America’s Annual Meeting when I saw this tweet:

As you might imagine, I did check out that talk.

For those of you who are wondering how you weaponise shark teeth, which are already regenerating, serrated meat knives at the business end of a streamlined, electric-sensing torpedo, here’s how. You drill a tiny hole in them, and then bind them in long rows to a piece of wood to make a sword. Or a trident. Or a four-metre-long lance. And then, presumably, you hit people really hard with them.

That’s what the people of the Gilbert Islands have been doing for centuries. Sharks are an ingrained part of their culture and their teeth have been an ingrained part of their weapons. Tiger sharks feature heavily – they have thick, cleaver-like teeth that can slice through turtle shells so they make a good cutting edge. But the weapons also include the teeth from spottail, dusky and bignose sharks (you can identify species from their teeth), and none of these actually live around the Gilbert Islands today.

Drew, who studied 124 of these weapons, says that their teeth reveal a “shadow diversity” – traces of sharks that disappeared from the surrounding waters before we even knew they were there. I wrote about this story for Nature News – head over there for the full details.

What Lurks In Logs

The world, it bears reminding, is far more complicated than what we can see. We take a walk in the woods and stop by a rotting log. It is decorated with mushrooms, and we faintly recall that fungus breaks down trees after they die. That’s true as far as it goes. But the truth goes much further. These days scientists do not have to rely on their eyes alone to observe the fungus on a log. They can drill into the wood, put the sawdust in a plastic bag, go to a lab, and fish the DNA out of the wood. A group of scientists did just this in Sweden recently, sequencing DNA from 38 logs in total. They published their results this week in the journal Molecular Ecology. In a single log, they found up to 398 species of fungi. Only a few species of fungi were living in all 38 logs; many species were limited to just one.

Consider that on your next walk in the woods. The one or two types of mushrooms you see on a log are an extroverted minority. The log is also filled with hundreds of other species that don’t make themselves known to you. Their invisible exuberance is a paradox. The fungi that live on rotting logs all make a living by releasing enzymes that break down wood. It’s puzzling that so many species can coexist in a log this way, instead of a single superior fungus.

The forces that drive up the diversity of fungi in a log are similar to the ones that fosterer the thousands of species of microbes in our bodies. For one thing, a log or a human body is not a uniform block of tissue. They both have geography. A microbe adapted to the acid bath of our stomach won’t fare well on the harsh desert of the skin. Likewise, what it takes to succeed as a fungus in a branch is different from what it takes in the heartwood of the trunk.

The human body changes over time, and a rotting log does, too. Babies are colonized by pioneer microbes, which alter the chemistry of their host and make it more welcoming to late-arriving species. The pioneers on a fallen log may include the spores of some species of fungi lurking in trees while they’re still alive. They burst into activity as soon as the tree crashes to the forest floor. Other species, delivered by the wind or snaking up through the soil, find it easier to infiltrate a log that’s already starting to rot. The early fungi may go after the easy sugar in the log, while later species unlock the energy in tougher tissues, like lignin and cellulose. Which particular pioneer starts to feed on a log first can make it inviting to certain species but not others.

Warfare also fosters diversity in a log. The fungi inside a log battle each other for food, spraying out chemicals that kill off their rivals. Each species has to balance the energy it puts into making enzymes to feed and weapons for war. Sometimes the war ends in victory for one species, but very often the result is a deadlock that leaves several species in an uneasy coexistence. There are more peaceful forces at work in a log, too. Many species of fungi in a log depend on each other. One species may feed on the waste produced by another, and supply another species with food in turn.

The world in a log influences the world as a whole. If it wasn’t for wood-rotting fungi, forests would be strewn with the durable remains of dead trees. When the first massive forests spread over the land 350 million years ago, fungi hadn’t yet adapted to decomposing logs. Instead of turning to soil, many trees ended up as coal. The great age of coal ended about 300 million years ago–right around the time that tree-rotting fungi emerged. Their emergence may have brought the age of coal to an end.

Three hundred million years later, that coal is coming back up to the surface of Earth to be burned. Some scientists are investigating fuels that could replace climate-warming ones like coal. One possibility is to pull out the energy-rich sugar locked up in the lignin and cellulose of crop wastes or switchgrass. On our own, we would not be able to perform the necessary alchemy. But fungi know how, and so scientists are sequencing the genomes of wood-rotting fungi to borrow their tricks. This is big-scale science: the genomes of over a dozen species have been sequenced or are in the sequencing pipeline. Yet a single log may contain twenty times more fungus genomes. At the moment, we can say for sure that the few mushrooms we see on a rotting log are far from its full reality. But it will be a long time before we know how all the parts of that reality fit together.

[Photo: Tom Gill (lapstrake) via Creative Commons]

A Blog by

Urban noise can turn sparrow females into bad mums

When Rachel Carson wrote her famous book Silent Spring, she envisioned a world in which chemical pollutants killed off wildlife, to the extent that singing birds could no longer be heard. Pesticides aside, we now know that humans have challenged birds with another type of pollution, which also threatens to silence their beautiful songs – noise.

A man-made world is a loud one. Between the din of cities and the commotion of traffic, we flood our surroundings with a chronic barrage of sound. This is bad news for songbirds. We know that human noise is a problem for them because some species go to great lengths to make themselves heard, from changing their pitch (great tits) to singing at odd hours (robins) to just belting their notes out (nightingales). We also know that some birds produce fewer chicks in areas affected by traffic noise.

Now, Julia Schroeder from the University of Sheffield has found one reason for this. She has shown that loud noises mask the communication between house sparrow mothers and their chicks, including the calls that the youngsters use to beg for food. Surrounded by sound, the chicks eat poorly. “City noise has the potential to turn sparrow females into bad mothers,” says Schroeder.


A Blog by

Californian condor not extinct yet, but still regularly poisoned by lead

The image above, which may be the worst photo of a Californian condor ever taken, was the best shot I snapped during a four-hour condor-watching trip in 2010. But even this grainy image is important, for it captures one of the 405 last Californian condors in the world.

Myra Finkelstein from the University of California, Santa Cruz writes that the condor is “a symbol of environmental tragedy and triumph”. The huge bird, with its three-metre wingspan and eerily smooth flight, was once widespread across North America. Between power lines, guns, and pesticides, their population plummeted. The birds were frequently poisoned by lead after scavenging off shot-filled carcasses, and that’s if poachers weren’t filling them with lead shot in a more direct way.

By 1982, there were just 22 Californian condors left in the world, and all of them were in captivity. An intense captive breeding programme began, and it has been an apparent success. There are currently around 400 birds, more than half of which fly free and wild.

But this might be a pyrrhic victory. Finkelstein has now shown that the condor’s fate is far from certain. Even though we have brought it back from the cusp of extinction, its old enemy – lead – is still a major threat. If conservation efforts are scaled back, the condor will disappear once more unless the use of lead-based ammo is severely or completely curtailed. (more…)

A Blog by

To control cannibal toads, you just need the right bait

Australians love to destroy cane toads. Ever since these animals were first introduced in 1935, they have run amok, eating local animals and poisoning any that try to eat them. They’re captured and slaughtered in traps, bludgeoned with golf clubs, and squished with veering tyres, but still they continue to spread. Now, Michael Crossland from the University of Sydney has discovered an unlikely ally in the quest to control the cane toad: the cane toad.

Along with their unappealing appearance and milky poison, cane toads are also cannibals. Older tadpoles will hunt and eat eggs that have been recently laid in the same pond, to do away with future competitors. Crossland reasoned that the eggs must release a substance that the tadpoles can detect, so he mushed them up in his lab and separated out their chemical components.

He discovered that the eggs secrete bufadienolides – the same substances that make the milky poisons of the adult toads so deadly to Australia’s fauna. Ironically, the same chemicals that protect the eggs later in life also attract cannibalistic tadpoles. And that makes them excellent bait.