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The rare coealacanth’s genome is slowly evolving—and contrary to prior speculation, it probably isn’t the common ancestor of all land animals. Image via Wikimedia Commons/Amelia Guo

On December 23, 1938, South African Hendrick Goosen, the captain of the fishing trawler Nerine, found an unusual fish in his net after a day of fishing in the Indian Ocean off of East London. He showed the creature to  local museum curator Marjorie Courtenay-Latimer, who rinsed off a layer of slime and described it as “the most beautiful fish I had ever seen…five foot long, a pale mauvy blue with faint flecks of whitish spots; it had an iridescent silver-blue-green sheen all over. It was covered in hard scales, and it had four limb-like fins and a strange puppy dog tail.”

The duo, it turned out, had made one of the most significant biological discoveries of the 20th century. The fish was a coelacanth, a creature previously known only from fossilized specimens and believed to have gone extinct about 80 million years earlier. Moreover, its prehistoric appearance and unusual leg-like lobed fins immediately suggested to biologists that it could be an ancient ancestor of all land animals—one of the pivotal sea creatures that first crawled onto solid ground and eventually evolved into amphibians, reptiles, birds and mammals.

Now, though, the coelacanth’s full genome has been sequenced for the first time, and the results, published by an international team of researchers today in Nature, suggest otherwise. Genetic analysis suggests that the coelacanth doesn’t appear to be the most recent shared ancestor between sea and land animals—so its lobed fins didn’t make that first fateful step onto land after all.

When the researchers used what they found out about the coelacanth’s genome to build an evolutionary tree of marine and terrestrial animals (below), they found it’s more likely that ancestors of closely-related class of fish called lungfish played this crucial role. The ancestors of coelacanths and lungfish split off from each other before the latter group first colonized any land areas.

The genetic sequencing showed that terrestrial animals share a more recent common ancestor with lungfish, rather than coelacanths. Image via Nature/Amemiya et. al.

Additionally, the coelacanth’s prehistoric appearance has led to it commonly being considered a “living fossil”: a rare, unchanging biological time capsule of a bygone prehistoric era. But the genomic sequencing indicated that the fish species is actually still evolving—just very, very slowly—supporting the recent argument that it’s time to stop calling the fish and other seemingly prehistoric creatures “living fossils.”

“We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at,” Jessica Alföldi, a scientist at MIT and Harvard’s Broad Institute and a co-author, said in a press statement. Small segments of the fish’s DNA had previously been sequenced, but now, she said, “This is the first time that we’ve had a big enough gene set to really see that.”

The fact that the fish is evolving isn’t surprising—like all organisms, it lives in a changing world, with continuously fluctuating selection pressures that drive evolution. What’s surprising (though reflected by its seemingly-prehistoric appearance) is that it’s evolving so slowly, compared to a random sampling of other animals. According to the scientists’ analysis of 251 genes in the fish’s genome, it evolved with an average rate of 0.89 base-pair substitutions for any given site, compared to 1.09 for a chicken and 1.21 for a variety of mammals (base-pair substitution refers to the frequency with with DNA base-pairs—the building blocks of genes—are altered over time).

The research team speculates that the coelacanth’s extremely stable deep Indian Ocean environment and relative lack of predators might explain why it has undergone such slow evolutionary changes. Without new evolutionary pressures that might result from either of these factors, the coelacanth’s genome and outward appearance have only changed slightly in the roughly 400 million years since it first appeared on the planet.

Drought and an increased demand for water have stressed the Colorado River, which flows nearly 1,500 miles through seven states and Mexico. Photo by Flickr user Alex E. Proimos

When Alexandra Cousteau, granddaughter of Jacques, recently went to Mexico to explore the southern terminus of the Colorado River, she found mud, sand and dust where water once raged. The expedition was videotaped for a short film (viewable below) produced in conjunction with Cousteau’s nonprofit, Blue Legacy, which raises awareness about water issues. The video was called Death of a River: The Colorado River Delta.

That title, it turns out, is an apt one: Today, the conservation organization American Rivers released its annual ranking of America’s most endangered rivers, and the Colorado topped the list.

The group cites outdated water management as the main malady attacking the Colorado’s health. “A century of water management policies and practices that have promoted wasteful water use have put the river at a critical crossroads,” a statement (PDF) released by the organization reads. “Demand on the river’s water now exceeds its supply, leaving the river so over-tapped that it no longer flows to the sea.”

At one time, the river emptied into the Gulf of California, between mainland Mexico and the Baja Peninsula. In fact, this river mouth can still be found on maps, including Google’s, because it’s supposed to be there. But a recent study (PDF) conducted by the Bureau of Reclamation (a division of the U.S. Department of Interior) determined that the entire river and its tributaries are siphoned off to meet the drinking, bathing and toilet-flushing needs of 40 million Americans throughout seven states, including Arizona, California, Colorado, New Mexico, Nevada, Utah, and Wyoming. It also irrigates 5.5 million acres of land and helps meet the electrical-power appetite of much of the West through hydro-power facilities. Nearly two dozen Native American tribes depend on it, and it’s the centerpiece of 11 national parks, most famously the Grand Canyon.

“Growing demands on the Colorado River system, coupled with the potential for reduced supplies due to climate change may put water users and resources relying on the river at risk of prolonged water shortages in the future,” the study authors write. “Ultimately,” they add, “the Study [sic] is a call to action.”

Low water levels at the Colorado River’s Hoover Dam, on the Arizona-Nevada border. Photo by Flickr user Remon Rijper

But what action is needed? Water conservation, water reuse and water augmentation–replacing water drawn from wells–the authors say. Specifically, landowners and municipalities must boost their agricultural, municipal and industrial water conservation agendas, as well as improve their energy water-use efficiency. Solutions for the most challenging regions include finding ways to import water, reuse waste water and desalinize ocean and brackish water.

Scientists acknowledge some solutions they’ve looked into are easier said than done and that not all are viable in every region. For instance, options like importing water to Southern California via submarine pipelines, water bags and icebergs (PDF), along with watershed management techniques like weather modification (aka cloud-seeding) are a bit pie-in-the-sky.

The Colorado isn’t the only endangered river, by far. Georgia’s Flint River, the San Saba River in Texas, Wisconsin’s Little Plover River, the Catawba River in the Carolinas and Minnesota’s Boundary Waters were all also red-flagged by American Rivers this year.

The challenge for all of these rivers, including the Colorado, only grows in the future. Climate-change-induced drought is working against them. American Rivers notes (PDF) that changes to climate are expected to reduce the Colorado River’s flow by as much as 10 to 30 percent by the year 2050. It could leave yet more sand and mud behind, making parts of the American West and Southwest even more parched.

A mixture of plant oils, bacterial spores and ozone is responsible for the powerful scent of fresh rain. Image via Wikimedia Commons/Juni

Step outside after the first storm after a dry spell and it invariably hits you: the sweet, fresh, powerfully evocative smell of fresh rain.

If you’ve ever noticed this mysterious scent and wondered what’s responsible for it, you’re not alone.

Back in 1964, a pair of Australian scientists (Isabel Joy Bear and R. G. Thomas) began the scientific study of rain’s aroma in earnest with an article in Nature titled “Nature of Agrillaceous Odor.” In it, they coined the term petrichor to help explain the phenomenon, combining a pair of Greek roots: petra (stone) and ichor (the blood of gods in ancient myth).

In that study and subsequent research, they determined that one of the main causes of this distinctive smell is a blend of oils secreted by some plants during arid periods. When a rainstorm comes after a drought, compounds from the oils—which accumulate over time in dry rocks and soil—are mixed and released into the air. The duo also observed that the oils inhibit seed germination, and speculated that plants produce them to limit competition for scarce water supplies during dry times.

These airborne oils combine with other compounds to produce the smell. In moist, forested areas in particular, a common substance is geosmin, a chemical produced by a soil-dwelling bacteria known as actinomycetes. The bacteria secrete the compound when they produce spores, then the force of rain landing on the ground sends these spores up into the air, and the moist air conveys the chemical into our noses.

“It’s a very pleasant aroma, sort of a musky smell,” soil specialist Bill Ypsilantis told NPR during an interview on the topic. “You’ll also smell that when you are in your garden and you’re turning over your soil.”

Because these bacteria thrive in wet conditions and produce spores during dry spells, the smell of geosmin is often most pronounced when it rains for the first time in a while, because the largest supply of spores has collected in the soil. Studies have revealed that the human nose is extremely sensitive to geosmin in particular—some people can detect it at concentrations as low as 5 parts per trillion. (Coincidentally, it’s also responsible for the distinctively earthy taste in beets.)

Ozone—O_3, the molecule made up of three oxygen atoms bonded together—also plays a role in the smell, especially after thunderstorms. A lightning bolt’s electrical charge can split oxygen and nitrogen molecules in the atmosphere, and they often recombine into nitric oxide (NO), which then interacts with other chemicals in the atmosphere to produce ozone. Sometimes, you can even smell ozone in the air (it has a sharp scent reminiscent of chlorine) before a storm arrives because it can be carried over long distances from high altitudes.

But apart from the specific chemicals responsible, there’s also the deeper question of why we find the smell of rain pleasant in the first place. Some scientists have speculated that it’s a product of evolution.

Anthropologist Diana Young of the University of Queensland in Australia, for example, who studied the culture of Western Australia’s Pitjantjatjara people, has observed that they associate the smell of rain with the color green, hinting at the deep-seated link between a season’s first rain and the expectation of growth and associated game animals, both crucial for their diet. She calls this “cultural synesthesia”—the blending of different sensory experiences on a society-wide scale due to evolutionary history.

It’s not a major leap to imagine how other cultures might similarly have positive associations of rain embedded in their collective consciousness—humans around the world, after all, require either plants or animals to eat, and both are more plentiful in rainy times than during drought. If this hypothesis is correct, then the next time you relish the scent of fresh rain, think of it as a cultural imprint, derived from your ancestors.

As the Arctic warms, more of it will be covered by shrubs (like the Arctic National Wildlife Refuge, above) and even by forest. Image via ANWR

You probably think of the Arctic as a cold, frozen tundra—home to lichen, polar bears and scattered herds of reindeer. In many places, this view would be accurate, but in a few relatively southern areas in Canada, Alaska and Russia, warming temperatures over the past few decades have allowed new types of plants, such as shrubs, to take root.

And by 2050—if current warming trends continue—we’ll see a dramatically different ecosystem across the Arctic, starting with something that’s largely unknown in the area currently: trees. According to research published today in Nature Climate Change, tree cover in the Arctic could increase by more than 50 percent over the next few decades.

The research team, which included scientists from a number of universities and was led by Richard Pearson of the American Museum of Natural History, made the calculation based off of current projections of how the Arctic’s climate will change by 2050. So far, temperatures in the region have risen about twice as fast as those for the planet as a whole.

They created a model that predicts which class of plants (various grasses, mosses, shrubs or trees) will grow given a particular temperature and precipitation range expected for the future; for each spot on a map of the Arctic, they fed in the 2050 projections. Doing this kind of vegetative modeling for the Arctic, they say, is relatively straightforward compared to doing it for somewhere like the tropics, because there are hard limits on the temperature and growing season length that given plant types can tolerate.

They found that tree cover will expand drastically, covering up to 52 percent more land area than currently, rising far north of the current tree line in Alaska and Canada. This new tree cover will mostly come at the expense of areas currently covered by shrubs, but shrubs will take over places now dominated by tundra plants (lichens and mosses), and some areas presently under ice will convert into tundra.

In effect, the area’s warming climate and lengthening growing season will shift all current vegetation zones to more northerly and colder regions. Already, these vegetation zones have shifted an average of five degrees of latitude over the past 30 years–in other words, the vegetation in one spot resembles how a location five degrees south looked 30 years ago.

But by 2050, this shift will be even more dramatic—perhaps equaling 20 degrees of latitude—and a projected 48 to 69 percent of the Arctic’s vegetated areas will switch to a different class of plants. Some rare plant species could be at risk of extinction if they’re not able to migrate as quickly as the vegetation zones move.

Presently (left), vegetated areas of Alaska are mostly covered by small shrubs and tundra mosses (represented by the pea green color). By 2050 (right), much of this area will be dominated forests (bright green). Image via Nature Climate Change/Pearson et. al.

In Canada, areas currently covered by tundra shrubs (purple at left) will be taken over by forest (bright green at right). Image via Nature Climate Change/Pearson et. al.

Because plants are the base of any food chain, this conversion will have wide-ranging effects, both locally and elsewhere. “These impacts would extend far beyond the Arctic region,” Pearson said in a press statement. “For example, some species of birds seasonally migrate from lower latitudes and rely on finding particular polar habitats, such as open space for ground-nesting.” Their migrations patterns would presumably be altered by the growth of forests on what had been open tundra.

Most troubling, the conversion of white, snow-covered land to dark vegetation will further affect the warming of the planet. Because darker colors absorb more radiation than the white of ice and snow, shifting large masses of land to a darker color is projected to further accelerate warming, creating a positive feedback loop: more warming leads to a greener Arctic, which leads to more warming.

Given all the other problems that the area is rapidly encountering as the climate changes—melting glaciers, increasing oil exploration and hybridizing bear species—it’s clear that the Arctic will be one of the most environmentally fragile regions of the planet over the coming century.

Beneath the seafloor, there is an ecosystem of microbes living in the oceanic crust, independent of sunlight. Here, the seafloor of McMurdo Sound in Antarctica. NSF/USAP photo by Steve Clabuesch

If you were to hit the seafloor and continue to travel down, you’d run into an ecosystem unlike any other on earth. Beneath several hundred meters of seafloor sediment is the Earth’s crust: thick layers of lava rock running with cracks that cover around 70% of the planet’s surface. Seawater flows through the cracks, and this system of rock-bound rivulets is enormous: it’s the largest aquifer on earth, containing 4% of global ocean volume, says Mark Lever, an ecologist who studies anaerobic (no-oxygen) carbon cycling at Aarhus University in Denmark.

The sub-seafloor crust may also be the largest ecosystem on earth, according to a new study by Lever, published this month in Science. For seven years, he incubated 3.5 million-year old basalt rock collected from 565 meters below the ocean floor–the depth of nearly two stacked Eiffel towers–and found living microbes. These microbes live far away from the thriving bacterial communities at mid-ocean ridges, and survive by slowly churning sulfur and other minerals into energy.

But just how big is this chemically-fueled ecosystem that survives entirely without oxygen? If the results from his sample, collected from below the seafloor off the coast of Washington state, are similar to those found across the planet, then diverse microbial communities could survive throughout the ocean’s crust, covering two-thirds of the earth’s surface and potentially going miles deep.

The sub-seafloor crust has plenty of space and energy-rich minerals–a welcoming potential habitat for a large microbial community–“but we have no idea what the ecosystem looks like,” says Julie Huber, a microbial oceanographer at the Marine Biological Laboratory in Woods Hole, Massachusetts. “Mark’s evidence would point to it being a very different world.”

Microbes that get their energy from minerals, rather than from sunlight, are far from rare. The most well known of these so-called chemoautotrophic or chemosynthetic bacteria are those found at hydrothermal vents in the deep sea. Some of these bacteria live symbiotically with giant tubeworms, mussels and clams, providing chemically-produced energy to these larger organisms as they “breathe” the sulfur-rich water erupting from the vent–not unlike how plants convert sunlight into energy at the surface. Chemosynthetic microbes are also found in the rotting and oxygen-poor muck of salt marshes, mangroves and seagrass beds—“any place you’ve got stinky black mud, you can have chemoautotrophy,” says Chuck Fisher, a deep-sea biologist at Pennsylvania State University in College Park.

But what makes Lever’s sub-seafloor microbes different is that they don’t use any oxygen at all. The symbiotic bacteria at hydrothermal vents are often described as “life without sunlight,” but they still rely on sunlight indirectly by using sun-produced oxygen in the chemical reaction to generate energy. Chemosynthetic microbes in salt marshes feed on decomposing plants and animals, which got their energy from sunlight. Even deep-sea sediment is accumulated from an assortment of dead animals, plants, microbes and fecal pellets that relies on light energy.

The oceanic crust microbes, on the other hand, rely entirely on non-oxygen-containing molecules derived from rock and completely removed from photosynthesis, such as sulfate, carbon dioxide and hydrogen. “In that sense it’s a parallel universe, in that it runs on a different type of energy,” says Lever. These molecules provide a lot less energy than oxygen, creating a sort of microbial slow food movement. So instead of dividing and growing quickly like many oxygen-based bacteria, Fisher suspects that microbes in the Earth’s crust may divide once every hundred or thousand years.

A hydrothermal vent, covered with tube worms, spews black sulfur smoke on the Juan de Fuca Ridge. The oceanic crust microbes were collected hundreds of meters under the seafloor beneath this same ridge. Photo via University of Washington; NOAA/OAR/OER

But just because they’re slow doesn’t mean they’re uncommon. “There are lots of data that there is a large, very productive biosphere under the surface,” says Fisher.

In addition, microbial population sizes in different areas of the crust may vary greatly, Huber notes. Through her studies on the fluid found between the cracks in the crust,  she says that in some areas the fluid contains about the same number of microbes as standard deep-sea water collected at ocean depths of 4,000 meters (2.5 miles): around 10,000 microbial cells per milliliter. In other regions, such as at the Juan de Fuca Ridge in the Pacific Ocean where Lever found his microbes, there are fewer cells, around 8,000 microbes per milliliter. And in other regions, such as in non-oxygenated fluid deep in hydrothermal vents, there can be around 10 times more.

It’s not just the number of microbes that vary depending on location–it’s possible that different microbial species are found in different types of crust. “Different types of rock and different types of chemistry should result in different types of microbes,” says Andreas Teske, a deep-sea microbial ecologist at the University of North Carolina at Chapel Hill and co-author on Lever’s paper. The Juan de Fuca Ridge is a relatively hot area bursting with new rock, which tends to be made of more reactive minerals and thus able to provide more energy. Other parts of the crust are older, composed of different minerals, and cooler. And, in some regions, oxygenated water reaches down to the cracks.

It’s this infiltrating seawater that keeps this sub-seafloor ecosystem from existing on a completely separate plane from our oxygenated one. “The crust plays a significant role in influencing the chemical composition of the ocean and the atmosphere, ultimately influencing [nutrient] cycles on earth,” says Lever. Some of the compounds created by oceanic crust microbes from rock are water soluble, and will eventually enter the ocean. Sulfur, for example, is present in magma—but after the microbes use it for energy, it’s converted to sulfate. Then it dissolves and becomes an important nutrient in the ocean food chain.

Lever’s find of a microbial community in the crust could catalyze the scientific community to answer these questions. For example, what kinds of microbes are found where, do they interact through interconnected cracks in the rock, and what role do they play in mineral and nutrient cycling? In some ways, it’s very basic exploratory work. “A lot of what we do on the seafloor is similar to what we’re doing on Mars right now,” says Huber. “Controlling [NASA’s Mars Rover] Curiosity is very similar to operating an ROV under the ocean.”

  Learn more about the deep sea from the Smithsonian’s Ocean Portal.