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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.

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.

A handsome tokay gecko. Photo: Ethan Knapp and Alyssa Stark

Anyone who lives in or has visited a tropical country is likely familiar with the chipper chirping of the gecko. These friendly little lizards inhabit homes and jungles stretching from Indonesia to Tanzania to the Dominican Republic. They emerge after sunset, taking advantage of their night vision eyesight—which is 350 times more powerful than a human’s—and are welcome guests in homes and hotels since they gobble up mosquitoes and other insect pests.

In addition to the locals, scientists also love these colorful lizards. Geckos possess the unique ability among lizards to run up flat walls and scamper across ceilings, even if the surface is very smooth. Researchers have been puzzling over this ability for years, and dozens of labs have tested gecko adhesion in the hopes of harnessing this superpower for potential use in everything from robotics to space technology to medicine to “gecko tape.”

Gecko toes, it turns out, contain hair-like structures that form a multicontact interface, meaning geckos grip with thousands of tiny adhesive structures rather than what appears to be a single uniform foot.

Gaps remain, however, in researchers’ understanding of how gecko feet interact with surfaces in their natural environment, especially in dry versus wet conditions. Scientists know that gecko toe pads are superhydrophobic, or water repelling, yet geckos lose their ability to cling to glass when it becomes wet. Why don’t they just repel the water and cling to the glass surface below? Similarly, scientists wonder how geckos deal with wet leaves in the forest during rain storms.

A new paper published in Proceedings of the National Academy of Sciences investigates these mysteries. The authors decided to test gecko grip on a range of wet and dry materials that both attract and repel water. To perform their experiments, they outfitted six tokay geckos with gecko-sized harnesses. They placed the geckos onto four different types of materials, such as glass, plastic and a substance designed to mimic waxy tropical leaves. After giving the lizards some time to adjust to their new surroundings, the researchers applied a uniform tugging pressure onto the geckos’ harnesses, pulling in the opposite direction of where the animals were walking. Eventually, the geckos could cling no longer and lost their grip. This allowed the team to measure the adhesive force required to displace the animals. They repeated the same experiments under very wet conditions, too.

The authors found that materials that are more “wettable”—an indication of the degree to which a surface attracts water molecules—the less force it took to disrupt the clinging geckos’ grips. Glass had the highest wettability of the surfaces the researchers tested, and geckos easily slipped from wet glass compared to dry glass. When that material gets wet, water forms a thin, attractive film that prevents the gecko’s tiny toe hairs from coming into contact with the surface.

The low wettability properties of waxy leaves, on the other hand, allow geckos to establish a sturdy grip, even in rain storms, because leaves actively repel water. Geckos performed equally well in wet and dry conditions on the leaf-mimicking surface, the researchers found. 

How the geckos interact with surfaces depends upon a thermodynamic theory of adhesion, the authors conclude. These features are dictated by Van der Waals force, or the sum of attractive and repulsive interactions between gecko toes and the characteristics of the surfaces they come into contact with. So long as those attractive forces jibe, geckos are in luck for getting a grip on whatever surface they come into contact with, regardless of whether it’s wet or dry.

Using our whole-animal adhesion results, we found that wet surfaces that are even weakly [water repulsive] allow the gecko adhesive system to remain functional for clinging and likely locomotion as well.

Our findings suggest a level of versatility in the gecko adhesive system that previously was not accounted for and calls into question interesting evolutionary, ecological, and behavioral predictions.

In addition to shedding light on how gecko adaptations help the lizards cope with their natural environment, the authors think their findings may contribute to designing new synthetic gecko robots that may overcome real-life geckos’ wet glass Achilles’ heel, useful perhaps for cleaning skyscraper windows, spying on suspected terrorists, or simply changing a hard-to-reach light bulb.

Polar bear-brown bear hybrids like this pair at Germany’s Osnabrück Zoo are becoming more common as melting sea ice forces the two species to cross paths. Photo by Corradox/Wikimedia Commons

Scientists and science writers have created catchy monikers for hybrid species, much the way tabloid writers merge the names of celebrity couples (Kimye, Brangelina, anyone?). Lions and tigers make ligers. Narwhals meet beluga whales in the form of narlugas. And pizzlies and grolar bears are a cross between polar bears and grizzlies. In coming years, their creativity may get maxed out to meet an expected spike in the number of hybrids. A driving force? Climate change. 

A new study published in the journal PLOS Genetics showed that there’s a historic precedent for cross-breeding among polar bears and brown bears–we’ll jump on the bandwagon and call them brolar bears. The researchers also asserted that such hybridization is currently occurring at an accelerated clip. As sea ice melts, polar bears are forced ashore to an Arctic habitat that’s increasingly hospitable to brown bears. There have been recent sightings in Canada of the resulting mixed-breed animals, which have coloring anomalies such as muddy-looking snouts and dark stripes down their backs, along with the big heads and humped backs typical of brown bears.

As it turns out, climate-change-induced hybridization extends well beyond bears. A 2010 study published in the journal Nature listed 34 possible and actual climate-change-induced hybridizations (PDF) of Arctic and near-Arctic marine mammals–a group that has maintained a relatively consistent number of chromosomes over time, making them particularly primed for hybridization. Here are some highlights from this list, along with some more recent discoveries. 

In 2009, a bowhead-right-whale hybrid was spotted in the Bering Sea by the National Oceanic and Atmospheric Administration’s (NOAA) National Marine Mammal Laboratory. Right whales, which typically hail from the North Pacific and North Atlantic, will increasingly be migrating north into the Arctic Ocean, the domain of bowheads, as a result of climate change–and co-mingling their DNA. The authors of the Nature study determined that “[d]iminishing ice will encourage species overlap.”

The narluga has a very big head, according to the scientists who found one in West Greenland. Its snout and lower jaw were particularly burly, and its teeth shared some similarities with both narwhals and belugas. Both species, which form a whale family called monodontidae, live in the Arctic Ocean and hunters have reported seeing more whales of similar stature in the region.

Harbor and Dall’s porpoises have already been mixing it up off the coast of British Columbia, and given that harbor porpoises are likely to keep moving north from the temperate seas of the North Atlantic and North Pacific into the home waters of the Dall’s, the trend is expected to continue. (Click here to see rare photos of the hybrid porpoise.)

Scientists in Ontario, Canada, are investigating inter-breeding between southern and northern flying squirrels as the southern rodents push into northern habitats. The hybrid squirrels have the stature of the southern species and the belly coloring of the northern one. The video below details the research.

Hybrid species often suffer from infertility, but some of these cross-breeds are having success at procreating. For example, researchers recently discovered the offspring of a female pizzly and a male grizzly bear (a subspecies of the brown bear) in Canada’s Northwest Territories. Despite cases like these, scientists are debating whether all of this hybridization is healthy. “Is this going to be a problem for the long-term existence of parental species? Are they going to merge into one big hybrid population?” asked University of California, Berkeley evolutionary biologist Jim Patton in an interview.

In the case of inter-bred polar bears, the concern is that the changing climate will be more welcoming to brown bears, and that while inter-species mating at first might appear to be an adaptive technique for polar bears, it could end up spelling their demise in all ways except cellular structure–much the way Neanderthals were folded into the human gene pool thanks to early humans in Europe more than 47,000 years ago.

Rare and endangered species are particularly vulnerable to the pitfalls of hybridization, according to the authors of the Nature study. “As more isolated populations and species come into contact, they will mate, hybrids will form and rare species are likely to go extinct,” they wrote. “As the genomes of species become mixed, adaptive gene combinations will be lost.”

Such is likely the case with the narluga. Scientists determined the animal’s lack of a tusk is a liability because the tusk is a measure of the narwhal’s breeding prowess. And a pizzly living at a German zoo showed seal-hunting tendencies, but lacked the swimming prowess of polar bears.

As Patton pointed out, it will be many years until we know the full consequences of hybridization. “We’re only going to find out in hindsight,” he said. But that’s not a reason to be complacent, according to the Nature authors, who called for the monitoring of at-risk species. “The rapid disappearance of sea ice,” they wrote, “leaves little time to lose.”

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A model of a giant squid versus sperm whale. Photo taken at the American Museum of Natural History by Mike Goren from New York

For centuries, monsters of the deep sea captivated the imagination of the public and terrified explorers–none more so than the many-tentacled kraken. In 13th century Icelandic sagas, the Vikings wrote of a terrifying monster that “swallows both men and ships and whales and everything that it can reach.” Eighteenth century accounts from Europe describe arms emerging from the ocean that could pull down the mightiest ships, attached to bodies the size of floating islands.

Today, we’re fairly confident that a tentacled beast will not emerge from the depths to swallow up a cruise ship, but the enduring allure of such creatures lingers. None of the ocean’s massive animals, perhaps, are as intriguing as the giant squid.

Now, scientists have come one step closer to unraveling the mysteries behind this rare animal. As it turns out, contrary to some squid enthusiasts’ former hypothesis, all giant squid belong to a single species. What’s more, those animals are extremely similar genetically.

To arrive at these findings, researchers from the University of Copenhagen’s Natural History Museum of Denmark along with collaborators from 7 other countries genetically analyzed bits and pieces of 43 of the animals–which can grow more than 40 feet long and weigh nearly 2,000 pounds–recovered from all over the world.

Photo by Winkelmann et. al.

Their results indicated that, unlike most marine animals, giant squid harbor almost no genetic diversity. Remarkably, individuals as far apart as Florida and Japan, from a statistical standpoint, shared almost the same DNA. The giant squid’s genetic diversity turned out to be 44 times lower than the Humboldt squid, another large species, and seven times lower than the diversity of a population of oval squids living in a restricted area and thus prone to inbreeding. In fact, the giant squid’s diversity was lower than all other measured oceanic species, save the basking shark, which scientists believe recently underwent a severe population bottleneck in which most animals died and only a few individuals survived and repopulated the species.

The researchers can only speculate about this finding’s underlying reasons–the giant squid’s genetic data alone cannot provide a plausible explanation. Perhaps something about the giant squid makes it advantageous to cull mutations from its genome? Alternatively, the animals may have undergone a recent bottleneck, similar to what happened to the basking sharks, meaning that all giant squid following that event are closely related. Or perhaps a few foundered squid somehow wandered in new stretches of ocean, so when they populated these new habitats their offspring shared the same squid family tree. The short answer, however, is that the researchers simply do not know.

“We cannot offer a satisfactory explanation for the low diversity, and this requires future studies to resolve,” they write in a paper published this week in Proceedings of the Royal Society B.

This has been a big year for giant squid. In January, a Japanese team released the first footage of a giant squid interacting in its natural environment. Yet much still remains to be learned about these enigmatic creatures. For example, researchers still have no idea how large of a range the adult squid patrol, how long they live, how quickly they grow and whether problems such as climate change affect their populations.

For the imagination’s sake, however, perhaps it’s best if some mysteries endure.

“Despite our findings, I have no doubt that these myths and legends will continue to get today’s children to open their eyes up–so they will be just as big as the real giant squid is equipped with to navigate the depths,” said lead researcher Tom Gilbert in a statement.