May 21, 2013
For nearly 150 years, starting in the late 17th century, millions of people living in Ireland subsisted largely off one crop: the potato. Then, in 1845, farmers noticed that their potato plants’ leaves were covered in mysterious dark splotches. When they pulled potatoes from the ground, most were shrunken, mushy and inedible. The blight spread alarmingly quickly, cutting yields from that year’s harvest in half. By 1846, harvest from potato farms had dropped to one quarter of its original size.
The disease—along with a political system that required Ireland to export large amounts of corn, dairy and meat to England—led to widespread famine, and nearly all of the few potatoes available were eaten, causing shortages of seed potatoes that ensured starvation would continue for nearly a decade. Ultimately, over one million people died, and another million emigrated to escape the disaster, causing Ireland’s population to fall by roughly 25 percent; the island has still not reached its pre-famine population levels today.
At the time, the science behind the blight was poorly understood, and most believed it was caused by a fungus. During the twentieth century, scientists determined that it was caused by an oomycete (a fungus-like eukaryote) called Phytophthora infestans. However, without access to the 1840s-era specimens, they couldn’t identify exactly which strain of the organism was responsible.
Now, an international group of scientists has gone back and sampled the DNA of Irish potato leaves preserved in the collections of London’s Kew Gardens since 1847. In doing so, they discovered that a unique, previously unknown strain of P. infestans that they call HERB-1 caused the blight.
The researchers, from the Sainsbury Laboratory in the UK and the Max Planck Institutes in Germany, came to the finding as part of a project sequencing DNA from 11 different preserved historial samples and 15 modern ones to track the evolution of the pathogen over time, published today in the journal eLife [PDF].
Currently, P. infestans is distributed worldwide, with the vast majority comprised of the destructive strain US-1. Most of the other strains of P. infestans occur only in Mexico’s Toluca Valley, where wild potato varieties are indigenous, so scientists long believed that US-1 had been responsible for the 1840s famine.
But when the researchers extracted small pieces of intact DNA from the old dried-out potato leaves, originally collected from from Ireland, Great Britain, Europe and North America, and compared them with present-day P. infestans specimens, they found that the strain responsible for the famine differed slightly from today’s US-1.
Based on their analysis of the genetic variation between the two strains and the other historical samples, they suggest that sometime in 1842 or 1843, the ancestor of the HERB-1 strain of P. infestans made it out of Mexico to North America and then to Europe, perhaps contained within the potatoes that ships carried as food for their passengers. Soon, it spread across the world, triggering famine in Ireland, and persisting until the 1970s, when it died out and was largely replaced by the US-1 strain. The two strains likely split apart sometime soon after their common ancestor made it out of Mexico.
The study is the first time that the genetics of a plant pathogen have been analyzed by extracting DNA from dried plant samples, opening up the possibility that researchers can study other plant diseases based on the historical collections of botanical gardens and herbaria around the world. Better understanding the evolution of plant diseases over time, the team says, could be instrumental in figuring out ways to breed more robust plant varieties that are resistant to the pathogens that infect plants today.
April 17, 2013
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.
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.
April 2, 2013
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—O3, 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.
March 21, 2013
Designing a robot that can easily move across loose terrain—say, a rover meant to traverse the surface of Mars—poses a unique engineering challenge: Wheels commonly sink into what engineers call “flowable ground” (mixtures of sand, soil, mud and grass).
Given the many biologically-inspired innovations in robotics, a team of researchers from Georgia Tech had an idea—to base a design on desert creatures such as zebra-tailed lizards that are able to scramble across a loose, sandy surface without slowing down. Their efforts allowed them to create this small six-legged device, presented in an article published today in Science, which can run across a granular surface in a way uncannily reminiscent of a reptile.
The research team, led by Chen Li, designed the device after studying the locomotion of various creatures and mathematically simulating the performance of different types of legs (varying in number, shape and length) in several distinct environments. They hope their research will spur the development of a field they’ve termed “terradynamics”—just as aerodynamics is concerned with the performance of winged vehicles in air, their field will study the motion of legged vehicles on granular surfaces.
To design their robot, they used these simulations to determine the exact leg lengths, movement speeds and levels of force that would propel devices across a loose surface without causing them to sink in too deeply. They then printed a variety of leg types with a 3D printer, and built robots to test them in the lab.
One of their most interesting findings is that the same types of design principles apply for locomotion on a variety of granular surfaces, including poppy seeds, glass beads and natural sand. Their simulations and real-world experiments revealed that C-shaped legs generally worked best, but that any type of bow-shaped limbs worked relatively well because they spread out the weight of the device over long (albeit narrow) leg surfaces as the legs come into contact with the ground over the course of a stride.
The applications of this kind research are broad: This particular robot, the researchers say, could be developed into a useful search-and-rescue or scouting device, while the principles derived from the field of terradynamics could be useful in designing probes to explore other planets in the future. They could also help biologists to better understand the how life forms here on earth have evolved to move across our planet’s surface.
March 19, 2013
In 2010, the surprising discovery that Neanderthals likely crossbred with our ancestors tens of thousands of years ago generated headlines around the world.
Now, we have a new finding about the sex lives of early Homo sapiens: It looks like they engaged in some inbreeding as well.
That is the conclusion of anthropologist Erik Trinkhaus of Washington University in St. Louis and Xiu-Jie Wu and Song Xing of the Chinese Academy of Sciences’ Institute of Vertebrate Paleontology and Paleoanthropology, based on a fractured 100,000-year-old skull excavated from China’s Nihewan Basin. Their finding, published yesterday in PLOS ONE, is that the skull shows evidence of an unusual genetic mutation that is likely the result of high levels of inbreeding.
The researchers used CT scanning and 3D modeling to join together for the first time the 5 pieces of the fractured skull—known as Xujiayao 11, named for the site where it was found back in 1977—and realized that it exhibited an unusual deformity. When the pieces are combined, they leave a hole on the crown of the skull, but there is no evidence that the fracture was caused by a traumatic injury or disease. As a result, they consider it most likely that the hole is a defect known as an enlarged parietal foramen.
Nowadays, this hole is mostly found in people with a particular pair of genetic mutations on chromosomes 5 and 11—most often a consequence of inbreeding—and occurs in about 1 of 25,000 live births. The mutation interferes with bone formation in the skull over the first five months of an infant’s life, when the pieces of the skull are supposed to fuse together to cover up the “soft spot.”
Given the tiny sample size of human skulls this old and the fact that similar kinds of genetic abnormalities have been seen so often in other prehistoric skulls—the researchers count 22 individuals with skull deformities discovered from this era—Trinkhaus thinks the simplest explanation is that small and unstable human populations forced our ancestors to inbreed.
If no inbreeding occurred, “the probability of finding one of these abnormalities in the small available sample of human fossils is very low, and the cumulative probability of finding so many is exceedingly small,” he said in a press statement. “The presence of the Xujiayao and other Pleistocene [2.6 million to 12,000 years ago] human abnormalities therefore suggests unusual population dynamics, most likely from high levels of inbreeding and local population instability.”
Such inbreeding was likely inevitable, given that most of humanity likely lived in small, isolated populations for most of our species’ evolution. For example, some scientists believe that an earlier population bottleneck that predated this skull may have driven the worldwide human population to as low as 2,000 individuals, at times making inbreeding a necessity. Our ancestors certainly didn’t understand the importance of genetic diversity and the dangerous consequences of inbreeding. But with such a scant population, the survival of our species might actually have depended on our ancient grandmothers procreating with their male relatives.
The good news? The researchers say that the genetic deformity preserved in this skull as a result of inbreeding may not have been too detrimental for this individual. Normally, it’s linked with major cognitive problems, but that’s doubtful in this case, given the demanding conditions of surviving in the Pleistocene. This prehistoric human appears to have survived to a ripe old age—which, in those days, probably means the individual lived into his or her thirties.