Evolution Right Under Our Noses
By CARL ZIMMER
To study evolution, Jason Munshi-South has tracked elephants in central Africa and proboscis monkeys in the wilds of Borneo. But for his most recent expedition, he took the A train.
Dr. Munshi-South and two graduate students, Paolo Cocco and Stephen Harris, climbed out of the 168th Street station lugging backpacks and a plastic crate full of scales, Ziploc bags, clipboards, rulers and tarps. They walked east to the entrance of Highbridge Park, where they met Ellen Pehek, a senior ecologist in the New York City Parks and Recreation Department. The four researchers entered the park, made their way past a basketball game and turned off the paved path into a ravine.
They worked their way down the steep slope, past schist boulders, bent pieces of rebar, oaks and maples, hunks of concrete and freakish poison ivy plants with leaves the size of a man’s hands. The ravine flattened out at the edge of Harlem River Drive. The scientists walked north along a guardrail contorted by years of car crashes before plunging back into the forest to reach their field site.
“We get police called on us a lot,” said Dr. Munshi-South, an assistant professor at Baruch College. “Sometimes with guns drawn.”
Dr. Munshi-South has joined the ranks of a small but growing number of field biologists who study urban evolution — not the rise and fall of skyscrapers and neighborhoods, but the biological changes that cities bring to the wildlife that inhabits them. For these scientists, the New York metropolitan region is one great laboratory.
White-footed mice, stranded on isolated urban islands, are evolving to adapt to urban stress. Fish in the Hudson have evolved to cope with poisons in the water. Native ants find refuge in the median strips on Broadway. And more familiar urban organisms, like bedbugs, rats and bacteria, also mutate and change in response to the pressures of the metropolis. In short, the process of evolution is responding to New York and other cities the way it has responded to countless environmental changes over the past few billion years. Life adapts.
The mice are the object of Dr. Munshi-South’s attention. Since 2008, he and his colleagues have fanned out across the city to study how the rise of New York influenced the evolution of the deer mice.
On this day in Highbridge Park his students, Mr. Cocco and Mr. Harris, spread a blue tarp on the forest floor, while Dr. Munshi-South walked to an orange flag planted in the ground. He picked up an aluminum box sitting next to the flag and pushed in a door at one end. At the other end of the box crouched a white-footed mouse. It gazed back at Dr. Munshi-South with bulging black eyes.
The researchers inspected 50 traps laid the day before and found seven mice inside. They plopped each mouse out of its trap and into a Ziploc bag. They clipped a scale to each bag to weigh the mice. Dr. Munshi-South gently took hold of the animals so his students could measure them with a ruler along their backs.
Dr. Munshi-South and his colleagues have been analyzing the DNA of the mice. He’s been surprised to find that the populations of mice in each park are genetically distinct from the mice in others. “The amount of differences you see among populations of mice in the same borough is similar to what you’d see across the whole southeastern United States,” he said.
White-footed mice live today in forests from Canada to Mexico. They arrived in the New York City region after ice age glaciers retreated 12,000 years ago. In the past few centuries, as their forest home became a city, they survived in New York’s patches of woods. (House mice, which New Yorkers battle in their apartments, arrived with European settlers.) Research by Dr. Munshi-South and his colleagues suggests that New York’s white-footed mice, which occupy isolated patches, are adapting to life in the city.
When Dr. Munshi-South opened the final trap, the seventh mouse had run out of patience. It shot out of its box and raced off into the brush.
Mr. Cocco shrugged. “They are New Yorkers, after all,” he said.
Pollution Forces Change
Evolution is one of life’s constants. New species emerge; old ones become extinct. Environmental changes have often steered evolution in new directions. And modern cities like New York have brought particularly swift changes to the environment. European settlers cut down most of New York’s original forest; towns grew and then merged into a sprawling metropolitan region. The chemical environment changed as well, as factories dumped chemical pollution into the water and soil.
Pollution has driven some of the starkest examples of evolution around New York. Hudson River fish faced a dangerous threat from PCBs, which General Electric released from 1947 to 1977. PCBs cause deformities in fish larvae. “These are important changes,” said Isaac I. Wirgin of New York University Medical Center. “If you’re missing your jaw, you’re not going to be able to eat.”
Dr. Wirgin and his colleagues were intrigued to discover that the Hudson’s population of tomcod, a bottom-dwelling fish, turned out to be resistant to PCBs. “There was no effect on them at all,” Dr. Wirgin said, “and we wanted to know why.”
In March, he and his colleagues reported that almost all the tomcod in the Hudson share the same mutation in a gene called AHR2. PCBs must first bind to the protein encoded by AHR2 to cause damage. The Hudson River mutation makes it difficult for PCBs to grab onto the receptor, shielding the fish from the chemical’s harm.
The AHR2 mutation is entirely missing from tomcod that live in northern New England and Canada. A small percentage of tomcod in Long Island and Connecticut carry the mutation. Dr. Wirgin and his colleagues concluded that once PCBs entered the Hudson, the mutant gene spread quickly.
“When these chemicals first starting getting released, if you had the normal form of the gene, you probably weren’t going to make it,” Dr. Wirgin said.
Evolution has also run in the opposite direction as government agencies cleaned up some of the pollution around New York. In 1989, Jeffrey Levinton of Stony Brook University and his colleagues discovered that a population of mud-dwelling worms in the Hudson had evolved resistance to cadmium. They lived in a place called Foundry Cove near a battery factory near West Point. Dr. Levinton and his colleagues found that the worms produced huge amounts of a protein that binds cadmium and prevents it from doing harm.
In the early 1990s, the federal Environmental Protection Agency hauled away most of the cadmium-laced sediment from Foundry Cove. Over nine generations, the Foundry Cove worm populations became vulnerable again. This shift occurred, Dr. Levinton and his colleagues reported last year, as worms from less contaminated parts of the river moved in. They are interbreeding with the resident worms, and the resistant mutations are becoming rarer.
Bacteria Adapt, Too
Today, scientists can scan the entire genomes of New York’s animals and plants to look for evolutionary changes. Last month, Mr. Harris presented new data on white-footed mice at the annual meeting of the Society for the Study of Evolution. Mr. Harris and his colleagues have identified mutations in more than 1,000 genes that are present in all New York City mice, but missing from mice in Harriman State Park, 45 miles north of the city.
The scientists are investigating whether these mutations have helped the mice adapt to life in New York City. Clues that some of them do are found in the functions of the mutated genes. Many of the genes are involved in fighting bacteria, while others are for reproduction and still others for coping with stress from exposure to chemicals. It’s possible that these new mutations are spreading independently in each of the parks in the city.
“The idea is that the urban pressures are the same everywhere, and they’re all adapting,” said Mr. Harris.
Cities attract only a small fraction of evolutionary biologists, who often work in lusher places like the Amazon. But urban evolution is attracting more research these days, because cities are fast-growing, and the urban environment is quickly taking over large areas of the Earth’s surface.
Evolution is not just taking place in New York’s rivers and parks. It’s also taking place inside its hospitals. In 1997, Dr. John Quale, an infectious diseases physician at SUNY Downstate Medical Center, discovered a newly evolved strain of bacteria in the city that is resistant to most antibiotics.
The bacterium, known as Klebsiella pneumoniae, is often found in hospitals, where it can cause pneumonia and other life-threatening infections. Doctors typically treat Klebsiella with a class of antibiotics called carbapenems. Dr. Quale and his colleagues discovered carbapenem-resistant Klebsiella in four hospitals in Brooklyn.
The new genetic recipe proved to be a winning solution. Dr. Quale’s surveys charted the strain as it spread from hospital to hospital throughout New York. “It’s one strain that’s adapted very well to the hospital environment, and it clearly has a survival advantage over other bacteria,” Dr. Quale said.
Once the new strain had established itself in New York, it began to spread out of the city. It’s now reached 33 other states, and has become a serious problem in other countries, including France, Greece and Israel.
Dr. Quale and his colleagues found that this new strain of Klebsiella is especially dangerous. About half of patients who get infected die. Doctors can cure some infections, but only by using toxic drugs that can cause nerve and kidney damage.
Fortunately, in recent years, New York has seen some modest success in fighting the bacterium. From 2006 to 2009, Brooklyn saw a decrease in the prevalence of the bacterium. But Dr. Quale doesn’t expect total eradication. “I think it’s always going to be with us — it’s so entrenched in our hospitals,” he said.
A Biological Melting Pot
While Dr. Quale studies evolution that happens out of sight, some scientists do their work in plain view. On a recent afternoon, James Danoff-Burg and Rob Dunn were clambering around in a narrow Broadway median on the Upper West Side. Dr. Danoff-Burg, a biologist at Columbia University, was digging up plastic cups from the ivy. Dr. Dunn, a biologist from North Carolina State University, was five feet in the air, crouched on a bough of a Japanese maple.
“New one! New one!” Dr. Dunn shouted over the traffic. He and Dr. Danoff-Burg were surveying the median for species of ants. Dr. Dunn had spotted Crematogaster lineolata, an ant species that he and Dr. Danoff-Burg had never found before in this particular urban habitat.
From his backpack, Dr. Dunn pulled out an aspirator, a rubber tube connected to a glass jar. Holding one end of the tube over the ant, he sucked it in. Instead of going into his mouth, the insect tumbled into the jar. (One hazard of urban evolutionary biology, said Dr. Dunn, is having your aspirator mistaken for a piece of drug paraphernalia.)
Dr. Danoff-Burg, Dr. Dunn and their colleagues chose to study the medians of Broadway to see how human activity alters biodiversity. In this artificial city, there is no environment more artificial than these medians, which sit on fill that was poured on top of subway tunnels. The scientists have found a blend of ant species, some that have been here since before the city existed, and others that have arrived more recently, hitching rides on ships, planes and trucks. The most common ant Dr. Danoff-Burg and Dr. Dunn encounter is the pavement ant (Tetramorium caespitum), which came from somewhere in Europe.
Biologists find a mixture of native and non-native in all the life forms they study in New York, from the trees in Central Park to the birds of Jamaica Bay. The biodiversity of New York today is the result of extinctions, invasions and adaptations. Manhattan was once home to 21 native species of orchids; today they’re all gone. In the current issue of Global Ecology and Biogeography, a team of scientists surveyed plant biodiversity in New York and 10 other cities. They found that 401 native plant species have vanished from New York since 1624, while 1,159 remain. New York’s native flora is vulnerable to extinction today in part because it was well adapted to the closed forests that once stood where the city is now.
Newcomers and Natives
As native species became extinct, new ones came to the city. As a major point of entry to the United States, New York is where many of North America’s invasive species first arrived. Some introductions were intentional. Starlings were brought to Central Park in 1890, for instance, as part of a project to bring every bird mentioned in Shakespeare to the United States. But most introduced species slipped in quietly.
Many non-native species quickly died out, but some fit comfortably into the city’s wildlife, and others wreaked havoc — first in New York and then beyond. New York was the port of entry for Dutch elm disease, chestnut blight, Asian longhorned beetles and other threats to trees across the country.
As the invaders adapted to New York, they put extra pressure on native species, competing with them for space and food. Recent research by the Brooklyn Botanic Garden found that American bittersweet vines are dwindling away within a 50-mile radius of New York City, outcompeted by Oriental bittersweet. At the same time, the two species are interbreeding, producing hybrids. “It’s a double-whammy,” said James D. Lewis, a plant ecologist at Fordham University.
Yet many native species still hold on. Dr. Danoff-Burg and Dr. Dunn were surprised to find that 9 out of the 13 ant species living in Broadway’s medians are native. Once the medians were built, the native species rushed in along with the invaders and created an ecosystem.
Dr. Danoff-Burg and Dr. Dunn are trying to figure out what controls the balance of native and new species in New York. They don’t understand why some medians have more biodiversity than others, for example. On natural islands, biodiversity tends to increase with the size of the islands. Dr. Danoff-Burg and Dr. Dunn find no such correlation in the medians on Broadway. They also have to determine how native species of ants are coexisting in such close quarters with invasive species.
New York, in other words, is an evolutionary experiment — one that some scientists find fascinating to observe. “It’s some new thing emerging around us,” Dr. Dunn said.
This article has been revised to reflect the following correction:
Correction: July 28, 2011
An article on Tuesday about the evolution of organisms in urban areas referred incorrectly to the treatment for infection with Klebsiella pneumoniae, a newly evolved strain of bacteria discovered in New York City. Doctors typically prescribe drugs from a large class of antibiotics known as carbapenems; there is no single antibiotic called carbapenem.
This article has been revised to reflect the following correction:
Correction: August 4, 2011
An article on July 26 about urban evolution described the rise of nonnative Oriental bittersweet vines incorrectly. The vines are outcompeting American bittersweet in a 50-mile radius of New York City, research by the Brooklyn Botanic Garden has found; they are not replacing American bittersweet at the Brooklyn Botanic Garden.
Category Archives: Evolution
Giant fungus discovered in China
The most massive fruiting body of any fungus yet documented has been discovered growing on the underside of a tree in China.
The fruiting body, which is equivalent to the mushrooms produced by other fungi species, is up to 10m long, 80cm wide and weighs half a tonne.
That shatters the record held previously by a fungus growing in Kew Gardens in the UK.
The new giant fungus is thought to be at least 20 years old.
The first example of the new giant fungus was recorded by scientists in 2008 in Fujian Province, China, by Professor Yu-Cheng Dai of the Herbarium of biology at the Chinese Academy of Sciences in Shenyang and his assistant Dr Cui.
“But the type collection was not huge,” Prof Dai told BBC Nature.
However, “we found [the] giant one in Hainan Province in 2010.”
The researchers were in the field studying wood-decaying fungi when they happened upon the specimen, which they describe in the journal Fungal Biology.
“We were not specifically looking for this fungus; we did not know the fungus can grow so huge,” he said.
“We were surprised when we found it, and we did not recognise it in the forest because it is too large.”
The fungus, F. ellipsoidea, is what mycologists call a perennial polypore – otherise known as a bracket fungus.
Being a perennial, it can live for a number of years, which may have enabled it to grow to such large size.
By colonising the underside of the large fallen tree, the fungus also had a huge amount of dead and decaying wood to feed on, helping to fuel its growth.
Fruiting bodies, such as mushrooms and toadstools, are the sexual stages of a many higher types of fungi, producing seeds or spores that produce further generations.
The giant fruiting body of F. ellipsoidea forms a long, brown shape up to 10.85m long, 82-88cm wide, and 4.6-5.5cm thick.
Tests on the density of the fruiting body suggest the whole thing weighs 400-500kg; it is also estimated to hold some 450 million spores.
“A small piece of the fruiting body is almost like my size,” said Prof Dai.
The previous record holder was a specimen of Rigidoporus ulmarius, a polypore with a pileate fruiting body found in Kew Gardens in the UK in 2003.
It measured approximately 150cm in diameter with a circumference of 425cm.
After their initial encounter with the new record-breaking fungus, the scientists took samples of it back to the lab where to be analysed.
These tests revealed that the fungus was the species Fomitiporia ellipsoidea, and the researchers made two subsequent trips to study the specimen further.
Why do seahorses resemble horses? – January 25, 2011
The wacky, curvaceous shape of a sea horse makes it easier to catch its prey without having to go to the trouble of swimming very far, a new study in Nature Communications has found.
Seahorses employ a sit-and-wait strategy, hiding behind lush sea grasses till their meal – small shrimp or fish larvae – happen along. At that point, they snap their heads upwards toward the prey and use suction to draw the meal into their snouts.
The tendons of the rotational muscles of the fish are like elastics that snap the head upward remarkably quickly as the prey passes by. The whole process is called pivot feeding and takes about 5 milliseconds. Pipefish and sea dragons, which also fall in the Syngnathid family of fishes, use the same mechanism.
But why the seahorse evolved a head that is bent in relation to the rest of the body in a horse-like manner has been a mystery. Their evolutionary ancestors resembled the pipefish, with their trunk and head in a straight line.
Sam Van Wassenbergh at the University of Antwerp and his colleagues now suggest the bent head gives the seahorse an advantage by allowing it to move its head further and strike at a greater distance.
Consider the linear pipefish, Syngnathus leptorhynchus, which also uses the pivot feeding mechanism. When the creature rotates its head toward the prey to capture it, the sudden momentum is transferred down the body to create movement in the trunk. The head movement itself is restricted.
This is not a problem for fish that swim around while hunting, such as the pipefish, because they can compensate for a decreased head strike range by moving themselves forward, say the scientists. But for a creature that refuses to budge to hunt for food, even small improvements in its strike range can confer a fitness advantage.
In seahorses, the trunk is at a sharp angle to the head and so has significant inertia. When the head rotates, the trunk reacts but less than in a pipefish. In addition, there is a compressed region in the bent neck that snaps the head forward to increase the speed of the strike.
“When you shoot a rifle, you get a recoil movement. Same thing happens with seahorses,” says Wassenberg.
The researchers created a biomechanical model to study feeding, and confirmed their model by studying real world data collected from videos of prey capture by various seahorse and pipefish species.
“Results were quite spectacular, I think,” says Wassenberg.
From Nature News:
Published online 22 July 1999 | Nature | doi:10.1038/news990722-2
Species without frontiers
140 years after the publication of Charles Darwin’s momentous Origin of Species, two groups of theorists seem to be making headway against one of evolutionary biology’s most difficult problems – how the formation of new species, or ‘speciation’, actually happens.
Understanding speciation is still a fundamental problem in biology. It is believed that speciation usually occurs when pre-existing populations are divided by a geographical barrier, such as a river or a range of mountains. Unable to interbreed, the sundered populations go their own way, until, eventually, two new species are found where there was one before. The central part of the argument is the barrier: without one, individuals have the potential to breed freely, mixing up parental traits and keeping the population homogeneous. Theorists have not been able to show convincingly how speciation might occur without physical separation of the founding populations, except in certain rather specialized circumstances.
This difficulty, though, is hard to reconcile with mounting evidence that many species form without physical barriers to interbreeding, so-called ‘sympatric’ speciation. Many lakes in Africa, for example, host ‘flocks’ of dozens or hundreds of closely related species of cichlid fish, all of which seem to have evolved in thge same body of water from a single, ancestral species, often within a few thousand years – an evolutionary eyeblink. Although similar in general anatomy, these fishes display a dazzling array of colours, habits and ecological specializations: some graze algae, whereas others eat other fishes. One species lives by plucking the eyes from other cichlids.
Ecological specialization is the key to driving sympatric speciation, according to a brace of reports in the 22 July issue of Nature. One study is from Alexey S. Kondrashov of the National Institutes of Health, Bethesda, Maryland, and Fyodor A. Kondrashov of Simon’s Rock College, Great Barrington, Massachusetts; the other from Ulf Dieckmann and Michael Doebeli of the Institute of Systems Analysis, Laxenberg, Austria, and the University of Basel, Switzerland.
Sympatric speciation ought to be simple. If a lake, newly colonized by a species of fish, contains two distinct prey items – large beetles and small shrimp, say – then natural selection should favour the evolution of large and small fishes, leaving medium-sized fishes at a disadvantage. Eventually, the population will become divided into large and small fishes, each of which will mate with their own kind.
The problem is sex. Sexual reproduction scrambles the genes in each generation, so that there will always be a proportion of medium-sized fishes in the population. This tendency can only be kept at bay by rigorously finicky fishes, which will only mate with fishes of their own general appearance.
Even then, there is a problem: that is, if the genes that govern mate choice (for attractive coloration, for example) are different from the genes that govern ecological specialization (such as size and shape), there is still the possibility that fishes specialized for one kind of life will prefer to mate with fishes specialized for another.
It is at this point that theorists have fudged, by assuming that genes for mate choice and ecological specialization are either the same, or can effectively be treated as such. But this assumption need not apply to real life. Where next?
This is where the new research comes in. Both sets of researchers model plausibly realistic scenarios, involving several genes for mate choice and ecological specialization. Although their results and methods differ in their technical details, both show how sympatric can be achieved by a steady build-up of genetic associations between genes for mate choice and genes for specialization, until a point comes when the two sub-populations become sexually isolated – the point where speciation can be said to have happened.
The Dieckmann and Doebeli model, in particular, provides a good account for what seems to have happened in some African crater lakes, which become colonized by fishes which then diversify into a range of different forms, despite the small size of each lake. Dieckmann and Doebeli envision a situation in which individuals of a single species compete for a single, abundant kind of food item. In such situations, competition can become so intense that some individuals diversify their tastes, switching to other food items which, although less abundant, are less popular, and so the individuals experience less competition. If choosy mating follows a taste for new food items, speciation soon follows. This process works best in new, empty habitats, such as a newly formed crater lake.
Published online 11 December 2008 | Nature | doi:10.1038/news.2008.1297
The genes that drive speciation
Mouse and fruitfly studies provide clues to the origins of species.
Geneticists have identified two genes, one in mice and one in fruitflies, that stop the offspring of different species from reproducing — driving the evolution of new species.
A species can be defined as a group of organisms that can interbreed to produce fertile offspring. Hybrid animals, bred from inter-species pairings — such as mules, from the pairing of a male donkey and a female horse — are usually infertile and many such hybrids do not survive. Sometimes, however, pairings of closely related species, or subspecies, produce hybrids with limited fertility.
Identifying the genes that block reproduction in hybrids can reveal the genetic forces that drive speciation. However, fewer than 10 such genes have been identified to date.
Now Jiri Forejt, a geneticist at the Academy of Sciences of the Prague-based Czech Republic, and his colleagues have identified a speciation gene in mice — the first to be found in mammals1.
Tracking down the gene “was terrible work”, says Forejt, who has spent the last 30 years trying to identity a suspected speciation gene in two subspecies of mice.
Relying on extensive crossing and genetic modification of animals, and thanks to whole-genome data that has only recently become available, Forejt found that male hybrids of these subspecies are infertile because of the Prdm9 gene.
The finding that Prdm9 encodes a protein that silences genes also confirms suspicions that epigenetic changes — traits that can be inherited without changes to the underlying DNA sequence — are important in speciation.
The fruit of the fruitfly hybrid
“The genetics of speciation are almost by definition inherently problematic — speciation means no crosses, and no crosses means it’s very difficult to do genetics,” says Nitin Phadnis, a geneticist at the Fred Hutchinson Cancer Research Center in Seattle.
Phadnis and his colleague, H. Allen Orr at Rochester University in New York, were searching for a speciation genes that caused peculiar hybrids when two related subspecies of Drosophila mated. These male hybrids are infertile for most of their lives, but recover some fertility in their old age — but then can produce only daughters.
The existence of these hybrids suggested to Phadnis and Orr that a segregation distorter — a gene that causes chromosomes bearing it to pass more frequently to offspring, in this case by controlling the sex of progeny — might be linked to speciation.
Because segregation distorters can be involved in an arms race with genes that try to prevent such distortion, they may evolve rapidly, says Phadnis. Although it has been proposed that the rapid evolution of ‘cheating’ genes and their repressors could cause functional divergence between populations resulting in speciation, evidence for this theory has been scarce.
Using similar techniques to the ones Forejt used, however, Phadnis showed that a single gene caused both hybrid sterility and segregation distortion2.
“What this works shows you is that speciation can happen not only because of adaptation to the external environment, but also because of adaptation to the internal genomic environment,” Phadnis says.
“Since there are so few speciation genes identified to the sequence level, adding one more to the list is exciting,” says Roger Butlin, a geneticist at Sheffield University, UK. “I think there will be a lot more interest in segregation distortion and its relationship to speciation.”
Both papers are published in Science and could pave the way to the discovery of more speciation genes in the near future. Forejt is already working to identify additional speciation genes that work with Prdm9 to cause infertility in hybrid mice, but says that other researchers are hot on his heels.
“There is no question that in this era of whole-genome sequences and genomic data it is much easier to identify speciation genes than it used to be” says Michael Nachman, who studies mouse genetics at the University of Arizona in Tucson.
With more genes should come greater insight into speciation. Some geneticists wonder whether only particular classes of genes are important in speciation — such as epigenetic genes or segregation distorters — or whether many sorts of genes help to drive species apart.
“What is surprising about the speciation genes that have been identified [so far] is that there is a whole hodgepodge of different kinds of genes with different functions,” says Nachman. “I don’t think we’re going to see [trends] until dozens of genes are identified, and there’s just a handful now.”