Natural Selection At Work In Dramatic Comeback Of Male Butterflies

ScienceDaily (July 14, 2007) — An international team of researchers has documented a remarkable example of natural selection in a tropical butterfly species that fought back - genetically speaking - against a highly invasive, male-killing bacteria.

Shown is a male Hypolimnas bolina, also called the Blue Moon or Great Eggfly butterfly. A male-killing bacteria has led to skewed sex ratios in populations of H. bolina in the South Pacific, but researchers have found that male butterflies on some islands have bounced back thanks to the rise of a suppressor gene. (Credit: Sylvain Charlat).

Within 10 generations that spanned less than a year, the proportion of males of the Hypolimnas bolina butterfly on the South Pacific island of Savaii jumped from a meager 1 percent of the population to about 39 percent. The researchers considered this a stunning comeback and credited it to the rise of a suppressor gene that holds in check the Wolbachia bacteria, which is passed down from the mother and selectively kills males before they have a chance to hatch.
"To my knowledge, this is the fastest evolutionary change that has ever been observed," said Sylvain Charlat, lead author of the study and a post-doctoral researcher with joint appointments at the University of California, Berkeley, and University College London. "This study shows that when a population experiences very intense selective pressures, such as an extremely skewed sex ratio, evolution can happen very fast."
Charlat pointed out that, unlike mutations that govern such traits as wing color or antennae length, a genetic change that affects the sex ratio of a population has a very wide impact on the biology of the species.
It is not yet clear whether the suppressor gene emerged from a chance mutation from within the local population, or if it was introduced by migratory Southeast Asian butterflies in which the mutation had already been established.
"We'll likely know more in three years' time when the exact location of the suppressor gene is identified," said Charlat. "But regardless of which of the two sources of the suppressor gene is correct, natural selection is the next step. The suppressor gene allows infected females to produce males, these males will mate with many, many females, and the suppressor gene will therefore be in more and more individuals over generations."
Charlat worked with Gregory Hurst, a reader in evolutionary genetics at University College London and senior author of the paper. Descriptions of all-female broods of H. bolina date back to the 1920s, but it wasn't until 2002 that Hurst and colleagues first identified Wolbachia bacteria as the culprit behind the distorted sex ratio.
"We usually think of natural selection as acting slowly, over hundreds or thousands of years," said Hurst. "But the example in this study happened in a blink of the eye, in terms of evolutionary time, and is a remarkable thing to get to observe."
The researchers noted that bacteria that selectively kill male offspring are found among a range of arthropods, so what was seen in this study may not be unusual, despite the fact that it has never before been described in the scientific literature. Previous research has revealed some of the extraordinary ways in which insects adapt to the pressures inherent when nearly all its members are of one gender.
Notably, Charlat and Hurst reported in an earlier study that, thanks to Wolbachia, when males of H. bolina, commonly known as the Blue Moon or Great Eggfly butterfly, become a rare commodity, the number of mating sessions for both males and females jumps, possibly as an attempt to sustain the population despite the odds.
Charlat added that the relationship between Wolbachia and the Blue Moon butterfly illustrates the so-called Red Queen Principle, an evolutionary term named after a scene in Lewis Carroll's famous book, "Through the Looking-Glass," in which the characters Alice and the Red Queen run faster and faster at the top of a hill, only to find that they remain in the same place.
"In essence, organisms must evolve or change to stay in the same place, whether it's a predator-prey relationship, or a parasite-host interaction," said Charlat. "In the case of H. bolina, we're witnessing an evolutionary arms race between the parasite and the host. This strengthens the view that parasites can be major drivers in evolution."
The researchers focused on the Samoan islands of Upolu and Savaii, where in 2001, males of the Blue Moon butterfly made up only 1 percent of the population. In 2006, the researchers embarked on a new survey of the butterfly after an increase in reports of male-sightings at Upolu.
They found that males that year made up about 41 percent of the Blue Moon butterfly population in Upolu. They hatched eggs from 14 females in the lab and confirmed that the male offspring from this group were surviving with sex ratios near parity. For Savaii, the population was initially 99 percent female at the beginning of 2006. By the end of the year, researchers found that males made up 39 percent of the 54 butterflies collected.
The researchers tested for the continued presence of Wolbachia in the butterflies. By mating infected females with males from a different island that did not have the suppressor gene, they also confirmed that the bacteria were still effective at killing male embryos. The male-killing ability of the bacteria emerged again after three generations. Thus, they could rule out a change in the bacteria as an explanation for the resurgence of the males in the butterfly populations studied.
The researchers' findings are described in the July 13 issue of the journal Science.
The field work for this study was based out of the UC Berkeley Richard B. Gump South Pacific Research Station on the island of Moorea in French Polynesia. The Gump station is part of the Moorea Coral Reef Long Term Ecological Research Site, one of 26 sites funded by the National Science Foundation to study long-term ecological phenomena.
The Gump Research Station is managed through UC Berkeley's Office of the Vice Chancellor for Research. George Roderick, UC Berkeley professor of environmental science, policy and management and curator of the Essig Museum of Entomology, is a former director of the station, and Neil Davies is the station's executive director and research scientist. Both Roderick and Davies are co-authors of this study.
Other study co-authors are Emily Hornett of University College London, James Fullard of the University of Toronto at Mississauga, and Nina Wedell of the University of Exeter in Cornwall, England.
The U.S. National Science Foundation, the U.K. Natural Environment Research Council and the Natural Sciences and Engineering Research Council of Canada helped support this research.
Adapted from materials provided by University of California - Berkeley, via EurekAlert!, a service of AAAS.

http://www.sciencedaily.com/releases/2007/07/070712143300.htm

Fossils From Animals And Plants Are Not Necessary For Crude Oil And Natural Gas, Swedish Researchers Find

ScienceDaily (Sep. 12, 2009) — Researchers at the Royal Institute of Technology (KTH) in Stockholm have managed to prove that fossils from animals and plants are not necessary for crude oil and natural gas to be generated. The findings are revolutionary since this means, on the one hand, that it will be much easier to find these sources of energy and, on the other hand, that they can be found all over the globe.

"There is no doubt that our research proves that crude oil and natural gas are generated without the involvement of fossils. All types of bedrock can serve as reservoirs of oil," says Vladimir Kutcherov. (Credit: Image courtesy of Vetenskapsrådet (The Swedish Research Council)).

“Using our research we can even say where oil could be found in Sweden,” says Vladimir Kutcherov, a professor at the Division of Energy Technology at KTH.
Together with two research colleagues, Vladimir Kutcherov has simulated the process involving pressure and heat that occurs naturally in the inner layers of the earth, the process that generates hydrocarbon, the primary component in oil and natural gas.
According to Vladimir Kutcherov, the findings are a clear indication that the oil supply is not about to end, which researchers and experts in the field have long feared.
He adds that there is no way that fossil oil, with the help of gravity or other forces, could have seeped down to a depth of 10.5 kilometers in the state of Texas, for example, which is rich in oil deposits. As Vladimir Kutcherov sees it, this is further proof, alongside his own research findings, of the genesis of these energy sources – that they can be created in other ways than via fossils. This has long been a matter of lively discussion among scientists.
“There is no doubt that our research proves that crude oil and natural gas are generated without the involvement of fossils. All types of bedrock can serve as reservoirs of oil,” says Vladimir Kutcherov, who adds that this is true of land areas that have not yet been prospected for these energy sources.
But the discovery has more benefits. The degree of accuracy in finding oil is enhanced dramatically – from 20 to 70 percent. Since drilling for oil and natural gas is a very expensive process, the cost picture will be radically altered for petroleum companies, and in the end probably for consumers as well.
“The savings will be in the many billions,” says Vladimir Kutcherov.
To identify where it is worthwhile to drill for natural gas and oil, Vladimir Kutcherov has used his research to arrive at a new method. It involves dividing the globe into a finely meshed grid. The grid corresponds to fissures, so-called ‘migration channels,’ through underlying layers under the surface of the earth. Wherever these fissures meet, it is suitable to drill.
According to Vladimir Kutcherov, these research findings are extremely important, not least as 61 percent of the world’s energy consumption derives from crude oil and natural gas.
The next step in this research work will involve more experiments, but above all refining the method will make it easier to find places where it is suitable to drill for oil and natural gas.
Vladimir Kutcherov, Anton Kolesnikov, and Alexander Goncharov’s research work was recently published in the scientific journal Nature Geoscience.
Journal reference:
Anton Kolesnikov, Vladimir G. Kutcherov, Alexander F. Goncharov. Methane-derived hydrocarbons produced under upper-mantle conditions. Nature Geoscience, 2009; 2 (8): 566 DOI: 10.1038/ngeo591
Adapted from materials provided by Vetenskapsrådet (The Swedish Research Council), via AlphaGalileo.
http://www.sciencedaily.com/releases/2009/09/090910084259.htm

Ancient pterosaurs were skilled fliers

Posted 2009/08/05 at 2:49 pm EDT

RIO DE JANEIRO, Aug. 5, 2009 (Reuters) — A fossil found in China of a pterosaur, the earliest known flying vertebrate, shows the creatures had unique and complex wing fibers that enabled them to fly with the precision and control of birds, researchers said on Wednesday.

A model of a pterosaurs called the Jeholopterus ningchengensis is shown during a news conference at Rio's Federal University in Rio de Janeiro August 5, 2009. The model is on display with a 130-million year-old fossil of the Jeholopterus ningchengensis which was discovered in China. REUTERS/Bruno Domingos

The finding by a team of Brazilian, German, Chinese and British researchers backs up the theory that the reptiles that dominated the skies from up to 220 million years ago, also known as pterodactyls, were not just basic gliders.

A new technique that involves shining ultra-violet rays on the well-preserved fossil found in Inner Mongolia brought out a detailed view of the tissue in the pterosaur's wing, researchers said at a news conference on Wednesday in Rio de Janeiro.

They also found hair-like fibers different from any other animal's that covered the creature's body and part of its wings. This could have helped the animals control their body temperature and shows they were warm-blooded, said Alexander Kellner, a paleontologist at Brazil's National Museum in Rio.

"They are different from other furs we find in mammals and they provide us another hint that these animals were able to control their body temperature, they were hot-blooded animals," said Alexander Kellner, a paleontologist at Brazil's National Museum in Rio.

"This is of great importance to understanding how the pterosaur functioned."

The UV analysis of the fossil showed that the creature had several layers of fibers to control its wings, rather than one as previously thought, suggesting it had more stability and control over its flight than flying animals such as bats.

The pterosaurs, which ranged in size from small up to the largest creatures known to have flown, went extinct about 65 million years ago, around the same time as the mass extinction of dinosaurs.

(Reporting by Stuart Grudgings and Alice Pereira; Editing by Phil Stewart)

http://www.newsdaily.com/stories/tre5745gj-us-china-pterosaur/

Malaria may have come from chimps

Posted 2009/08/04 at 2:17 am EDT

WASHINGTON, Aug. 4, 2009 (Reuters) — Malaria may have jumped to humans from chimpanzees much as AIDS did, U.S. researchers reported on Monday in a study they hope could help in developing a vaccine against the infection.

A chimpanzee sits in his enclosure in Berlin Zoo, June 9, 2009. REUTERS/Fabrizio Bensch

They found evidence the parasite that causes most cases of malaria is a close genetic relative of a parasite found in chimpanzees. Genetic analysis suggests the human parasite is a direct descendant of the chimp parasite, they reported in the Proceedings of the National Academy of Sciences.

The malaria-causing parasite Plasmodium falciparum may have been transmitted to human beings as recently as 10,000 years ago, Francisco Ayala of the University of California Irvine and colleagues said.

"When malaria transferred to humans, it became very severe very quickly," Ayala said in a statement.

"The disease in humans has become resistant to many drugs. It's my hope that our discovery will bring us closer to making a vaccine."

Malaria kills an estimated 1 million people a year, mostly children, according to the World Health Organization. The mosquito-borne parasite causes severe disease in more than 300 million every year.

Ayala's team sampled blood samples from 94 chimpanzees in Cameroon and Ivory Coast to find the apes' version of the parasite.

"The closest known relative of P. falciparum is a chimpanzee parasite, Plasmodium reichenowi," they wrote. They found eight samples of P. reichenowi.

Their genetic testing of the samples showed all known P. falciparum parasites originated from P. reichenowi.

Researchers are trying to make a vaccine against malaria but are having difficulty. Understanding how it became adapted to humans could help in this work.

The finding is the latest to show that some of humanity's worst diseases originated in animals. AIDS came from chimpanzees -- and French researchers reported on Sunday that they found a Cameroonian woman had been infected with an HIV virus that apparently came from gorillas.

Swine flu, H5N1 avian influenza and in fact all influenza viruses are believed to have originated in animals. Other animal-to-human infections include severe acute respiratory syndrome, or SARS, which killed 800 people in 2003-2004, Ebola and Marburg viruses, and plague.

(Editing by Xavier Briand)

http://www.newsdaily.com/stories/tre5725r6-us-malaria-source/

Swine Flu: What Does It Do To Pigs?

ScienceDaily (May 12, 2009) — The effects of H1N1 swine flu have been investigated in a group of piglets. Scientists studied the pathology of the virus, finding that all infected animals showed flu-like symptoms between one and four days after infection and were shedding virus two days after infection.

Roongroje Thanawongnuwech led a team of researchers from Chulalongkorn University, Bangkok, who infected 22-day old pigs with both the H1N1 strain of swine flu and the less dangerous H3N2 subtype.

He said, “The results demonstrated that both swine flu subtypes were able to induce flu-like symptoms and lung lesions in weanling pigs. However the severity of the disease with regard to both gross and microscopic lung lesions was greater in the H1N1-infected pigs”.

All infected pigs developed respiratory symptoms such as nasal discharge, coughing, sneezing and conjunctivitis. Upon pathological examination, lung lesions large enough to be seen by the naked eye were observed.

According to Thanawongnuwech, “These lesions were characterized by dark plum-colored, consolidated areas on lung lobes and were most severe two days after infection, especially in the H1N1-infected pigs, where approximately a third of the lung was covered”.

The course of infection was limited to less than a week and none of the animals died.

---

Journal reference:

1. Sreta et al. Pathogenesis of swine influenza virus (Thai isolates) in weanling pigs: an experimental trial. Virology Journal, 2009; 6 (1): 34 DOI: 10.1186/1743-422X-6-34

Adapted from materials provided by BioMed Central.

http://www.sciencedaily.com/releases/2009/05/090511091905.htm

Researchers Describe The 90-year Evolution Of Swine Flu

ScienceDaily (July 5, 2009) — The current H1N1 swine flu strain has genetic roots in an illness that sickened pigs at the 1918 Cedar Rapids Swine Show in Iowa, report infectious disease experts at the University of Pittsburgh Graduate School of Public Health in the New England Journal of Medicine. Their paper, published online June 29 and slated for the July 16 print issue, describes H1N1's nearly century-long and often convoluted journey, which may include the accidental resurrection of an extinct strain.

"At the same time the 1918 flu pandemic was rapidly spreading among humans, pigs were hit with a respiratory illness that closely resembled symptoms seen in people," said senior author Donald S. Burke, M.D., dean, University of Pittsburgh Graduate School of Public Health. "Early experiments confirmed that this 1918 swine virus and a human strain emerged about the same time. Since then, this ancestor virus has re-assorted genetically with other influenza strains at least four times, leading to the emergence of the new 2009 strain, which has retained some similarities to the original virus."

In the paper, Dr. Burke and lead author Shanta M. Zimmer, M.D., assistant professor, University of Pittsburgh School of Medicine, describe the temporary "extinction" of the H1N1 virus from humans in 1957 and its subsequent re-emergence 20 years later. They note a small 230-person outbreak of H1N1 in 1976 among soldiers in Fort Dix, New Jersey that did not extend outside the military base. Then, H1N1 influenza re-emerged in 1977 among people in the former Soviet Union, Hong Kong and northeastern China. Careful study of the genetic origin of the 1977 strain showed that it was not the Fort Dix strain, but, surprisingly, was related closely to a 1950 human strain. Given the genetic similarity of these strains, re-emergence was likely due to an accidental release during laboratory studies of the 1950 strain that had been preserved as a 'freezer' virus, they said.

The authors hypothesize that concerns about the Fort Dix outbreak stimulated a flurry of research on H1N1 viruses in 1976, which led to an accidental release and re-emergence of the previously extinct virus a year later. The re-emerged 1977 H1N1 strain has continued to circulate among humans as seasonal flu for the past 32 years.

Although originally traced to Mexico, the exact physical origins of the 2009 H1N1 pandemic virus are unknown. Because the current strain shares common ancestry with older flu strains, it is possible that portions of the population may have partial immunity to the new pandemic virus.

The authors also go on to explain that the danger posed by a virus isn't based solely on its lethality, but also on its transmissibility, which is the ability to jump from animals to humans and to survive by mutating to adapt to its new human host. H1N1 influenza viruses have demonstrated this ability throughout their history.

"Studying the history of emergence and evolution of flu viruses doesn't provide us with a blueprint for the future, but it does reveal general patterns, and this kind of information is critical if we are to be as prepared as possible," said Dr. Burke.

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Adapted from materials provided by University of Pittsburgh Schools of the Health Sciences, via EurekAlert!, a service of AAAS.

http://www.sciencedaily.com/releases/2009/06/090629200641.htm

A Fading Field

Traditional taxonomists are an endangered species. Could their unique brand of knowledge disappear, too?

By Bob Grant
Anthony Cognato, an entomologist at Michigan State University, is a bark beetle expert. He's made a career out of collecting, identifying, and classifying the insects—members of the subfamily Scolytinae—that make a living by cultivating fungal gardens in tunnels they bore in dead trees. Even though he's an expert in bark beetles, Cognato can still be surprised by the organisms he's devoted his career to studying.

A few years ago, Cognato's graduate student, Jiri Hulcr, spent 18 months in the rainforests of Papua New Guinea, surveying the island's bark beetle fauna across a 1,000-kilometer transect. Hulcr set up three sampling sites, each 500 kilometers apart, by felling trees and waiting for bark beetles to inhabit the dead wood and establish their fungal gardens, called galleries. As he collected beetles, Hulcr began to notice a pattern that he showed to his advisor during Cognato's visit to the field sites. "When you collected this one smaller species, it was always associated with this other larger species," Cognato recalls. "Their galleries were always located right next to each other."

Cognato encouraged Hulcr to collect data on the frequency of this phenomenon, in which the smaller, yellowish species of beetle seemed to bore its tunnel within a centimeter of the larger, long-legged species. "He had the data and it was pretty obvious," Cognato says. "Basically you always found these species together."

With the pattern established, the researchers next sought to get to the bottom of the two beetles' relationship. They hypothesized that the smaller species was somehow leaching off of the larger species by stealing fungi rather than collecting and seeding their own spores. To test their hypothesis, they needed to look at the insects' morphology, so they temporarily set aside the molecular tools that are de rigueur among most biologists, rolled up their sleeves, and used some of the microscopes and dissection tools that have sat in the taxonomic toolbox for centuries.

Back in Cognato's Michigan State University lab, Hulcr dissected hundreds of specimens of the smaller beetle species that he had collected in the field. He dipped their heads in paraffin and made multiple histological slices, looking for specialized fungal spore-carrying structures, called mycangia, that virtually every species of bark beetle harbors in their mandibles. He found none, demonstrating that the smaller species did, in fact, depend on another source for its fungi. To confirm, Hulcr sequenced the DNA of the fungal communities he sampled from the tunnels of both the larger and smaller beetles, and showed they matched. The two taxonomists had identified a completely new ecological phenomenon that they dubbed "mycocleptism," or fungi-stealing. While comparing the DNA of the fungi was an important confirmation of mycocleptism, the scientists would never have spotted the behavior if they hadn't observed it in the field and taken a close look at the insects' morphology.

"You get more out of your systematic studies if you can actually go and collect your organism of interest," Cognato says. "It allows you to observe so much more that you can't observe in a DNA sequence." The subfamily to which these bark beetles belong contains the most commonly imported exotic beetles into the United States, and some species are currently contributing to the decimation of tree populations in the coastal southeast. There is no known control method at the moment, but knowing more about how the beetles make their livings may provide key insights into how to control the pest.

However, there are fewer and fewer biologists who practice traditional taxonomy, or the collection, description, naming and categorization of organisms through intense study of their physical attributes. In general, the field of taxonomy, or systematics as it is often called, has been leaning towards the molecular end of the spectrum since genetic technology matured in the late 1970s and 1980s, and traditional taxonomic skills have been dwindling as older taxonomic experts retire. Many taxonomists blend traditional methods, such as morphological and behavioral study, with modern molecular techniques, such as DNA sequencing, to fully characterize their pet taxa. But taxonomists like Cognato and Hulcr, who rely on fieldwork and morphological study as core aspects of their taxonomic work, appear to be slowly going extinct.

Most children are born taxonomists. Exploring, discovering, and naming the living things in one's environment, whether it's a backyard or a city block, seem to come naturally. Some of the first scientists, such as Aristotle, focused intense efforts on exploring and cataloging the living world around them, and at the height of global exploration from the 15th to 19th centuries, taxonomists were in great demand, as new lands and species were discovered. Other notable Western taxonomists include Ernst Haeckel, Carolus Linnaeus, and Charles Darwin.
A mycocleptic (fungus-stealing) ambrosia beetle Biuncus duodecimspinatus from Papua New Guinea.
Courtesy of Jiri Hulcr

Describing, naming, and preserving new taxonomic groups—specifically using the morphological skills that are traditionally central to the discipline's methodology—is just as important today, as researchers continue to uncover new genera and species in the unexplored corners of the globe. "Taxonomy provides the language of biodiversity," says Quentin Wheeler, an Arizona State University insect taxonomist and dean of that university's college of liberal arts and sciences.

By some estimates, scientists have discovered, described, and named only 6 percent of the planet's species—less than 2 million of the 30 million that exist, at most.

That remaining 94% of species tend to reside in rapidly vanishing ecosystems—biodiversity hotspots—where scores of species likely slip into extinction without ever attracting scientific attention. Research published in 2004 estimated that certain areas on Earth will lose up to 37% of their species by 2050 due to climate change alone.1
The danger is that our planet's biodiversity is disappearing quicker than our accumulated mass of taxonomic expertise can catalog it.

The danger is that our planet's biodiversity is disappearing quicker than our accumulated mass of taxonomic expertise can catalog it. And in order to stop these extinctions, scientists have to understand how the species within each ecosystem live and relate. To fix a clock, you have to know how the individual parts work and interact, says Wheeler—and the same is true for ecosystems.
An ambrosia beetle Hadrodemius globus, male, size: 2.5 mm.
Courtesy of Jiri Hulcr

Despite the importance of taxonomic expertise in the face of such a precarious situation, children these days with an interest in the natural world typically don't grow up to be taxonomists like Haeckel and Linnaeus, but instead study life using PCR, mass spectrometers, and DNA sequencers.

Montgomery Wood, the world's foremost taxonomic expert in a family of globally distributed black flies, spent idle summer days turning over rocks, fording creeks, collecting bird nests, and catching insects. "I had nothing to do in the summer time, and I just chased things," says Wood, 76.
An ambrosia beetle Hadrodemius globus, female, size: 5 mm.
Courtesy of Jiri Hulcr

Growing up on the fringes of London, Ontario, in the 1930s and 40s, Wood's peregrinations were not unusual, but his eye was perhaps keener, his curiosity sharper. Though he may not have realized it then, the young Wood was embarking on a scientific career that would span nearly five decades. He can identify many of family Tachinidae's approximately 10,000 named black fly species by sight. "I'm weak in [the black fly species of] Africa and China," he concedes.

Wood honed expertise in identifying thousands of species of flies the old-fashioned way: through exhaustive examination of the organisms' morphology and natural history. "What made me an expert in Tachinidae was to stay at them for an entire lifetime," he says.
Various views of the male copulatory organ (pedipalp) of the pimoid (family Pimoidae) spider Putaoa huaping, a new species from China.
Drawings by Gustavo Hormiga, reproduced with permission from Zootaxa

Perhaps Wood should have seen the demise of his chosen profession coming. He recalls that when he was starting his PhD work on the taxonomy of Ontario's tachinids in the early 1960s, a fellow biologist at the University of Toronto questioned his decision to enter the field, with the promise of new and exciting technologies and methodologies—namely DNA analysis—poised to revolutionize modern biology. "He didn't say I was wasting my time," Wood remembers, "but he implied that."
"This is not about being modern or crusty or anything. It's about having data." —Gustavo Hormiga

Just like the organisms taxonomists study, the discipline of systematics and biology as a whole was evolving. By the 1980s, the field of systematics, like many other fields, became entranced by the promise of DNA analysis and its ability to decipher genetic codes, enabling taxonomists to look past an animal's skin and into its cells. Walter Judd, a University of Florida botanist, had a front row seat for this evolution in taxonomy. "When the excitement of molecular analyses hit, people started spending a lot of time in the lab," and less in the field, he says. As younger botanists sought to validate molecular analyses as taxonomic tools, they necessarily focused their study on more well-studied plant species, such as Arabidopsis, rather than seeking out undiscovered taxa in the field, according to Judd.

Now older taxonomists like Wood and Judd are retiring from museum and university positions, with institutions tending not to replace them with more taxonomists. The United Kingdom's Royal Botanic Gardens Kew, for example, has not had a gymnosperm taxonomist since the last one there retired in 2006, and has not replaced its last fern specialist, who retired in 2007.

Judd, whose work centers largely on the morphology of tropical flowering plants, says that taxonomic expertise could slip through our fingers in alarmingly short order. "I'm worried that in perhaps a generation or two we'll be in rough shape because there won't be people who know how to use the morphological features" to identify a species.

The primary federal funder of systematic research in the United States is the National Science Foundation. This year, the agency put $2.5 million (0.04% of its total budget) towards a program designed to help experts train young students in taxonomy.

Through the Partnerships for Enhancing Expertise in Taxonomy (PEET) program, graduate students and postdocs of Gustavo Hormiga, a George Washington University spider systematist, learn to observe, measure, and draw their spiders while at the same time studying them with scanning electron microscopy and taking genetic samples to be analyzed for key diagnostic markers. Hormiga strongly encourages his students to complete taxonomic monographs—detailed publications that describe the taxonomy of organismal groups—and compile taxonomic keys, which give other researchers a map to identifying organisms. In this way, Hormiga says, his students are grounded in the traditional methods of taxonomy while utilizing modern methods to extract as much useful information from their specimens as possible. "This is not about being modern or crusty or anything," Hormiga says. "It's about having data."

The PEET program doled out its first round of grants in 1995 in the face of a rapid decline of experts in the field. An NSF survey conducted in the mid-1990s found only 940 systematic biologists working at doctorate-granting institutions, and one quarter of those were only adjunct faculty members. More than 80% of the institutions that responded to the NSF survey said that they would not hire systematists in the future if new positions opened up.2 "There was a strong perception in the scientific community that many of the folks that were doing taxonomics and systematics were getting old and retiring and weren't being replaced by their institutions," according to Scott Snyder, a PEET program officer at NSF. Since its inception, PEET, a biennial program that awards 5-year grants of $750,000 to successful applicants, has helped train hundreds of graduate students and postdoctoral fellows in taxonomic science. However, there are indications that the dwindling of taxonomy has reached a point of no return, and even this influx of funding may not be enough to reverse the trend.
(1) Fruiting structures (stromata) of Moelleriella sloaneae. (2) Hypocrella hirsuta and (3) Hypocrella disciformis on dead scale insects or whiteflies on leaves. The fungi have completely covered and consumed the insect. The size of these structures are 2–3 mm in diameter.
© P. Chaverri, Stud. Mycol. 60 (2008)

When Pricila Chaverri arrived at the University of Maryland about a year ago with a PEET grant in hand, she advertised on campus for undergraduate students to work on revising the taxonomy of fungi in the order Hypocreales, which she studies. Herself a graduate of the PEET program, she waited for the expressions of interest to roll in. None came. Frustrated, she changed her advertisement to highlight the fact that students would also learn molecular techniques, such as PCR and DNA sequence analysis, as they sought to fully characterize fungal specimens in her lab. "I got, like, a hundred applications," Chaverri recalls. "And they all wanted to learn molecular biology."

Chaverri realizes that emphasizing the modernity of her research is a surefire way to attract attention from students and funding agencies alike. She's used the tactic so many times that she's begun to wonder about how she herself conducts research. "Sometimes I worry that I'm wasting my time looking at the morphology of fungi," Chaverri sighs, standing in her lab this spring as graduate students peer through microscopes at dead twigs harboring her fungal quarry. "But I like my fungi, so I'm going to keep looking at them."

Looking at her fungi, in fact, led Chaverri to an unprecedented insight into a group of neotropical species that infect scale insects and other agricultural pests. Last year, Chaverri was studying genus Hypocrella, which contained several brightly colored species grouped together based on DNA sequence data. But Chaverri decided to look more closely at the morphology of the sprawling genus, and when she trained her microscope on the ascospores—long, sexual reproductive structures—of the species, she noticed some interesting differences. Some of the species in the genus had large ascospores that could disarticulate into many smaller parts, while others had smaller ascospores that did not disarticulate. Her study of the fungi resulted in the creation of two new genera, Moelleriella (the species with the large, disarticulating ascosporse) and Samuelsia (the species with the smaller ascospores).3

Far from being an arcane taxonomic revision, Chaverri's research may help to improve the way that researchers use particular species of fungi to control agricultural insect pests. For example, using fungi of genus Moelleriella may lead to more effective control of the scale insects or whiteflies that plague citrus growers in Florida, Chaverri says. "One can hypothesize that [Moelleriella] would be more successful on spreading to new trees or insects."

"I think [taxonomy and systematics are] healthy enough in terms of how they're executed. The sickness is that there are no jobs anymore." —Oliver Flint

Though Chaverri has managed to continue her taxonomic work, a 2007 survey by PEET graduates Ingi Agnarsson and Matja Kuntner found that 47% of PEET alumni no longer worked in taxonomy, and a further 9% had positions where taxonomy played only a minor role. In addition, 6% of the PEET program alumni were unemployed when contacted by Agnarsson and Kuntner. And the authors stress that the survey findings are likely overly rosy, because their ability to find and survey PEET graduates in part relied on their closeness to the field of taxonomy—in other words, some of the graduates they couldn't track down are likely so far removed from the field they couldn't be found. Some of the comments recorded by the two authors convey the disconcerting realities facing taxonomists today. "As it is now," one survey respondent wrote, "[PEET] trains students in skills absolutely not required by the job market."

Nearly all the classically trained taxonomists with whom I spoke echoed this sentiment.

Ralph Holzenthal, a Michigan State University entomologist and caddisfly expert, says that he's been fighting to fund his lab for 3 years, ever since his last round of PEET funding ran out. He once supported six graduate students with two overlapping NSF grants, but now can support only one with money from the NSF. Holzenthal adds that he's in his fourth round of revisions of an NSF grant application to update the taxonomy of caddisflies in Brazil, which are severely understudied. Fewer than 350 species have been recorded in a country that spans 8.5 million square kilometers, and Holzenthal estimates that as many as 850 species await discovery and description in the southeastern corner of Brazil. He says that cataloging these species could ultimately benefit the health of tropical streams and rivers, which are intimately tied to the health and life history of caddisflies in the area.

Jerome Regier, an NSF-funded systematist at the University of Maryland, says that some classical taxonomists need to do a better job of convincing the scientific and funding communities of the importance of cataloguing the world's species before they disappear. "[Taxonomists have] got to interest graduate students in the [scientific] problems that they have. Species descriptions aren't problems as such," Regier says. "It's species loss that's a problem. It's habitat destruction that's a problem. You have to relate your species drawings to those bigger questions. The fact is you've got to get funding to carry this out."

In some sense, administrators are justified in shunning taxonomists when it comes time to hire new faculty. A taxonomist has access to essentially a fraction of a percentage of the NSF budget, while a molecular biologist has at her fingertips the budget from the National Institutes of Health, typically four times larger than the NSF's. "If your objective is just to get a job, you probably shouldn't be in taxonomy at all, molecular or descriptive," said Holzenthal.
http://images.the-scientist.com/content/images/articles/55708/38-1.gif
James Rodman, a botanist and former NSF program director who was instrumental in creating the PEET program in the mid-1990s, says that the disappearance of traditional taxonomy is only part of a larger problem. "More broadly speaking, organismal biology is dying out," Rodman says, now in semi-retirement as museum research associate at the University of Washington's Burke Museum. He says that colleagues tell him all the time that even in high schools, biology field trips are seldom, if ever, taken—a trend that ripples up through the university level as survey courses in entomology, mycology, and other organismal disciplines cease to exist. "We're no longer interested in knowing about the organisms of the world. That's the sadder tragedy."

Some taxonomists feel that their legacies will live on even though they are retiring and leaving the lifelong studies that often began with an organic fascination in the natural world around them. Ralph Holzenthal's mentor and PhD advisor in the 1980s was Oliver Flint, a curator emeritus at the Smithsonian Institution and a world-class caddisfly expert. Flint says that his lasting appreciation for the field assuages any feelings of loss for the lack of jobs available to traditional taxonomists. "I think [taxonomy and systematics are] healthy enough in terms of how they're executed. The sickness is that there are no jobs anymore."

Monty Wood echoes Flint's sentiment. He says that he has no desire to lament the downfall of the type of taxonomy in which he was trained. "I have thought about it," Wood admits. "But I don't lose any sleep over it. There's nothing I can do about it."

Instead, Wood says that he focuses on studying and preserving as many specimens as possible. Quentin Wheeler, the Arizona State University entomologist who is also director of the newly-created International Institute for Species Exploration, says that he hopes to create a "cyber-infrastructure," including digital images and virtual networks, that will give researchers around the world access to all of the nearly 3 billion biological specimens currently housed at natural history museums. He says that if modern technologies and more funding are successfully combined with continued taxonomic work, taxonomists have a good chance of describing and naming 8 million new species in the next 50 years.

Ironically, the demise of taxonomy and systematics might be attributable to its most fervent champions. "I think in the past there's been a tradition in classical taxonomy that it's OK to isolate yourself from the world to work in the museum," says Regier. "There has to be somewhat of a shift in culture." Indeed, because it formed the bedrock of biology for centuries, taxonomy carries with it a lot of perceptual baggage. "It's hard to get over this image of the systematist being just a stamp collector," says Cognato. But nothing could be further from the truth, he says. "Properly done, [traditional taxonomy] gets you out in the field and discovering many new things that wouldn't have been found without them."

Have a comment? Email us at mail@the-scientist.com
References
1. C. Thomas et al., "Extinction risk from climate change," Nature, 427:145–48, 2004.
2. M. Claridge, "Introducing systematics agenda 2000," Biodivers. Conserv., 4:451–54, 1995.
3. P. Chaverri et al., Studies in Mycology 60: Neotropical Hypocrella (anamorph Aschersonia), Moelleriella, and Samuelsia, Utrecht: Centraalbureau voor Schimmelcultures (CBS), 2008, 68 pp.

Fossils suggest earlier land-water transition of tetrapod

April 17th, 2009

New evidence gleaned from CT scans of fossils locked inside rocks may flip the order in which two kinds of four-limbed animals with backbones were known to have moved from fish to landlubber.

Both extinct species, known as Ichthyostega and Acanthostega, lived an estimated 360-370 million years ago in what is now Greenland. Acanthostega was thought to have been the most primitive tetrapod, that is, the first vertebrate animal to possess limbs with digits rather than fish fins.

But the latest evidence from a Duke graduate student's research indicates that Ichthyostega may have been closer to the first tetrapod. In fact, Acanthostega may have had a terrestrial ancestor and then returned full time to the water, said Viviane Callier, who is the first author of a report on the findings to be published in today's issue of the journal Science.

"If there is one take-home message, it is that the evolutionary relationship between these early tetrapods is not well resolved," Callier said.

Co-author Jennifer Clack of the University Museum of Zoology in Cambridge, England -- where she supervised Callier's work for a master's degree -- found the fossils embedded in rocks collected from East Greenland.

Rather than trying to remove them -- an action that would have destroyed much of the evidence -- the researchers studied the fossils inside the stone with computed tomography (CT) scanning. Callier "reconstructed" the animals using imaging software (Amira and Mimics) to analyze the CT scans, focusing on the shapes of the two species' upper arm bones, or humeri.

The CT slices revealed that Clack had found the first juvenile forms of Ichthyostega. Previously known fossils of Ichthyostega had come from adults.

Anatomies can morph as animals move towards adulthood, Callier said. And such shifts can help scientists deduce when in development the animal acquired the terrestrial habit. The fossils suggest that Ichthyostega juveniles were aquatically adapted, and that the terrestrial habit was acquired relatively late in development. The fossils bore evidence that the muscle arrangement in adults was better suited to weight-bearing, terrestrial locomotion than the juvenile morphology. It is possible that Ichthyostega came out of the water only as a fully mature adult.

In contrast, in Acanthostega "there is less change from the juvenile to the adult. Although Acanthostega appears to be aquatically adapted throughout the recorded developmental span, its humerus exhibits subtle traits that make it more similar to the later, fully terrestrial tetrapods," Callier said

Because the shapes of its adult limbs seemed the most fin-like, scientists had previously concluded that Acanthostega was "more primitive," Callier said. "But now, if we look at the details of the humeri, Ichthyostega's are actually more similar to earlier fishes."

Ironically, the shape of Acanthostegas limb's, in both adult and the newly-discovered juvenile forms, is more "paddle-like" than Ichthyostega's, Callier said. "They would have been really good swimmers. So, although Acanthostega had limbs with digits, we don't think it was really terrestrial. We think even the adults were aquatic."

"If Ichthyostega is actually more primitive than Acanthostega, then maybe animals evolved towards a terrestrial existence a lot earlier than originally believed," she said. "Maybe Acanthostega was actually derived from a terrestrial ancestor, and then, went back to an aquatic lifestyle."

Per Ahlberg, a Swedish paleontologist who was previously Clack's graduate student, also joined Clack in a comparative analysis of other more fish-like species living at about the same time as Ichthyostega and Acanthostega.

Those include Tiktaalik, another animal that has made the news because of scientists' deductions that it was in transition from water to land.

"It seems like there were different species evolving the same or similar traits independently -- evidence of parallel evolution," Callier said. "The terrestrial environment posed new challenges like feeding and moving on land and breathing air, to which the first tetrapods had to evolve solutions. Sometimes different lineages stumbled upon similar solutions."

Ahlberg, now professor at the University of Uppsala in Sweden, is corresponding author of the new Science report. The research was funded by the Winston Churchill Foundation and the Swedish Research Council.

Source: Duke University (news : web)

http://www.physorg.com/news159190294.html

Fossils suggest earlier land-water transition of tetrapod

April 17th, 2009

New evidence gleaned from CT scans of fossils locked inside rocks may flip the order in which two kinds of four-limbed animals with backbones were known to have moved from fish to landlubber.

Both extinct species, known as Ichthyostega and Acanthostega, lived an estimated 360-370 million years ago in what is now Greenland. Acanthostega was thought to have been the most primitive tetrapod, that is, the first vertebrate animal to possess limbs with digits rather than fish fins.

But the latest evidence from a Duke graduate student's research indicates that Ichthyostega may have been closer to the first tetrapod. In fact, Acanthostega may have had a terrestrial ancestor and then returned full time to the water, said Viviane Callier, who is the first author of a report on the findings to be published in today's issue of the journal Science.

"If there is one take-home message, it is that the evolutionary relationship between these early tetrapods is not well resolved," Callier said.

Co-author Jennifer Clack of the University Museum of Zoology in Cambridge, England -- where she supervised Callier's work for a master's degree -- found the fossils embedded in rocks collected from East Greenland.

Rather than trying to remove them -- an action that would have destroyed much of the evidence -- the researchers studied the fossils inside the stone with computed tomography (CT) scanning. Callier "reconstructed" the animals using imaging software (Amira and Mimics) to analyze the CT scans, focusing on the shapes of the two species' upper arm bones, or humeri.

The CT slices revealed that Clack had found the first juvenile forms of Ichthyostega. Previously known fossils of Ichthyostega had come from adults.

Anatomies can morph as animals move towards adulthood, Callier said. And such shifts can help scientists deduce when in development the animal acquired the terrestrial habit. The fossils suggest that Ichthyostega juveniles were aquatically adapted, and that the terrestrial habit was acquired relatively late in development. The fossils bore evidence that the muscle arrangement in adults was better suited to weight-bearing, terrestrial locomotion than the juvenile morphology. It is possible that Ichthyostega came out of the water only as a fully mature adult.

In contrast, in Acanthostega "there is less change from the juvenile to the adult. Although Acanthostega appears to be aquatically adapted throughout the recorded developmental span, its humerus exhibits subtle traits that make it more similar to the later, fully terrestrial tetrapods," Callier said

Because the shapes of its adult limbs seemed the most fin-like, scientists had previously concluded that Acanthostega was "more primitive," Callier said. "But now, if we look at the details of the humeri, Ichthyostega's are actually more similar to earlier fishes."

Ironically, the shape of Acanthostegas limb's, in both adult and the newly-discovered juvenile forms, is more "paddle-like" than Ichthyostega's, Callier said. "They would have been really good swimmers. So, although Acanthostega had limbs with digits, we don't think it was really terrestrial. We think even the adults were aquatic."

"If Ichthyostega is actually more primitive than Acanthostega, then maybe animals evolved towards a terrestrial existence a lot earlier than originally believed," she said. "Maybe Acanthostega was actually derived from a terrestrial ancestor, and then, went back to an aquatic lifestyle."

Per Ahlberg, a Swedish paleontologist who was previously Clack's graduate student, also joined Clack in a comparative analysis of other more fish-like species living at about the same time as Ichthyostega and Acanthostega.

Those include Tiktaalik, another animal that has made the news because of scientists' deductions that it was in transition from water to land.

"It seems like there were different species evolving the same or similar traits independently -- evidence of parallel evolution," Callier said. "The terrestrial environment posed new challenges like feeding and moving on land and breathing air, to which the first tetrapods had to evolve solutions. Sometimes different lineages stumbled upon similar solutions."

Ahlberg, now professor at the University of Uppsala in Sweden, is corresponding author of the new Science report. The research was funded by the Winston Churchill Foundation and the Swedish Research Council.

Source: Duke University (news : web)

http://www.physorg.com/news159190294.html

Humans, chimps may have bred after split

By Gareth Cook, Globe Staff | May 18, 2006

Boston scientists released a provocative report yesterday that challenges the timeline of human evolution and suggests that human ancestors bred with chimpanzee ancestors long after they had initially separated into two species.

The researchers, working at the Cambridge-based Broad Institute of Harvard and MIT, used a wealth of newly available genetic data to estimate the time when the first human ancestors split from the chimpanzees. The team arrived at an answer that is at least 1 million years later than paleontologists had believed, based on fossils of early, humanlike creatures.

The lead scientist said that this jarring conflict with the fossil record, combined with a number of other strange genetic patterns the team uncovered, led him to a startling explanation: that human ancestors evolved apart from the chimpanzees for hundreds of thousands of years, and then started breeding with them again before a final break.

''Something very unusual happened," said David Reich, one of the report's authors and a geneticist at the Broad and Harvard Medical School.

The suggestion of interbreeding was met with skepticism by paleontologists, who said they had trouble imagining a successful breeding between early human ancestors, which walked upright, and the chimpanzee ancestors, which walked on all fours. But other scientists said the work is impressive and will probably force a reappraisal of the story of human origins. And one leading paleontologist said he welcomed the research as a sign that new genetic information will yield more clues to our deep history than once thought.

''I find this terrifically exciting and important work," said David Pilbeam, a Harvard paleontologist who was not part of the Broad team.

Pilbeam helped discover an early human ancestor known as Toumai, which walked on two legs and is thought to have lived in present-day Chad 6.5 million to 7.4 million years ago. The new report, published in today's issue of the journal Nature, estimates that final break between the human and chimpanzee species did not come until 6.3 million years ago at the earliest, and probably less than 5.4 million years ago.

This contradiction could be resolved, Reich said, if early creatures like Toumai then interbred with chimpanzee ancestors, leaving a population of hybrids that developed into today's humans. (In this scenario, the line of Toumai creatures then went extinct.) But it is also possible, he said, that the dating of the early human fossils is wrong, or that the dating of other, older fossils used in his calculations is wrong, which would partially undercut the interbreeding theory. Scientists said that the report will probably bring intense scrutiny, as researchers look for potential flaws in the work or other explanations for its findings.

The work will also probably inspire biologists to devote more attention to hybrids, the term for offspring with parents of different species, and the role that they may play in fueling evolution. Biologists have long known about hybrids -- a half-grizzly bear, half-polar bear was recently discovered in Canada -- but it has been assumed that these were generally lone animals that had had little impact on the story of evolution. The Nature paper joins a wave of work showing that the lines between species are hazy, according to James Mallet, a biologist who studies hybrids at University College London.

As two species evolve, they can develop new abilities. Some hybrids could combine the best of both species, Mallet said, though the biological barriers to the creation of hybrids increase the longer the species are apart. It is thought that human ancestors were adapting to life on the savannah instead of the forest, where chimpanzees still live today. It is not known why human ancestors would have begun mating with chimpanzee ancestors again, or why they would have stopped.

To understand how long ago humans split from chimpanzees, Reich and his colleagues did a close study of DNA from the two. This technique rests on the idea that once the populations separate, the DNA will slowly drift apart as natural mutations accumulate. If they can count the number of changes, and determine how quickly the changes happened, then they can calculate how long the two populations have been separate, according to Nick Patterson, a scientist who was part of the Broad team.

Previous studies have used this idea and found that the two species split between about 5 million and 8 million years ago.

The Broad team sought to get a more precise answer by looking at how different the DNA of chimps and humans is at many locations, instead of calculating an average difference. The DNA of humans and chimpanzees is quite similar, meaning that scientists can readily identify many segments of DNA that are so similar they must have been handed down by a common ancestor, deep in the past. Scientists can then use a computer to put the segments of human and chimp DNA into alignment, placing side by side the segments that are very similar.

For each pair of segments, they then calculated how long it would have taken to accumulate all the differences. The team used sophisticated statistical techniques to calculate these ''divergence times."

This analysis brought surprises that the team could explain only by suggesting human ancestors and chimpanzee ancestors interbred. First, they found that the divergence times varied widely. Some parts of the DNA seemed to indicate the human and chimpanzee species had been apart much longer than others, by millions of years. If humans split from chimps and then interbred before splitting again, the more divergent DNA sequences could date to before the first split, while the less divergent sequences could date to just before the second split.

The other surprise was that sequences from the X chromosome, one of two chromosomes that determine gender, gave consistently more recent divergence times, instead of the range seen on other chromosomes. This, too, would be explained by the idea of interbreeding, according to the report. The X chromosome is thought to be the focus of fertility problems in hybrids, and population models suggest that all of the X chromosomes in a hybrid population would quickly come to match those of one of the parent species. This would explain why the human and chimpanzee X chromosomes are so similar.

Although the idea is controversial, there will soon be a wealth of more information to test it. Part of the Broad team's analysis relied on using DNA sequences from the gorilla and other primates as a kind of baseline to interpret their results. Only a relatively small amount of DNA has been sequenced from gorillas, limiting the amount of data the team could use. By the end of 2007, there should be a full sequence of the gorilla, allowing the scientists to do a much fuller analysis, Reich said.

The team also plans on looking at genetic data for other groups of closely related species to try to determine whether those species split apart fairly abruptly, or whether there is evidence that hybridization is a common part of evolution, bringing together the best of two species.

Gareth Cook can be reached at cook@globe.com.
© Copyright 2006 Globe Newspaper Company.

http://www.boston.com/news/science/articles/2006/05/18/humans_chimps_may_have_bred_after_split/

Microbial Ocean Study Reels In RNA Surprise

By News Staff | May 13th 2009 01:00 AM

To study small RNA, snippets of RNA that act as switches to regulate gene expression in single-celled creatures, you need lab-cultured microorganisms but a new method of obtaining marine microbe samples while preserving the microbes' natural gene expression has shown the presence of many varieties of small RNAs.

The discovery of its presence in a natural setting may make it possible finally to learn on a broad scale how microbial communities living at different ocean depths and regions respond to environmental stimuli.

Microbes are ultra-sensitive environmental sensors that respond in the blink of an eye to minute changes in light, temperature, chemicals or pressure and modify their protein expression accordingly. But that sensitivity creates a quandary for the scientists who study them. Sort of like the observer effect in quantum physics, by entering the environment or removing the microbes from it, the observer causes the microbes to change their protein expression. That same sensitivity makes some of these creatures exceedingly difficult to grow in lab cultures.

"Microbes are exquisite biosensors," said Edward Delong, a professor of civil and environmental engineering (CEE) and biological engineering. "We had developed this methodology to look at protein-encoding genes, because if we know which proteins the microbes are expressing under what conditions, we can learn about the environmental conditions and how these microbes influence those. The unexpected presence and abundance of these small RNAs, which can act as switches to regulate gene expression, will allow us to get an even deeper view of gene expression and microbial response to environmental changes.

DeLong and co-authors Yanmei Shi, a graduate student in CEE, and postdoctoral associate Gene Tyson describe this work in the May 14 issue of Nature. The team used a technique called metatranscriptomics, which allows them to analyze the RNA molecules of wild microbes, something that previously could be done only with lab-cultured microbes.

To overcome the hurdle of quickly collecting and filtering microbial samples in seawater before the microbes change their protein expression, the research team — collaboratively with CEE Professor Sallie (Penny) Chisholm and her research team, which has successfully grown and studied the photosynthetic microbe, Prochlorococcus, in the lab — created a method for amplifying the RNA extracted from small amounts of seawater by modifying a eukaryotic RNA amplification technique.

When Shi began lab studies of the RNA in their samples, she found that much of the novel RNA they expected to be protein-coding was actually small RNA (or sRNA), which can serve as a catalyst or regulator for metabolic pathways in microbes.

"What's surprising to me is the abundance of novel sRNA candidates in our data sets," said Shi. "When I looked into the sequences that cannot be confidently assigned as protein-coding, I found that a big percentage of those sequences are non-coding sequences derived from yet-to-be-cultivated microorganisms in the ocean. This was very exciting to us because this metatranscriptomic approach — using a data set of sequences of transcripts from a natural microbial community as opposed to a single cultured microbial strain — opens up a new window of discovering naturally occurring sRNAs, which may further provide ecologically relevant implications."

"We've found an incredibly diverse set of molecules and each one is potentially regulating a different protein encoding gene," said DeLong. "We will now be able to track the protein expression and the sRNA expression over time to learn the relevance of these little switches."

If we think of marine bacteria and their proteins as tiny factories performing essential biogeochemical activities — such as harvesting sunlight to create oxygen and synthesize sugar from carbon dioxide — then the sRNAs are the internal switches that turn on and off the factories' production line. Their discovery in the ocean samples opens the way to learning even more detailed information in the lab: the researchers can now conduct lab experiments to look at the effects of environmental perturbation on microbial communities. These new sRNAs also expand our general knowledge of the nature and diversity of these recently recognized regulatory switches.

"Being able to track the dynamics of small RNA expression in situ provides insight into how microbes respond to environmental changes such as nutrient concentration and physical properties like light and pressure," said Shi. "A very interesting question to follow up in the lab is how much fitness advantage a small RNA confers to microbes. Can the microbes with a specific small RNA perform better in competing for nutrients in a tough situation, for instance? The discovery of naturally occurring small RNAs is a first step towards addressing such questions."

This work was supported by the Gordon and Betty Moore Foundation, the National Science Foundation and the U.S. Department of Energy.

http://www.scientificblogging.com/news_articles/microbial_ocean_study_reels_rna_surprise

'Hobbit' Skull Study Finds Hobbit Is Not Human

ScienceDaily (Jan. 21, 2009) — In a an analysis of the size, shape and asymmetry of the cranium of Homo floresiensis, Karen Baab, Ph.D., a researcher in the Department of Anatomical Scienes at Stony Brook University, and colleagues conclude that the fossil, found in Indonesia in 2003 and known as the “Hobbit,” is not human.

They used 3-D shape analysis to study the LB1 skull of the hobbit and found the shape of the skull to be consistent with a scaled down human ancestor but not modern humans. Their findings, reported in the current online edition of the Journal of Human Evolution, add to the evidence that the hobbit is a new species.

The question as to whether the hobbit was human or another species remains controversial. Some scientists claim the hobbit was a diminutive human that suffered from some type of disease that causes microcephaly, which results in abnormal growth of the brain and causes the cranium to be much smaller than the normal human cranium. But Dr. Baab and co-author Kieran McNulty, Professor of Anthropology at the University of Minnesota, believe their findings counter the microcephaly theory.

“A skull can provide researchers with a lot of important information about a fossil species, particularly regarding their evolutionary relationships to other fossil species,” explains Dr. Baab. “The overall shape of the LB1 skull, particularly the part that surrounds the brain (neurocranium) looks similar to fossils more than 1.5 million years older from Africa and Eurasia, rather than modern humans, even though Homo floresiensis is documented from 17,000 to 95,000 years ago.”

To carry out the study, Dr. Baab and colleagues collected 3D landmark data on the LB1 skull and a large sample of fossils representing other extinct hominin species, as well as a comparative sample of modern humans and apes. They performed several analyses of different regions of the skulls. Taken together, these analyses indicated that the LB1 skull shape is that of a scaled down Homo fossil not a scaled down modern human.

The results of the analysis of the asymmetry of the skulls, which refers to differences between the right and left sides of the skull, refutes the suggestion that the LB1 skull was that of a modern human with a diagnosis of microcephaly. In modern humans, a high degree of asymmetry may indicate that the individual was diseased. At least one scientific study on the asymmetry of LB1 supported the argument that this individual had microcephaly. Conversely, Dr. Baab and colleagues found the degree of asymmetry of the LB1 skull was not unexpectedly high and therefore not supportive of the diagnosis of microcephaly.

“The degree of asymmetry in LB1 was within the range of apes and was very similar to that seen in other fossil skulls,” says Dr. Baab. “We suggest that the degree of asymmetry is within expectations for this population of hominins, particular given that the conditions of the cave in Indonesia in which the skull was preserved may have contributed to asymmetry.”

Dr. Baab recognizes that the controversy as to the evolutionary origins of Homo floresiensis will continue, perhaps without an answer. However, all the evidence that she and colleagues illustrate in their article “Size, shape, and asymmetry in fossil hominins: The status of the LB1cranium based on 3D morphometric analyses,” suggest that Homo floresiensis was most likely the diminutive descendant of a species of archaic Homo.

The results of this study are also in line with what other researchers in the Department of Anatomical Sciences at Stony Brook University have found regarding the rest of the hobbit skeleton. Drs. William Jungers and Susan Larson have documented a range of primitive features in both the upper and lower limbs of Homo floresiensis, highlighting the many ways that these hominins were unlike modern humans.

Adapted from materials provided by Stony Brook University Medical Center.
http://www.sciencedaily.com/releases/2009/01/090120144508.htm

Neandertals Sophisticated And Fearless Hunters

ScienceDaily (May 14, 2009) — Neandertals, the 'stupid' cousins of modern humans were capable of capturing the most impressive animals. This indicates that Neandertals were anything but dim. Dutch researcher Gerrit Dusseldorp analysed their daily forays for food to gain insights into the complex behaviour of the Neandertal. His analysis revealed that the hunting was very knowledge intensive.

Although it is now clear that Neandertals were hunters and not scavengers, their exact hunting methods are still something of a mystery. Dusseldorp investigated just how sophisticated the Neandertals' hunting methods really were. His analysis of two archaeological sites revealed that Neandertals in warm forested areas preferred to hunt solitary game but that in colder, less forested areas they preferred to hunt the more difficult to capture herding animals.

The Neandertals were not easily intimated by their game. Rhinoceroses, bisons and even predators such as the brown bear were all on their menu. Dusseldorp established that just as for modern humans, the environment and the availability of food determined the choice of prey and the hunting method adopted. If the circumstances allowed it, Neandertals lived in large groups and even the most attractive and difficult to catch prey were within their reach.

Coordination and communication

Although herding animals are difficult to surprise and isolate, many such game lived on the open steppes. This large supply attracted large groups of Neandertals. That the Neandertals were capable of hunting down such elusive game demonstrates that they had good coordination skills and could communicate well with each other.

Each prey has a specific cost-benefit scenario. For example, game that are more difficult to catch yield more calories and have a more usable, thick fleece. Dusseldorp used these data to examine the Neandertal's preferences. He also analysed the prey of hyenas in the same manner. Hyenas were important competitors of Neandertals as they had a similar dietary pattern.

Dusseldorp demonstrated that Neandertals, thanks to their intelligence, even surpassed hyenas at capturing the strongest game. All things being considered, the Neandertals were skilled and highly intelligent hunters. So the idea that Neandertals were brute musclemen can be dismissed.

This study was part of NWO project Thoughtful Hunters? The Archaeology of Neandertal Communication and Cognition. Dusseldorp is continuing his research with a postdoc position in Johannesburg. There he shall focus on the modern humans that evolved in Africa.

---

Adapted from materials provided by Netherlands Organization for Scientific Research, via AlphaGalileo.

http://www.sciencedaily.com/releases/2009/05/090514084115.htm