Chimp and Human Y Chromosomes Evolving Faster Than Expected

ScienceDaily (Jan. 15, 2010) — Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation.

By conducting the first comprehensive interspecies comparison of Y chromosomes, Whitehead Institute researchers have found considerable differences in the genetic sequences of the human and chimpanzee Ys -- an indication that these chromosomes have evolved more quickly than the rest of their respective genomes over the 6 million years since they emerged from a common ancestor. The findings are published online this week in the journal Nature.

"The region of the Y that is evolving the fastest is the part that plays a role in sperm production," say Jennifer Hughes, first author on the Nature paper and a postdoctoral researcher in Whitehead Institute Director David Page's lab. "The rest of the Y is evolving more like the rest of the genome, only a little bit faster."

The chimp Y chromosome is only the second Y chromosome to be comprehensively sequenced. The original chimp genome sequencing completed in 2005 largely excluded the Y chromosome because its hundreds of repetitive sections typically confound standard sequencing techniques. Working closely with the Genome Center at Washington University, the Page lab managed to painstakingly sequence the chimp Y chromosome, allowing for comparison with the human Y, which the Page lab and the Genome Center at Washington University had sequenced successfully back in 2003.

The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content. The chimp Y, for example, has lost one third to one half of the human Y chromosome genes--a significant change in a relatively short period of time. Page points out that this is not all about gene decay or loss. He likens the Y chromosome changes to a home undergoing continual renovation.

"People are living in the house, but there's always some room that's being demolished and reconstructed," says Page, who is also a Howard Hughes Medical Institute investigator. "And this is not the norm for the genome as a whole."

Wes Warren, Assistant Director of the Washington University Genome Center, agrees. "This work clearly shows that the Y is pretty ingenious at using different tools than the rest of the genome to maintain diversity of genes," he says. "These findings demonstrate that our knowledge of the Y chromosome is still advancing."

Hughes and Page theorize that the divergent evolution of the chimp and human Y chromosomes may be due to several factors, including traits specific to Y chromosomes and differences in mating behaviors.

Because multiple male chimpanzees may mate with a single female in rapid succession, the males' sperm wind up in heated reproductive competition. If a given male produces more sperm, that male would theoretically be more likely to impregnate the female, thereby passing on his superior sperm production genes, some of which may be residing on the Y chromosome, to the next generation.

Because selective pressure to pass on advantageous sperm production genes is so high, those genes may also drag along detrimental genetic traits to the next generation. Such transmission is allowed to occur because, unlike other chromosomes, the Y has no partner with which to swap genes during cell division. Swapping genes between chromosomal partners can eventually associate positive gene versions with each other and eliminate detrimental gene versions. Without this ability, the Y chromosome is treated by evolution as one large entity. Either the entire chromosome is advantageous, or it is not.

In chimps, this potent combination of intense selective pressure on sperm production genes and the inability to swap genes may have fueled the Y chromosome's rapid evolution. Disadvantages from a less-than-ideal gene version or even the deletion of a section of the chromosome may have been outweighed by the advantage of improved sperm production, resulting in a Y chromosome with far fewer genes than its human counterpart.

To determine whether this rapid rate of evolution affects Y chromosomes beyond those of chimps and humans, the Page lab and the Washington University Genome Center are now sequencing and examining the Y chromosomes of several other mammals.

This research was funded by the National Institutes of Health (NIH) and the Howard Hughes Medical Institute (HHMI).

http://www.sciencedaily.com/releases/2010/01/100113131505.htm

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.

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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