[Centraal] Evolutie in het nieuws

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Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3′ flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty (“green animals”) and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.

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How the turtle's shell evolved

A newly discovered fossil from China has shed light on how the turtle's shell evolved.

The 220 million-year-old find, described in Nature journal, shows that the turtle's breast plate developed earlier than the rest of its shell.

The breast plate of this fossil was an extension of its ribs, but only hardened skin covered its back.

Researchers say the breast plate may have protected it while swimming.

The turtle fossil, found near Guangling in south-west China, is thought to be the ancestor of all modern turtles, although it differs markedly; it has teeth rather than a bony plate, the shell only covers its underside and it has a long tail.

The fossil find helps to answer key questions about the evolution of turtles, Dr Xiao-Chun Wu from the Canadian Museum of Nature was one of the first to examine the fossil.

Aquatic life

"Since the 1800s, there have been many hypotheses about the origin of the turtle shell," explained Dr. Wu. "Now we have these fossils of the earliest known turtle. They support the theory that the shell would have formed from below as extensions of the backbone and ribs, rather than as bony plates from the skin as others have theorised," Dr Wu explained.

The researchers say this idea is supported by evidence from the way modern turtle embryos develop. The breast plate grows before the shell covering their backs.

The fossilised turtle ancestor, which has been named Odontochelys semitestacea, meaning half-shelled turtle with teeth, probably inhabited the river deltas or coastal shallows of China's Nanpanjiang trough basin - the area where the fossil was unearthed.

Researchers say the development of the shell to first protect the underside points to a mainly aquatic lifestyle.

Dr Olivier Rieppel from Chicago's Field Museum also examined the fossil.

"This strongly suggests Odontochelys was a water dweller whose swimming exposed its underside to predators. Reptiles living on the land have their bellies close to the ground with little exposure to danger," he said.

The researchers say further evidence to support the idea that this species lived mainly in water comes from the structure and proportions of the fossil's forelimbs, which closely resemble those of modern turtles that live in similar conditions.

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All for One and One for All
Few scientists win a Pulitzer Prize. In 1991, Bert Hölldobler and Edward O. Wilson did for their magisterial The Ants (1). Now these distinguished collaborators offer The Superorganism: The Beauty, Elegance, and Strangeness of Insect Societies. In this ambitious book, they seemingly have three goals. Hölldobler and Wilson reprise and update themes from The Ants while broadening their survey to include other social insects (most notably honeybees). In a thread woven throughout the narrative, they argue that colonies of social insects should be seen and studied as superorganisms, a naturally selected level of organization a step above individual organisms. And they present the work in a format apparently intended to attract the broadest possible readership of both specialists and nonspecialists. This suggests the authors' probable primary motivation--they are advocating a conceptual framework for understanding insect sociality that has been out of favor for four decades.

Hölldobler and Wilson begin by updating the superorganism concept. They hold that "[t]he principal target of natural selection in the social evolution of insects is the colony, while the unit of selection is the gene." They then treat this claim in detail through a historical and theoretical dissection of gene-centered, altruistic worker-centered, and colony-centered perspectives along with the controversies, sometimes heated, that have accompanied them. They seek synthesis under the umbrella of multilevel selection, which Wilson and David Sloan Wilson have recently advocated in general and specialist articles (2, 3). Ensuing chapters address the "sociogenesis" of colonies and two main organizing principles for social insect colonies, division of labor and communication. Several chapters on ants, the forte of both authors, round out the book. Each chapter after the introduction is a stand-alone review of its topic, rich in content and sometimes daunting in detail. The chapter on ponerine ants, in particular, exemplifies the quantity, quality, and diversity of research on ants during the past two decades.

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Amish gene 'limits heart disease'

A gene mutation which protects the heart against a high-fat diet has been found in the Amish population.

Researchers found 5% of the US Amish population in Lancaster, Pennsylvania have a mutation in a protein which breaks down fatty particles.

Those with the mutation had higher levels of "good" HDL-cholesterol and lower levels of "bad" LDL-cholesterol, the journal Science reported.

It is hoped the finding will lead to new therapies to reduce cholesterol.

The researchers used blood samples from 800 volunteers in the Old Order Amish community to look for DNA markers that might be associated with levels of fat particles called triglycerides in the blood stream.

High blood levels of triglycerides, one of the most common types of fat in food, have been linked to heart disease.

They found a mutation in the APOC3 gene, which encodes a protein - apoC-III - that inhibits the breakdown of triglycerides.

As part of the study, participants drank a high-fat milkshake and were monitored for the next six hours.

Individuals with the mutation produced half the normal amount of apoC-III and had the lowest blood triglyceride levels - seemingly because they could break down more fat.

They also had relatively low levels of artery-hardening - a sign of cardiovascular disease.

Protection

Study leader Dr Toni Pollin, assistant professor of medicine at the University of Maryland School of Medicine, said: "Our findings suggest that having a lifelong deficiency of apoC-III helps to protect people from developing cardiovascular disease.

"The discovery of this mutation may eventually help us to develop new therapies to lower triglycerides and prevent cardiovascular disease," she added.

The researchers believe the mutation was first introduced into the Amish community in Lancaster County by a person who was born in the mid-1700s.

It appears to be rare or absent in the general population.

Cathy Ross, cardiac nurse at the British Heart Foundation said the benefits of high HDL cholesterol and low LDL cholesterol are already being achieved by drugs such as statins.

"If new drugs can be developed that mimic the effect of this mutation, it may afford more ways in which individuals could be protected from developing cardiovascular disease.

"There are also lots of other simple ways people can reduce your risk of cardiovascular disease such as eating a diet low in saturated fat, having five portions of fruit and vegetables a day and taking regular physical activity."

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Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection.

T. Hofer, N. Ray, D. Wegmann, L. Excoffier (2009).
Annals of Human Genetics, 73 (1), 95-108

Several studies have found strikingly different allele frequencies between continents. This has been mainly interpreted as being due to local adaptation. However, demographic factors can generate similar patterns. Namely, allelic surfing during a population range expansion may increase the frequency of alleles in newly colonised areas. In this study, we examined 772 STRs, 210 diallelic indels, and 2834 SNPs typed in 53 human populations worldwide under the HGDP-CEPH Diversity Panel to determine to which extent allele frequency differs among four regions (Africa, Eurasia, East Asia, and America). We find that large allele frequency differences between continents are surprisingly common, and that Africa and America show the largest number of loci with extreme frequency differences. Moreover, more STR alleles have increased rather than decreased in frequency outside Africa, as expected under allelic surfing. Finally, there is no relationship between the extent of allele frequency differences and proximity to genes, as would be expected under selection. We therefore conclude that most of the observed large allele frequency differences between continents result from demography rather than from positive selection.

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Life makes more of itself.

And now so can a set of custom-designed chemicals. Chemists have shown that a group of synthetic enzymes replicated, competed and evolved much like a natural ecosystem, but without life or cells.

"So long as you provide the building blocks and the starter seed, it goes forever," said Gerald Joyce, a chemist at the Scripps Research Institute and co-author of the paper published Thursday in Science. "It is immortalized molecular information."

Joyce's chemicals are technically hacked RNA enzymes, much like the ones we have in our bodies, but they don't behave anything like those in living creatures. But, these synthetic RNA replicators do provide a model for evolution — and shed light on one step in the development of early living systems from on a lifeless globe.

Scientists believe that early life on Earth was much more primitive than what we see around us today. It probably didn't use DNA like our cells do. This theory of the origin of life is called the RNA World hypothesis, and it posits that life began using RNA both to store information, like DNA does now, and as a catalyst allowing the molecules to reproduce. To try to understand what this life might have looked like, researchers are trying to build models for early life forms and in the process, they are discovering entirely new lifelike behavior that nonetheless isn't life, at least as we know it.

As Joyce put it, "This is more of a Life 2.0 thing."

The researchers began with pairs of enzymes they've been tweaking and designing for the past eight years. Each member of the pairs can only reproduce with the help of the other member.

"We have two enzymes, a plus and a minus," Joyce explains. "The plus assembles the pieces to make the minus enzyme, and the minus enzyme assembles the pieces to draw the plus. It's kind of like biology, where there is a DNA strand with plus and minus strands."

From there, Joyce and his graduate student Tracey Lincoln, added the enzymes into a soup of building blocks, strings of nucleic bases that can be assembled into RNA, DNA or larger strings, and tweaked them to find pairs of enzymes that would reproduce. One day, some of the enzymes "went critical" and produced more RNA enzymes than the researchers had put in.

It was an important day, but Joyce and Lincoln wanted more. They wanted to create an entire population of enzymes that could replicate, compete and evolve, which is exactly what they did.

"To put it in info speak, we have a channel of 30 bit capacity for transferring information," Joyce said. "We can configure those bits in different ways and make a variety of different replicators. And then have them compete with each other."

But it wasn't just a bunch of scientist-designed enzymes competing, like a miniature molecular BattleBots sequence. As soon as the replicators got into the broth, they began to change.

"Most of the time they breed true, but sometimes there is a bit flip — a mutation — and it's a different replicator," explained Joyce.

Most of these mutations went away quickly, but — sound familiar? — some of the changes ended up being advantageous to the chemicals in replicating better. After 77 doublings of the chemicals, astounding changes had occurred in the molecular broth.

"All the original replicators went extinct and it was the new recombinants that took over," said Joyce. "There wasn't one winner. There was a whole cloud of winners, but there were three mutants that arose that pretty much dominated the population."

It turned out that while the scientist-designed enzymes were great at reproducing without competition, when you put them in the big soup mix, a new set of mutants emerged that were better at replicating within the system. It almost worked like an ecosystem, but with just straight chemistry.

"This is indeed interesting work," said Jeffrey Bada, a chemist at the Scripps Institution of Oceanography, who was not involved with the work. It shows that RNA molecules "could have carried out their replication in the total absence" of the more sophisticated biological machinery that life now possesses.

"This is a nice example of the robustness of the RNA world hypothesis," he said. However, "it still leaves the problem of how RNA first came about. Some type of self-replicating molecule likely proceeded RNA and what this was is the big unknown at this point."

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Op zondag 1 februari 2009 20:40 schreef pfaf het volgende:

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Uiteraard. En dat zie ik in deze tijd nog niet zo snel gebeuren. Of heel vrouwelijk moet op 6 vingers gaan vallen.

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Op maandag 2 februari 2009 04:53 schreef vaarsuvius het volgende:
Prachtige utizending van David Attenborough gisteravond weer op de BBC. in een uur Darwin uitgelegd zonder dat het te moeilijk werd, maar toch met alle belangrijke zaken erin. BBC kwaliteit. Waarom hebben we dat niet in Nederland?

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A research team at the Broad Institute of Harvard and MIT and Beth Israel Deaconess Medical Center has uncovered a vast new class of previously unrecognized mammalian genes that do not encode proteins, but instead function as long RNA molecules.

Their findings, published in the February 1st advance online issue of the journal Nature, demonstrate that this novel class of "large intervening non-coding RNAs" or "lincRNAs" plays critical roles in both health and disease, including cancer, immune signaling and stem cell biology.

Standard "textbook" genes encode RNAs that are translated into proteins, and mammalian genomes harbor about 20,000 such protein-coding genes. Some genes, however, encode functional RNAs that are never translated into proteins. These include a handful of classical examples known for decades and some recently discovered classes of tiny RNAs, such as microRNAs.

[..]

By contrast, the newly discovered lincRNAs are thousands of bases long. Because only about ten examples of functional lincRNAs were known previously, they seemed more like genomic oddities than critical components. The new Nature study shows that there are actually thousands of such genes and that they have been conserved across mammalian evolution.

[..]

To uncover this large collection of new genes, the Broad scientific team looked not at the RNA molecules themselves but at telltale signs in the DNA called chromatin modifications or epigenomic marks. They searched for genomic regions that have the same chromatin patterns as protein-coding genes, but do not encode proteins. By surveying the genomes of four different types of mouse cells (including embryonic stem cells and cells from various tissue types), they found an astounding 1,586 such loci that had not been previously described. The researchers also found that the vast majority of these genomic regions are transcribed into lincRNAs, and that these are conserved across mammals.

"The epigenomic marks revealed where these genes were hiding," said Mitch Guttman, a MIT graduate student working at the Broad Institute. "Analysis of their sequence then revealed that the genes are highly conserved in mammalian genomes, which strongly suggested that these genes play critical biological functions."

By correlating the expression patterns of lincRNAs in various cell types with the expression patterns of known critical protein-coding genes in those same cells, the scientists observed that lincRNAs likely play critical roles in helping to regulate a variety of different cellular processes, including cell proliferation, immune surveillance, maintenance of embryonic stem cell pluripotency, neuronal and muscle development, and gametogenesis. Further experimental evidence from several of the identified lincRNAs verified these observations.

Because of the stringent experimental conditions imposed by the researchers in identifying the 1,600 lincRNAs in the Nature study, it is likely that there are many more lincRNA genes hiding in plain sight in the genome, as well as other RNA-encoding genes that are as important to genome function as their better-recognized protein-coding counterparts.

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Guttman, M. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, advance online

There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. Although there are some well-characterized examples, most (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise5, 6. Here we report a new approach to identifying large non-coding RNAs using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci. Our approach identified approx1,600 large multi-exonic RNAs across four mouse cell types. In sharp contrast to previous collections, these large intervening non-coding RNAs (lincRNAs) show strong purifying selection in their genomic loci, exonic sequences and promoter regions, with greater than 95% showing clear evolutionary conservation. We also developed a functional genomics approach that assigns putative functions to each lincRNA, demonstrating a diverse range of roles for lincRNAs in processes from embryonic stem cell pluripotency to cell proliferation. We obtained independent functional validation for the predictions for over 100 lincRNAs, using cell-based assays. In particular, we demonstrate that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFkappaB, Sox2, Oct4 (also known as Pou5f1) and Nanog. Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes.

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Rapidly Evolving Gene Contributes To Origin Of Species

ScienceDaily (Feb. 7, 2009) — A gene that helped one species split into two species shows evidence of adapting much faster than other genes in the genome, raising questions about what is driving its rapid evolution.

The paper in the Feb 5 issue of Science shows that the gene has connections to another previously identified "speciation gene." Both genes code for key proteins that control molecular traffic into and out of a cell's nucleus. The researchers believe an arms race of sorts inside the cell drives these genes to evolve rapidly—and as a consequence makes closely related species genetically incompatible with one another.

"When we cross two species of fruit fly, which had split from one another 3 million years ago, some of the hybrid offspring die," says Daven Presgraves, professor of biology at the University of Rochester and Grass Fellow at the Radcliffe Institute for Advanced Study at Harvard University. "This tells us that genes from one species are no longer compatible with genes from the other species. We've now found that a functionally related group of genes is responsible, with different versions of the genes having evolved in the two species. And just as Darwin predicted 150 years ago, they evolved by natural selection."

Presgraves has some ideas why two of the genes in particular, called Nup160 and Nup96, have evolved so quickly: they act as gatekeepers of a cell's nucleus, a favorite target for viruses and even malicious genes within the fly's own genome. Presgraves says that these genes probably experience constant assault and thus must constantly adapt. That these genes also prevent genetic mixing between closely related species is incidental—the origin of new species is just a by-product of evolutionary arms races, he says.

When two populations become separated by a geographic barrier—a mountain range or an ocean—they evolve independently. Presgraves and his graduate student Shanwu Tang studied a fruit fly species from Madagascar that long ago become separated from its sister species in Africa. Separated by an expanse of the Indian Ocean, the two independently evolving species accumulated genetic differences. Tang and Presgraves's unexpected finding, however, was that in both species, the Nup160 and Nup96 genes became so different so quickly that they are no longer compatible.

"When the same genes in two different species evolve quickly, they become so different that they can be incompatible," says Tang. "The genes from one species can't talk to the genes in the other species any more."

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Biologists Find Gene Network That Gave Rise To First Tooth

ScienceDaily (Feb. 10, 2009) — A new paper in PLoS Biology reports that a common gene regulatory circuit controls the development of all dentitions, from the first teeth in the throats of jawless fishes that lived half a billion years ago, to the incisors and molars of modern vertebrates, including you and me.

"It's likely that every tooth made throughout the evolution of vertebrates has used this core set of genes," said Gareth Fraser, postdoctoral fellow at Georgia Tech's School of Biology.

The first vertebrates to have teeth were a group of eel-like jawless fish known as the conodonts that had teeth not in their mouth, but lining the throat. This particular group is long since extinct, but some modern fish retain teeth in the throat (pharynx). Dr. Fraser and colleagues studied tooth formation in a group of fish known for their rapid rate of evolution, the cichlids of Africa's Lake Malawi. The cichlids have teeth both in their oral jaws, like humans, and deep in their throats on a pharyngeal jaw. A co-author of the paper, Darrin Hulsey, first identified a surprising positive correlation between the number of teeth in the oral jaw and in the throat in these fish.

"Originally, I thought there wouldn't be a correlation due to the developmental differences and the evolutionary distinction between the two jaw regions, but it turns out there is," explained Fraser. "So fish that have fewer oral teeth also have fewer pharyngeal teeth. This shows that on some level there's a genetic control that governs the number of teeth in both regions."

The team investigated what this control might be by using a technique localizing gene expression in the cells during tooth development, known as in situ hybridization, and found that a common genetic network governs teeth in the two locations.

"So seemingly, regardless of where you grow a tooth, whether it's in the jaw or the pharynx, you use the same core set of genes to do it," said co-author J. Todd Streelman. "We also think it's probable that this network is not just acting in teeth, but also in other similarly patterned structures like hair and feathers."

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Deducing Diet Of Prehistoric Hominid With Mathematical Models

ScienceDaily (Feb. 11, 2009) — In an unusual intersection of materials science and anthropology, researchers from the National Institute of Standards and Technology (NIST) and The George Washington University (GWU) have applied materials-science-based mathematical models to help shed light on the dietary habits of some of mankind’s prehistoric relatives. Their work forms part of a newly published, multidisciplinary analysis of the early hominid Australopithecus africanus by anthropologists at the State University of New York at Albany and elsewhere.

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A. africanus presented a puzzle. Classical analysis of the skull—large molars and premolars with thick enamel, thick heavy jawbones, strong chewing muscles as evidenced by their anchor points on the bone—pointed to a diet of small, hard seeds. The finite-element analysis threw a spanner in the works. It suggested that A. africanus’s facial and jaw anatomy was optimized to handle stress on the premolars, teeth located farther forward in the mouth and most useful for chewing larger hard objects. But recent studies had shown that the teeth lacked the microscopic wear patterns characteristic of chewing hard objects, a contradiction.

Here, work by NIST researcher Brian Lawn and a group at GWU headed by Peter Lucas came in handy. Driven by an interest in tooth restoration materials, they had been studying teeth using fracture mechanics, a field that considers how materials fail under excessive loads. “Our analytical approach produces equations that predict how each mode of damage will occur under different conditions and this enables us to determine trends for different tooth sizes, different food sizes, different food hardness and so on,” explained Lawn. “What they show is that, under some conditions, teeth will actually fracture before they wear.” This explained the absence of microwear patterns in the teeth, which would normally not be used for chewing small hard seeds. “A lot of people have thought the most important part of the survival of the tooth is wear, but it’s now becoming evident that the fracture properties are also very important because there’s a limit to the force that you can apply. Wear is important, but when you start to bite on harder, larger objects, fracture becomes more important,” Lawn said.

“This is a neat example of how really basic materials science—fracture mechanics—has important implications for biological sciences and anthropology,” Strait observed. In the bigger picture, said Strait, the new understanding about A. africanus’s diet may help to explain its successful adaptation to changing climates. A large hard nut that had to be cracked with the premolars may not have been a preferred meal, but it could be something to fall back on when other foods were scarce.

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Did Burst Of Gene Duplication Set Stage For Human Evolution?

ScienceDaily (Feb. 12, 2009) — Roughly 10 million years ago, a major genetic change occurred in a common ancestor of gorillas, chimpanzees, and humans. Segments of DNA in its genome began to form duplicate copies at a greater rate than in the past, creating an instability that persists in the genome of modern humans and contributes to diseases like autism and schizophrenia. But that gene duplication also may be responsible for a genetic flexibility that has resulted in some uniquely human characteristics.

"Because of the architecture of the human genome, genetic material is constantly being added and deleted in certain regions," says Howard Hughes Medical Institute investigator and University of Washington geneticist Evan Eichler, who led the project that uncovered the new findings. "These are really like volcanoes in the genome, blowing out pieces of DNA."

Eichler and his colleagues focused on the genomes of four different species: macaques, orangutans, chimpanzees, and humans. All are descended from a single ancestral species that lived about 25 million years ago. The line leading to macaques broke off first, so that macaques are the most distantly related to humans in evolutionary terms. Orangutans, chimpanzees, and humans share a common ancestor that lived 12-16 million years ago. Chimps and humans are descended from a common ancestral species that lived about 6 million years ago.

By comparing the DNA sequences of the four species, Eichler and his colleagues identified gene duplications in the lineages leading to these species since they shared a common ancestor. They also were able to estimate when a duplication occurred from the number of species sharing that duplication. For example, a duplication observed in orangutan, chimpanzees, and humans but not in macaques must have occurred sometime after 25 million years ago but before the orangutan lineage branched off.

Eichler's research team found an especially high rate of duplications in the ancestral species leading to chimps and humans, even though other mutational processes, such as changes in single DNA letters, were slowing down during this period. "There's a big burst of activity that happens where genomes are suddenly rearranged and changed," he says. Surprisingly, the rate of duplications slowed down again after the lineages leading to humans and to chimpanzees diverged. "You might like to think that humans are special because we have more duplications than did earlier species," he says, "but that's not the case."

These duplications have created regions of our genomes that are especially prone to large-scale reorganizations. "That architecture predisposes to recurrent deletions and duplications that are associated with autism and schizophrenia and with a whole host of other diseases," says Eichler.

Yet these regions also exhibit signs of being under positive selection, meaning that some of the rearrangements must have conferred advantages on the individuals who inherited them. Eichler thinks that uncharacterized genes or regulatory signals in the duplicated regions must have created some sort of reproductive edge. "I believe that the negative selection of these duplications is being outweighed by the selective advantage of having these newly minted genes, but that's still unproven," he said.

An important task for future studies is to identify the genes in these regions and analyze their functions, according to Eichler. "Geneticists have to figure out the genes in these regions and how variation leads to different aspects of the human condition such as disease. Then, they can pass that information on to neuroscientists and physiologist and biochemists who can work out what these proteins are and what they do," he says. "There is the possibility that these genes might be important for language or for aspects of cognition, though much more work has to be done before we'll be able to say that for sure."

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Survival Of The Weakest? Cyclical Competition Of 3 Species Favors Weakest As Victor

ScienceDaily (Feb. 13, 2009) — The extinction of species is a consequence of their inability to adapt to new environmental conditions, and also of their competition with other species. Besides selection and the appearance of new species, the possibility of adaptation is also one of the driving forces behind evolution. According to the interpretation that has been familiar since Darwin, these processes increase the “fitness” of the species overall, since, of two competing species, only the fittest would survive.

LMU researchers have now simulated the progression of a cyclic competition of three species. It means that each participant is superior to one other species, but will be beaten by a third interaction partner. “In this kind of cyclical concurrence, the weakest species proves the winner almost without exception,” reports Professor Erwin Frey, who headed the study. “The two stronger species, on the other hand, die out, as experiments with bacteria have already shown. Our results are not only a big surprise, they are important to our understanding of evolution of ecosystems and the development of new strategies for the protection of species.”

Ecosystems are composed of a large number of different species, which interact and compete with one another for scarce resources. This competition between species in turn affects the probability with which the individual can reproduce and survive – a matter of life and death, as it were. All of these processes are also largely probabilistic and lead to fluctuations that ultimately lead to the extinction of species. We know that up to 50 species become extinct every day on Earth, which at this high rate can be attributed to the influence of man.

Yet, the phenomenon of extinction of species itself cannot be avoided altogether – and is still only barely understood. Theoretical ecologists and biophysicists are therefore intensively researching conditions and mechanisms that affect the biodiversity of Earth. Cyclic dominance is a particularly interesting constellation of species competing with each other. It means that each participant is superior to one other interaction partner, but will be beaten by a third. In ecosystems, this would be three subpopulations – in the simplified model – which dominate in turn. In fact, communities of subpopulations following such rules have been identified in numerous ecosystems, ranging from coral reef invertebrates to lizards in the inner Coast Range of California.

Such cyclical interaction is also familiarly termed “rock-paper-scissors” interaction. This is where the rock blunts the scissors, which cut the paper, which in turn wraps around the rock. Together, these non-hierarchical relationships form a cyclical motion. “The game can help describe the diversity of species,” explains Frey. “The background is a branch of mathematics called game theory, and in this case evolutionary game theory. It helps analyze systems that involve multiple actors whose interactions are similar to those in parlor games.”

Using game theory, one can also study the collective development of populations. In their study, the scientists working with Frey developed elaborate computer simulations in order to calculate the probabilities with which species in cyclical competition will survive. The games started off with three species coexisting in the systems, and ran until two species became extinct – with the third being the only remaining survivors. “What we saw was that in large populations, the weakest species would – with very high probability – come out as the victor,” says Frey.

This “law of the weakest” even held true when the difference between the competing species was slight. “This result was just as unexpected for us,” reports Frey. “But it shows once more that chance plays a big part in the dynamics of an ecosystem. Incidentally, in experiments that were conducted a couple of years ago on bacterial colonies, in order to study cyclical competition, there was one clear result: The weakest of the three species emerged victorious from the competition.”

The project was supported by the cluster of excellence “Nanoinitiative Munich (NIM)”, of which Professor Erwin Frey is a principal investigator.

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HIV Is Evolving To Evade Human Immune Responses

ScienceDaily (Feb. 28, 2009) — HIV is evolving rapidly to escape the human immune system, an international study led by Oxford University has shown. The findings, published in Nature, demonstrate the challenge involved in developing a vaccine for HIV that keeps pace with the changing nature of the virus.

'The extent of the global HIV epidemic gives us a unique opportunity to examine in detail the evolutionary struggle being played out in front of us between an important virus and humans,’ says lead researcher Professor Philip Goulder of the Peter Medawar Building for Pathogen Research at Oxford University.

‘Even in the short time that HIV has been in the human population, it is doing an effective job of evading our best efforts at natural immune control of the virus. This is high-speed evolution that we’re seeing in the space of just a couple of decades.’

The study better describes HIV's ability to adapt by spelling out at least 14 different "escape mutations" that help keep the virus alive after it interacts genetically with immunity molecules that normally attack HIV.

"Key genetic regions of HIV introduced into individuals of different ancestry in different places have been evolving to a greater or lesser degree according to inherited factors controlling immune response," said Richard Kaslow, M.D., a professor in the UAB School of Public Health and a co-author of the study. "If HIV adapts differently in genetically distinct hosts, the challenge ahead in vaccine design is formidable," he said.

HIV has already killed 25 million people, and an estimated 33 million are currently infected. However, HIV does not kill all people at the same rate. On average, an adult with HIV will survive for ten years without anti-HIV drugs before developing AIDS. But some people will progress to AIDS within 12 months while others can make effective immune responses to the virus and survive without any anti-HIV therapy for over 20 years.

Genes encoding a key set of molecules in the human immune system called the human leucocyte antigens (HLA) are critically important. HLA determine the progress of many infectious diseases including HIV, and enable the recognition and killing of HIV-infected cells. Humans differ from each other in the exact HLA genes they have, and small differences can make the difference in how long it takes to progress to AIDS.

The research team set out to determine whether HIV is adapting to human immune responses. They looked at HIV genetic sequences in different countries around the world, including the UK, South Africa, Botswana, Australia, Canada, and Japan, wanting to see whether the HIV sequences could be related to the different HLA genes present in the different populations.

The collaboration between Oxford University, the Ragon Institute at Massachusetts General Hospital, Kumamoto University in Japan, the Royal Perth Hospital and Murdoch University in Australia and others analysed the genetic sequences of the HIV virus and human leucocyte antigen (HLA) genes in over 2,800 people.

Mutations that allow HIV to get round immune responses directed by a particular HLA gene were found more frequently in populations with a high prevalence of that HLA gene. This is strong evidence for HIV adaptation to the human immune system at the level of populations.

‘Where a favourable HLA gene is present at high levels in a given population, we see high levels of the mutations that enable HIV to resist this particular gene effect,’ says author Professor Rodney Phillips, co-director of the James Martin Institute for Emerging Infections at Oxford University. ‘The virus is outrunning human variation, you might say.’

‘The temptation is to see this as bad news, that these results mean the virus is winning the battle,’ says Professor Goulder. ‘That’s not necessarily the case. It could equally be that as the virus changes, different immune responses come into play and are actually more effective.’

The results are important because it is our most effective immune responses that vaccines against HIV would try and boost to a level that would protect against the virus.

‘The implication is that once we have found an effective vaccine, it would need to be changed on a frequent basis to catch up with the evolving virus, much like we do today with the flu vaccine,’ explains Professor Goulder.

‘In this anniversary year of Darwin’s birth, we are accustomed to think of evolution happening over thousands, tens of thousands and even millions of years,’ says Professor Goulder. ‘But we are seeing changes in HIV, and our immune response to the virus, in just a couple of decades.’

The work was funded by a number of organisations including the Wellcome Trust, the Medical Research Council, the US National Institutes of Health, and Oxford’s James Martin 21st Century School.

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McEvoy, B.P. et al. (2009) Geographical structure and differential natural selection amongst North European populations. Genome Research, in press.


Population structure can provide novel insight into the human past and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, UK, Netherlands, Denmark, Sweden, Finland, Australia and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and -American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogenous region. There is evidence from FST based analysis of genic and non-genic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to HLA-G gene on chromosome 6. Evidence of the sweep extends over 8Mb/3.5cM region. Overall the results illustrate the power of dense genotype and sample data to explore regional population variation, the events that have crafted it and their implications in both explaining disease prevalence and mapping these genes by association

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Gallet, R. (2009) Ecological Conditions Affect Evolutionary Trajectory in a Predator-Prey system. Evolution, 63, 641 - 651.

The arms race of adaptation and counter adaptation in predator–prey interactions is a fascinating evolutionary dynamic with many consequences, including local adaptation and the promotion or maintenance of diversity. Although such antagonistic coevolution is suspected to be widespread in nature, experimental documentation of the process remains scant, and we have little understanding of the impact of ecological conditions. Here, we present evidence of predator–prey coevolution in a long-term experiment involving the predatory bacterium Bdellovibrio bacteriovorus and the prey Pseudomonas fluorescens, which has three morphs (SM, FS, and WS). Depending on experimentally applied disturbance regimes, the predator–prey system followed two distinct evolutionary trajectories, where the prey evolved to be either super-resistant to predation (SM morph) without counter-adaptation by the predator, or moderately resistant (FS morph), specialized to and coevolving with the predator. Although predation-resistant FS morphs suffer a cost of resistance, the evolution of extreme resistance to predation by the SM morph was apparently unconstrained by other traits (carrying capacity, growth rate). Thus we demonstrate empirically that ecological conditions can shape the evolutionary trajectory of a predator–prey system.

Conclusion
From one single ancestral strain, we observed two distinct evolutionary outcomes depending on the experimental ecological treatments. When disturbances were frequent or moderate, the FS morph usually went to fixation. When disturbances were relatively infrequent and not intense, it was possible for the SM morph to go to fixation. Antagonistic coevolution with specialization between predator and prey was observed where the FS morph went to fixation and not where the SM morph went to fixation. The predator failed to counter-adapt to the form of the SM morph that emerged. Only where the disturbance regime favored the SM morph did it persist long enough to evolve extreme resistance to predation. This suggests that there may be several alternative evolutionary or genetic pathways that a prey or host may follow to develop resistance to predation or parasitism. These alternative pathways seem to be favored by different disturbance regimes. In other words, in our experiment, disturbance seems to have driven predator–prey populations toward different features on their evolutionary landscape, with either the evolution of prey resistance (SM) or an antagonistic predator–prey coevolution (FS). This suggests that microorganisms evolve on much more complex and changing adaptive landscapes than previously thought, warranting the exploration of more than one culturing regime (in contrast to most experimental evolution designs).

Our results also provide information about the adaptive capacities of B. bacteriovorus. Thus far, this predatory bacterium was known as a generalist preying on various Gram− bacteria strain. Ours is the first report of specialization to a specific prey by B. bacteriovorus; further, we showed that the predation efficiency of B. bacteriovorus increased only on certain prey morphs. This result might be viewed as surprising and intriguing, given B. bacteriovorus's profile as a generalist. Our results also contradict the notion that resistance to B. bacteriovorus is rare. Unfortunately, nothing is known about the mechanistic details of this prey–predator system, so we do not know if resistance to predation by B. bacteriovorus in P. fluorescens is the result of a reduced ability to enter the periplasm of the prey or less accessible cytoplasm, among other possibilities. A better understanding of the mechanisms involved in the predator–prey interaction between B. bacteriovorus and P. fluorescens might allow us to identify the cause of high resistance to predation by the SM morph and the constraints acting on resistance to predation in the FS morph.

This should also inspire caution about the use of B. bacteriovorus as an environmental prophylactic or as an alternative to antibiotic therapy (Sockett and Lambert 2004). Many diseases have evolved resistance to antibiotics (e.g., tuberculosis; Abdel Aziz and Wright 2005). "Living antibiotics" must also be considered carefully regarding the way their efficiency might be shaped by evolution. Successful long-term control of diseases, pests, and invasive species will require a better understanding of coevolutionary dynamics in an ecological context.

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Cretaceous Octopus With Ink And Suckers -- The World's Least Likely Fossils?

ScienceDaily (Mar. 18, 2009) — New finds of 95 million year old fossils reveal much earlier origins of modern octopuses. These are among the rarest and unlikeliest of fossils. The chances of an octopus corpse surviving long enough to be fossilized are so small that prior to this discovery only a single fossil species was known, and from fewer specimens than octopuses have legs.

Even if you have never encountered an octopus in the flesh, the eight arms, suckers, and sack-like body are almost as familiar a body-plan as the four legs, tail and head of cats and dogs. Unlike our vertebrate cousins, however, octopuses don't have a well-developed skeleton. And while this famously allows them to squeeze into spaces that a more robust animal could not, it does create problems for scientists interested in evolutionary history. When did octopuses acquire their characteristic body-plan, for example? Nobody really knows, because fossil octopuses are rarer than, well, pretty much any very rare thing you care to mention.

The body of an octopus is composed almost entirely of muscle and skin, and when an octopus dies, it quickly decays and liquefies into a slimy blob. After just a few days there will be nothing left at all. And that assumes that the fresh carcass is not consumed almost immediately by hungry scavengers. The result is that preservation of an octopus as a fossil is about as unlikely as finding a fossil sneeze, and none of the 200-300 species of octopus known today has ever been found in fossilized form. Until now, that is.

Palaeontologists have just identified three new species of fossil octopus discovered in Cretaceous rocks in Lebanon. The five specimens, described in the latest issue of the journal Palaeontology, are 95 million years old but, astonishingly, preserve the octopuses' eight arms with traces of muscles and those characteristic rows of suckers. Even traces of the ink and internal gills are present in some specimens. '

"These are sensational fossils, extraordinarily well preserved," says Dirk Fuchs of the Freie University Berlin, lead author of the report. But what surprised the scientists most was how similar the specimens are to modern octopus: "these things are 95 million years old, yet one of the fossils is almost indistinguishable from living species." This provides important evolutionary information. "The more primitive relatives of octopuses had fleshy fins along their bodies. The new fossils are so well preserved that they show, like living octopus, that they didn't have these structures." This pushes back the origins of modern octopus by tens of millions of years, and while this is scientifically significant, perhaps the most remarkable thing about these fossils is that they exist at all.

Publicatie
Fuchs et al. New Octopods (Cephalopoda: Coleoidea) from the Late Cretaceous (Upper Cenomanian) of Hakel and Hadjoula, Lebanon. Palaeontology, 2009; 52 (1): 65

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Somel, M. et al. (2009) Transcriptional neoteny in the human brain. PNAS, advance online.

In development, timing is of the utmost importance, and the timing of developmental processes often changes as organisms evolve. In human evolution, developmental retardation, or neoteny, has been proposed as a possible mechanism that contributed to the rise of many human-specific features, including an increase in brain size and the emergence of human-specific cognitive traits. We analyzed mRNA expression in the prefrontal cortex of humans, chimpanzees, and rhesus macaques to determine whether human-specific neotenic changes are present at the gene expression level. We show that the brain transcriptome is dramatically remodeled during postnatal development and that developmental changes in the human brain are indeed delayed relative to other primates. This delay is not uniform across the human transcriptome but affects a specific subset of genes that play a potential role in neural development.

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Op dinsdag 24 maart 2009 15:39 schreef barthol het volgende:

[..]

Interessant artikel. Gould suggereerde indertijd ook al die neotenie.

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Gunz, P. et al. (2009) Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario. PNAS, advance online

The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil Homo and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa

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Food Choices Evolve Through Information Overload

ScienceDaily (Mar. 30, 2009) — Ever been so overwhelmed by a huge restaurant menu that you end up choosing an old favourite instead of trying something new?

Psychologists have long since thought that information overload leads to people repeatedly choosing what they know. Now, new research has shown that the same concept applies equally to hundreds of animal species, too.

Researchers from the University of Leeds have used computer modelling to examine the evolution of specialisation, casting light on why some animal species have evolved to eat one particular type of food. For example some aphids choose to eat garden roses, but not other plants which would offer similar nutritional values.

"This is a major leap forward in our understanding of the way in which animals interact with their environment," says lead researcher Dr Colin Tosh from the University's Faculty of Biological Sciences. "Our computer models show the way in which neural networks operate in different environments. They have made it possible for us to see how different species make decisions, based on what's happening – or in this case, which foods are available - around them."

Despite the prevalence of specialisation in the animal kingdom, very little is known about why it occurs. The work conducted at Leeds has provided strong evidence in support of the 'neural limitations' hypothesis put forward by academics in the 1990s. This hypothesis, derived from human psychology, is based on the concept of information overload.

"There are several hypotheses to explain specialisation: one suggests that animals adapt to eat certain foods and this prevents them from eating other types of food," says Dr Tosh.

"For example, cows have evolved flat teeth which allow them to chew grass but they are unable to efficiently process meat. However, the problem with these hypotheses is that they don't apply across the board. Some species – such as many plant eating insects – have evolved to specialise even though there are many other available foods they could eat perfectly well."

This is the first study to provide a realistic representation of neural information processing in animals and how these interact with their environment. The research team believe that it could also have major implications for predicting the effects of environmental change.

"A good example of a struggling specialist is the giant panda, which relies on high mountain bamboo," says Dr Tosh. "In understanding how neural processes work, we may be able to gain an insight into how future environmental conditions – such as the dying out of particular types of plants - may affect a range of different animal species that utilise them for food."

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New Theory On Largest Known Mass Extinction In Earth's History

ScienceDaily (Mar. 31, 2009) — The largest mass extinction in the history of the earth could have been triggered off by giant salt lakes, whose emissions of halogenated gases changed the atmospheric composition so dramatically that vegetation was irretrievably damaged.

At least that is what an international team of scientists has reported in the most recent edition of the Proceedings of the Russian Academy of Sciences (Dokladi Earth Sciences). At the Permian/Triassic boundary, 250 million years ago, about 90 percent of the animal and plant species ashore became extinct. Previously it was thought that volcanic eruptions, the impacts of asteroids, or methane hydrate were instigating causes.

The new theory is based on a comparison with today's biochemical and atmospheric chemical processes. "Our calculations show that airborne pollutants from giant salt lakes like the Zechstein Sea must have had catastrophic effects at that time", states co-author Dr. Ludwig Weißflog from the Helmholtz-Center for Environmental Research (UFZ). Forecasts predict an increase in the surface areas of deserts and salt lakes due to climate change. That is why the researchers expect that the effects of these halogenated gases will equally increase.

The team of researchers from Russia, Austria, South Africa and Germany investigated whether a process that has been taking place since primordial times on earth could have led to global mass extinctions, particularly at the end of the Permian. The starting point for this theory was their discovery in the south of Russia and South Africa that microbial processes in present-day salt lakes naturally produce and emit highly volatile halocarbons such as chloroform, trichloroethene, and tetrachloroethene.

They transcribed these findings to the Zechstein Sea, which about 250 million years ago in the Permian Age, was situated about where present day Central Europe is. The Zechstein Sea with a total surface area of around 600.000 km2 was almost as large as France is today. The hyper saline flat sea at that time was exposed to a predominantly dry continental desert climate and intensive solar radiation – like today’s salt seas. "Consequently, we assume that the climatic, geo-chemical and microbial conditions in the area of the Zechstein Sea were comparable with those of the present day salt seas that we investigated," Weißflog said.

In their current publication the authors explain the similarities between the complex processes of the CO2-cycle in the Permian Age as well as between global warming from that time and at present. Based on comparable calculations from halogenated gas emissions in the atmosphere from present-day salt seas in the south of Russia, the scientists calculated that from the Zechstein Sea alone an annual VHC emissions rate of at least 1.3 million tonnes of trichloroethene, 1.3 million tonnes of tetrachloroethene, 1.1 million tonnes of chloroform as well as 0.050 million tonnes of methyl chloroform can be assumed. By comparison, the annual global industrial emissions of trichloroethene and tetrachloroethene amount to only about 20 percent of that respectively, and only about 5 percent of the chloroform from the emissions calculated for the Zechstein Sea by the scientists. Incidentally, the industrial production of methyl chloroform, which depletes the ozone layer, has been banned since 1987 by regulation of the Montreal Protocol.

"Using steppe plant species we were able to prove that halogenated gases contribute to speeding up desertification: The combination of stress induced by dryness and the simultaneous chemical stressor „halogenated hydrocarbons“ disproportionately damages and destabilize the plants and speeds up the process of erosion," Dr. Karsten Kotte from the University of Heidelberg explained.

Based on both of these findings the researchers were able to form their new hypothesis: At the end of the Permian Age the emissions of halogenated gases from the Zechstein Sea and other salt seas were responsible in a complex chain of events for the world's largest mass extinction in the history of the earth, in which about 90 percent of the animal and plant species of that time became extinct.

According to the forecast from the International Panel on Climate Change (IPCC), increasing temperatures and aridity due to climate change will also speed up desertification, increasing with it the number and surface area of salt seas, salt lagoons and salt marshlands. Moreover, this will then lead to an increase in naturally formed halogenated gases. The phytotoxic effects of these substances become intensified in conjunction with other atmospheric pollutants and at the same time increasing dryness and exponentiate the eco-toxicological consequences of climate change.

The new theory could be like a jigsaw piece that contributes to solving the puzzle of the largest mass extinction in the history of the earth. "The question as to whether the halogenated gases from the giant salt lakes alone were responsible for it or whether it was a combination of various factors with volcanic eruptions, the impact of asteroids, or methane hydrate equally playing their role still remains unanswered," Ludwig Weißflog said. What is fact however is that the effects of salt seas were previously underestimated.

In their publication the researchers working with Dr. Ludwig Weißflog from the UFZ and Dr. Karsten Kotte from the University of Heidelberg want to showed that recent salt lakes and salt deserts of south-east Europe, Middle Asia, Australia, Africa, America can not only influence the regional but also the global climate. The new findings on the effects of these halogenated gases are important for revising climate models, which form the basis for climate forecasts.

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Evolution-proof Insecticides May Stall Malaria Forever

ScienceDaily (Apr. 7, 2009) — Killing just the older mosquitoes would be a more sustainable way of controlling malaria, according to entomologists who add that the approach may lead to evolution-proof insecticides that never become obsolete.

Each year malaria -- spread through mosquito bites -- kills about a million people, but many of the chemicals used to kill the insects become ineffective. Repeated exposure to an insecticide breeds a new generation of mosquitoes that are resistant to that particular insecticide.

"Insecticides sprayed on house walls or bed nets are some of the most successful ways of controlling malaria," said Andrew Read, professor of biology and entomology, Penn State. "But they work by killing the insects or denying them the human blood they turn into eggs. This imposes an enormous selection in favor of insecticide-resistant mosquitoes."

Read and his colleagues Matthew Thomas, professor of entomology, Penn State, and Penelope Lynch, doctoral student, Open University, UK, argue that insecticides -- chemical or biological -- that kill only older mosquitoes are a more sustainable way to fight the deadly disease.

"If we killed only older mosquitoes we could control malaria and solve the problem of resistant mosquitoes," said Read. "This could be done by changing the way we use existing insecticides, even by simply diluting them," he added.

Aging mosquitoes are easier to kill with insecticides like DDT but new generation pesticides could do it too. Read and his colleagues are working with a biopesticide that kills older mosquitoes.

"It is one of the great ironies of malaria," explained Read, whose team's findings appear today (April 7) in PLoS Biology. "Most mosquitoes do not live long enough to transmit the disease. To stop malaria, we only need to kill the old mosquitoes."

Since most mosquitoes die before they become dangerous, late-acting insecticides will not have much impact on breeding, so there is much less pressure for the mosquitoes to evolve resistance, explained Read, who is also associated with the Penn State Center for Infectious Disease Dynamics. "This means that late-life insecticides will be useful for much, much longer -- maybe forever -- than conventional insecticides," he added. "Insects usually have to pay a price for resistance, and if only a few older mosquitoes gain the benefits, evolutionary economics can stop resistance from ever spreading."

"We are working on a fungal pesticide that kills mosquitoes late in life," said Thomas. "We could spray it onto walls or onto treated materials such as bed nets, from where the mosquito would get infected by the fungal spores." The fungi take 10 to 12 days to kill the insects. This achieves the benefit of killing the old, dangerous mosquitoes, while dramatically reducing the selection for the evolution of resistance, Thomas explained.

To study the impact of late-acting insecticides on mosquito populations, the researchers constructed a mathematical model of malaria transmission using factors such as the egg laying cycle of the mosquito and the development of parasites within the insect.

Once malaria parasites infect a mosquito, they need at least 10 to 14 days -- or two to six cycles of egg production -- to mature and migrate to the insect's salivary glands. From there they can pass into humans when a mosquito bites.

Analyses of the model using data on mosquito lifespan and malaria development from hotspots in Africa and Papua New Guinea reveal that insecticides killing only mosquitoes that have completed at least four cycles of egg production reduce the number of infectious bites by about 95 percent.

Critically, the researchers also found that resistance to late-acting insecticides spreads much more slowly among mosquitoes, compared to conventional insecticides, and that in many cases, it never spreads at all.

Read says the development of biological or chemical insecticides that are more effective against older, malaria-infected mosquitoes could save the millions dollars that will have to be spent to endlessly find new insecticides to replace ones that have become ineffective.

"Insecticides that kill indiscriminately impose maximal selection for mosquitoes that render those insecticides useless. Late-life acting insecticides would avoid that fate," Read added. "Done right, a one-off investment could create a single insecticide that would solve the problem of mosquito resistance forever."

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Op dinsdag 14 april 2009 02:10 schreef SpecialK het volgende:
tot vandaag nog nooit zelfs maar iets gehoord over Histones. Dank je!

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An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence.

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New Nucleotide In DNA Could Revolutionize Epigenetics

ScienceDaily (Apr. 17, 2009) — Anyone who studied a little genetics in high school has heard of adenine, thymine, guanine and cytosine – the A, T, G and C that make up the DNA code. But those are not the whole story. The rise of epigenetics in the past decade has drawn attention to a fifth nucleotide, 5-methylcytosine (5-mC), that sometimes replaces cytosine in the famous DNA double helix to regulate which genes are expressed. And now there's a sixth: 5-hydroxymethylcytosine.

In experiments to be published online April 16 by Science, researchers reveal an additional character in the mammalian DNA code, opening an entirely new front in epigenetic research.

The work, conducted in Nathaniel Heintz's Laboratory of Molecular Biology at The Rockefeller University, suggests that a new layer of complexity exists between our basic genetic blueprints and the creatures that grow out of them. "This is another mechanism for regulation of gene expression and nuclear structure that no one has had any insight into," says Heintz, who is also a Howard Hughes Medical Institute investigator. "The results are discrete and crystalline and clear; there is no uncertainty. I think this finding will electrify the field of epigenetics."

Genes alone cannot explain the vast differences in complexity among worms, mice, monkeys and humans, all of which have roughly the same amount of genetic material. Scientists have found that these differences arise in part from the dynamic regulation of gene expression rather than the genes themselves. Epigenetics, a relatively young and very hot field in biology, is the study of nongenetic factors that manage this regulation.

One key epigenetic player is DNA methylation, which targets sites where cytosine precedes guanine in the DNA code. An enzyme called DNA methyltransferase affixes a methyl group to cytosine, creating a different but stable nucleotide called 5-methylcytosine. This modification in the promoter region of a gene results in gene silencing.

Some regional DNA methylation occurs in the earliest stages of life, influencing differentiation of embryonic stem cells into the different cell types that constitute the diverse organs, tissues and systems of the body. Recent research has shown, however, that environmental factors and experiences, such as the type of care a rat pup receives from its mother, can also result in methylation patterns and corresponding behaviors that are heritable for several generations. Thousands of scientific papers have focused on the role of 5-methylcytosine in development.

The discovery of a new nucleotide may make biologists rethink their approaches to investigating DNA methylation. Ironically, the latest addition to the DNA vocabulary was found by chance during investigations of the level of 5-methylcytosine in the very large nuclei of Purkinje cells, says Skirmantas Kriaucionis, a postdoctoral associate in the Heintz lab, who did the research. "We didn't go looking for this modification," he says. "We just found it."

Kriaucionis was working to compare the levels of 5-methylcytosine in two very different but connected neurons in the mouse brain — Purkinje cells, the largest brain cells, and granule cells, the most numerous and among the smallest. Together, these two types of cells coordinate motor function in the cerebellum. After developing a new method to separate the nuclei of individual cell types from one another, Kriaucionis was analyzing the epigenetic makeup of the cells when he came across substantial amounts of an unexpected and anomalous nucleotide, which he labeled 'x.'

It accounted for roughly 40 percent of the methylated cytosine in Purkinje cells and 10 percent in granule neurons. He then performed a series of tests on 'x,' including mass spectrometry, which determines the elemental components of molecules by breaking them down into their constituent parts, charging the particles and measuring their mass-to-charge ratio. He repeated the experiments more than 10 times and came up with the same result: x was 5-hydroxymethylcytosine, a stable nucleotide previously observed only in the simplest of life forms, bacterial viruses. A number of other tests showed that 'x' could not be a byproduct of age, DNA damage during the cell-type isolation procedure or RNA contamination. "It's stable and it's abundant in the mouse and human brain," Kriaucionis says. "It's really exciting."

What this nucleotide does is not yet clear. Initial tests suggested that it may play a role in demethylating DNA, but Kriaucionis and Heintz believe it may have a positive role in regulating gene expression as well. The reason that this nucleotide had not been seen before, the researchers say, is because of the methodologies used in most epigenetic experiments. Typically, scientists use a procedure called bisulfite sequencing to identify the sites of DNA methylation. But this test cannot distinguish between 5-hydroxymethylcytosine and 5-methylcytosine, a shortcoming that has kept the newly discovered nucleotide hidden for years, the researchers say. Its discovery may force investigators to revisit earlier work. The Human Epigenome Project, for example, is in the process of mapping all of the sites of methylation using bisulfite sequencing. "If it turns out in the future that (5-hydroxymethylcytosine and 5-methylcytosine) have different stable biological meanings, which we believe very likely, then epigenome mapping experiments will have to be repeated with the help of new tools that would distinguish the two," says Kriaucionis.

Providing further evidence for their case that 5-hydroxymethylcytosine is a serious epigenetic player, a second paper to be published in Science by an independent group at Harvard reveals the discovery of genes that produce enzymes that specifically convert 5-methylcytosine into 5-hydroxymethylcytosine. These enzymes may work in a way analogous to DNA methyltransferase, suggesting a dynamic system for regulating gene expression through 5-hydroxymethylcytosine. Kriaucionis and Heintz did not know of the other group's work, led by Anjana Rao, until earlier this month. "You look at our result, and the beautiful studies of the enzymology by Dr. Rao's group, and realize that you are at the tip of an iceberg of interesting biology and experimentation," says Heintz, a neuroscientist whose research has not focused on epigenetics in the past. "This finding of an enzyme that can convert 5-methylcytosine to 5-hydroxymethylcytosine establishes this new epigenetic mark as a central player in the field."

Kriaucionis is now mapping the sites where 5-hydroxymethylcytosine is present in the genome, and the researchers plan to genetically modify mice to under- or overexpress the newfound nucleotide in specific cell types in order to study its effects. "This is a major discovery in the field, and it is certain to be tied to neural function in a way that we can decipher," Heintz says.

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The Story Of X: Evolution Of A Sex Chromosome

ScienceDaily (Apr. 25, 2009) — Move over, Y chromosome – it's time X got some attention.

In the first evolutionary study of the chromosome associated with being female, University of California, Berkeley, biologist Doris Bachtrog and her colleagues show that the history of the X chromosome is every bit as interesting as the much-studied, male-determining Y chromosome, and offers important clues to the origins and benefits of sexual reproduction.

"Contrary to the traditional view of being a passive player, the X chromosome has a very active role in the evolutionary process of sex chromosome differentiation," said Bachtrog, an assistant professor of integrative biology and a member of UC Berkeley's Center for Theoretical Evolutionary Genomics.

Bachtrog, UC Berkeley post-doctoral fellow Jeffrey D. Jensen and former UC San Diego post-doc Zhi Zhang, now at the University of Munich, detail their findings in this week's edition of the open-access journal PLoS Biology.

"In our manuscript, we demonstrate for the first time the flip side of the sex chromosome evolution puzzle: The X chromosome undergoes periods of intense adaptation in the evolutionary process of creating new sections of the genome that govern sexual differentiation in many species, including our own," she said.

Not all animals and plants employ genes to determine if an embryo becomes male or female. Many reptiles, for example, rely on environmental cues such as temperature to specify male or female.

But in life forms that do set aside a pair of chromosomes to specify sex – from fruit flies to mammals and some plants – the two X chromosomes inherited by females look nearly identical to the other non-sex chromosomes, so-called autosomes, Bachtrog said. The Y chromosome, however, which is inherited by males in concert with one X chromosome, is a withered version of the X, having lost many genes since it stopped recombining with the X chromosome.

In mammals, that probably took place about 150 million years ago, while in the fruit fly Drosophila melanogaster, a laboratory favorite, the sex chromosomes arose independently about 100 million years ago. In both humans and fruit flies, the Y chromosome has dwindled from a few thousand genes to a few dozen.

Hence the intense interest in why and how the Y chromosome lost genes once it stopped interacting with the X. Scientists have found that, as the only chromosome pair that doesn't break and recombine every time a cell divides, the XY pair in males is unable to take advantage of the main way deleterious genetic mutations are eliminated. The XX pair in females does recombine, but for the Y, the only way to get rid of a bad mutation in a gene is to inactivate or delete the entire gene. Over millions of years, inactive genes are lost, and the Y shrinks.

"If you have no recombination, natural selection is less effective at removing detrimental genes," said Bachtrog. "Y is an asexual chromosome, and it pays a price for that: It keeps losing genes."

Bachtrog, whose career has revolved mostly around the study of the degeneration of the Y chromosome, decided to focus on the X chromosome several years ago and went about searching for sex chromosome pairs that have arisen more recently – and thus might be in the process of adapting to their new role. Her paper centers around study of the three sex chromosomes in a rare western fruit fly, Drosophila miranda, a darker-colored cousin of D. melanogaster. (Many creatures have more than one pair of sex chromosomes; the platypus, for example, has five pairs, all inherited together.)

While one of D. miranda's sex chromosomes is descended from the original sex chromosome that appeared in Drosophila nearly 100 million years ago, a second originated perhaps 10 million years ago, and the third about a million years ago. The older two look much alike, Bachtrog said: The Y chromosome in each pair has lost genes to become a shadow of its former self, while the two X chromosomes are indistinguishable from each other.

The third and youngest sex chromosome is different. The Y is not yet shriveled, though it contains many non-functional genes – about half the total – that will eventually be lost. The X, which is dubbed neo-X, is undergoing rapid change, however, with about 10 times the normal amount of adaptation seen in the autosomes, according to the researchers.

By adaptation, Bachtrog means that the gene sequences in the X chromosome are becoming fixed as random mutations have finally settled on a few beneficial changes that accommodate the increasingly irrelevant Y chromosome. Between 10 and 15 percent of neo-X genes show adaptation, compared to only 1-3 percent of autosome genes.

"In hindsight, that is not surprising," Bachtrog said. "Neo-X is facing a much more challenging situation than the autosomes because its pair, the Y chromosome, is degenerating. Its genes are no longer producing proteins, so neo-X has to compensate by up-regulating its genes. We find a lot of genes on the X chromosome are involved in dosage compensation."

In humans, for example, all genes on the X chromosome are twice as active to account for the lack of genes on the Y. Women accommodate this by inactivating one entire X chromosome so as not to produce too much protein, Bachtrog said.

Another change in neo-X that Bachtrog suspects is taking place is the elimination of genes that are harmful to females. Biologists have realized recently that some genes have opposite effects in males and females, and evolution is a tug of war between males jettisoning genes that they find detrimental only to have females put them back, and vice versa.

"A good place to put sexually antagonistic genes that are beneficial to one sex but detrimental to the other is on the sex chromosomes," she said. The Y always ends up in the male, she said, so genes on the Y chromosome won't affect females.

"Conversely, the X chromosome becomes feminized with genes that are good for the female but detrimental to the male," said Bachtrog, adding that the X also becomes demasculinized, losing genes that are of use only in the male.

In search of more insights into the evolution of the X chromosome, Bachtrog said she is looking for fruit fly species with older and younger sex chromosomes "to study sex chromosome evolution in action." She said evidence suggests that adaptation to being a sex chromosome is most intense between 1 and 10 million years after it starts. Bachtrog also is completing assembly of the genome sequence for D. miranda, which is not among the 12 species of Drosophila currently targeted by the genome sequencing community. She hopes that the fly will become a model system like D. melanogaster.

"Now, finally, we are within reach of studying model systems like D. miranda that we couldn't think of several years ago," she said, predicting that "whole genome comparisons will revolutionize evolutionary biology, ecology and many other fields."

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Evolution Of Human Sex Roles More Complex Than Described By Universal Theory

ScienceDaily (Apr. 27, 2009) — A new study challenges long-standing expectations that men are promiscuous and women tend to be more particular when it comes to choosing a mate. The research suggests that human mating strategies are not likely to conform to a single universal pattern and provides important insights that may impact future investigations of human mating behaviors.

In 1948, Angus J. Bateman's performed some now famous studies in fruit flies that showed that males exhibit greater variance in mating success (the number of sexual partners) and in reproductive success (the number of offspring) when compared to females. In addition, Bateman demonstrated that there was a stronger relationship between reproductive success and mating success in males than females.

Bateman concluded that, because a single egg is more costly to produce than a single sperm, the number of offspring produced by a female fruit fly was mainly limited by her ability to produce eggs, while a male's reproductive success was limited by the number of females he inseminated. These studies supported the conventional assumption that male animals are competitive and promiscuous while female animals are non-competitive and choosy.

"The conventional view of promiscuous, undiscriminating males and coy, choosy females has also been applied to our own species," says lead study author Dr. Gillian R. Brown from the School of Psychology at the University of St. Andrews. "We sought to make a comprehensive review of sexual selection theory and examine data on mating behavior and reproductive success in current human populations in order to further our understanding of human sex roles."

Dr. Brown and colleagues examined the general universal applicability of Bateman's principles. To test one of Bateman's assumptions, they collated data on the variance in male and female reproductive success in 18 human populations. While male reproductive success varied more than female reproductive success overall, huge variability was found between populations; for instance, in monogamous societies, variances in male and female reproductive success were very similar.

The researchers also examined factors that might explain variations across human populations that are not in keeping with the prediction of universal sex roles. "Recent advances in evolutionary theory suggest that factors such as sex-biased mortality, sex-ratio, population density and variation in mate quality, are likely to impact mating behavior in humans," concludes Dr. Brown. "The insights gained from this new perspective will have important implications for how we conceive of male and female sexual behavior."

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Neandertals Sophisticated And Fearless Hunters, New Analysis Shows

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.

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Hutchinson, J.R. and Allen, V. (2009) The evolutionary continuum of limb function from early theropods to birds. Naturwissenschaften, 96, 423-448

The bipedal stance and gait of theropod dinosaurs evolved gradually along the lineage leading to birds and at some point(s), flight evolved. How and when did these changes occur? We review the evidence from neontology and palaeontology, including pectoral and pelvic limb functional morphology, fossil footprints/trackways and biomechanical models and simulations. We emphasise that many false dichotomies or categories have been applied to theropod form and function, and sometimes, these impede research progress. For example, dichotomisation of locomotor function into ‘non-avian’ and ‘avian’ modes is only a conceptual crutch; the evidence supports a continuous transition. Simplification of pelvic limb function into cursorial/non-cursorial morphologies or flexed/columnar poses has outlived its utility. For the pectoral limbs, even the classic predatory strike vs. flight wing-stroke distinction and separation of theropods into non-flying and flying—or terrestrial and arboreal—categories may be missing important subtleties. Distinguishing locomotor function between taxa, even with quantitative approaches, will always be fraught with ambiguity, making it difficult to find real differences if that ambiguity is properly acknowledged. There must be an ‘interpretive asymptote’ for reconstructing dinosaur limb function that available methods and evidence cannot overcome. We may be close to that limit, but how far can it be stretched with improved methods and evidence, if at all? The way forward is a combination of techniques that emphasises integration of neontological and palaeontological evidence and quantitative assessment of limb function cautiously applied with validated techniques and sensitivity analysis of unknown variables.

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High Population Density Triggers Cultural Explosions

ScienceDaily (June 5, 2009) — Increasing population density, rather than boosts in human brain power, appears to have catalysed the emergence of modern human behaviour, according to a new study by UCL (University College London) scientists published in the journal Science.

High population density leads to greater exchange of ideas and skills and prevents the loss of new innovations. It is this skill maintenance, combined with a greater probability of useful innovations, that led to modern human behaviour appearing at different times in different parts of the world.

In the study, the UCL team found that complex skills learnt across generations can only be maintained when there is a critical level of interaction between people. Using computer simulations of social learning, they showed that high and low-skilled groups could coexist over long periods of time and that the degree of skill they maintained depended on local population density or the degree of migration between them. Using genetic estimates of population size in the past, the team went on to show that density was similar in sub-Saharan Africa, Europe and the Middle-East when modern behaviour first appeared in each of these regions. The paper also points to evidence that population density would have dropped for climatic reasons at the time when modern human behaviour temporarily disappeared in sub-Saharan Africa.

Adam Powell, AHRC Centre for the Evolution of Cultural Diversity, says: "Our paper proposes a new model for why modern human behaviour started at different times in different regions of the world, why it disappeared in some places before coming back, and why in all cases it occurred more than 100,000 years after modern humans first appeared.

"By modern human behaviour, we mean a radical jump in technological and cultural complexity, which makes our species unique. This includes symbolic behavior, such as abstract and realistic art, and body decoration using threaded shell beads, ochre or tattoo kits; musical instruments; bone, antler and ivory artefacts; stone blades; and more sophisticated hunting and trapping technology, like bows, boomerangs and nets.

Professor Stephen Shennan, UCL Institute of Archaeology, says: "Modern humans have been around for at least 160,000 to 200,000 years but there is no archaeological evidence of any technology beyond basic stone tools until around 90,000 years ago. In Europe and western Asia this advanced technology and behaviour explodes around 45,000 years ago when humans arrive there, but doesn't appear in eastern and southern Asia and Australia until much later, despite a human presence. In sub-Saharan Africa the situation is more complex. Many of the features of modern human behaviour – including the first abstract art – are found some 90,000 years ago but then seem to disappear around 65,000 years ago, before re-emerging some 40,000 years ago.

"Scientists have offered many suggestions as to why these cultural explosions occurred where and when they did, including new mutations leading to better brains, advances in language, and expansions into new environments that required new technologies to survive. The problem is that none of these explanations can fully account for the appearance of modern human behaviour at different times in different places, or its temporary disappearance in sub-Saharan Africa."

Dr Mark Thomas, UCL Genetics, Evolution and Environment, says: "When we think of how we came to be the sophisticated creatures we are, we often imagine some sudden critical change, a bit like when the black monolith appears in the film 2001: A Space Odyssey. In reality, there is no evidence of a big change in our biological makeup when we started behaving in an intelligent way. Our model can explain this even if our mental capacities are the same today as they were when we first originated as a species some 200,000 years ago.

"Ironically, our finding that successful innovation depends less on how smart you are than how connected you are seems as relevant today as it was 90,000 years ago."

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Geography And History Shape Genetic Differences In Humans

ScienceDaily (June 7, 2009) — New research indicates that natural selection may shape the human genome much more slowly than previously thought. Other factors -- the movements of humans within and among continents, the expansions and contractions of populations, and the vagaries of genetic chance – have heavily influenced the distribution of genetic variations in populations around the world.

The study, conducted by a team from the Howard Hughes Medical Institute, the University of Chicago, the University of California and Stanford University, is published June 5 in the open-access journal PLoS Genetics.

In recent years, geneticists have identified a handful of genes that have helped human populations adapt to new environments within just a few thousand years—a strikingly short timescale in evolutionary terms. However, the team found that for most genes, it can take at least 50,000-100,000 years for natural selection to spread favorable traits through a human population. According to their analysis, gene variants tend to be distributed throughout the world in patterns that reflect ancient population movements and other aspects of population history.

"We don't think that selection has been strong enough to completely fine-tune the adaptation of individual human populations to their local environments," says co-author Jonathan Pritchard. "In addition to selection, demographic history -- how populations have moved around -- has exerted a strong effect on the distribution of variants."

To determine whether the frequency of a particular variant resulted from natural selection, Pritchard and his colleagues compared the distribution of variants in parts of the genome that affect the structure and regulation of proteins to the distribution of variants in parts of the genome that do not affect proteins. Since these neutral parts of the genome are less likely to be affected by natural selection, they reasoned that studying variants in these regions should reflect the demographic history of populations.

The researchers found that many previously identified genetic signals of selection may have been created by historical and demographic factors rather than by selection. When the team compared closely related populations they found few large genetic differences. If the individual populations' environments were exerting strong selective pressure, such differences should have been apparent.

Selection may still be occurring in many regions of the genome, says Pritchard. But if so, it is exerting a moderate effect on many genes that together influence a biological characteristic. "We don't know enough yet about the genetics of most human traits to be able to pick out all of the relevant variation," says Pritchard. "As functional studies go forward, people will start figuring out the phenotypes that are associated with selective signals," says lead author Graham Coop. "That will be very important, because then we can figure out what selection pressures underlie these episodes of natural selection."

But even with further research, much will remain unknown about the processes that have resulted in human traits. In particular, Pritchard and Coop urge great caution in trying to link selection with complex characteristics like intelligence. "We're in the infancy of trying to understand what signals of selection are telling us," says Coop, "so it's a very long jump to attribute cultural features and group characteristics to selection."

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Op maandag 8 juni 2009 11:10 schreef SpecialK het volgende:
De ene keer gaat menselijke evolutie weer sneller dan gedacht. De andere keer langzamer. Make up your mind already

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Discovery Raises New Doubts About Dinosaur-bird Links

ScienceDaily (June 9, 2009) — Researchers at Oregon State University have made a fundamental new discovery about how birds breathe and have a lung capacity that allows for flight – and the finding means it's unlikely that birds descended from any known theropod dinosaurs.

The conclusions add to other evolving evidence that may finally force many paleontologists to reconsider their long-held belief that modern birds are the direct descendants of ancient, meat-eating dinosaurs, OSU researchers say.

"It's really kind of amazing that after centuries of studying birds and flight we still didn't understand a basic aspect of bird biology," said John Ruben, an OSU professor of zoology. "This discovery probably means that birds evolved on a parallel path alongside dinosaurs, starting that process before most dinosaur species even existed."

These studies were just published in The Journal of Morphology, and were funded by the National Science Foundation.

It's been known for decades that the femur, or thigh bone in birds is largely fixed and makes birds into "knee runners," unlike virtually all other land animals, the OSU experts say. What was just discovered, however, is that it's this fixed position of bird bones and musculature that keeps their air-sac lung from collapsing when the bird inhales.

Warm-blooded birds need about 20 times more oxygen than cold-blooded reptiles, and have evolved a unique lung structure that allows for a high rate of gas exchange and high activity level. Their unusual thigh complex is what helps support the lung and prevent its collapse.

"This is fundamental to bird physiology," said Devon Quick, an OSU instructor of zoology who completed this work as part of her doctoral studies. "It's really strange that no one realized this before. The position of the thigh bone and muscles in birds is critical to their lung function, which in turn is what gives them enough lung capacity for flight."

However, every other animal that has walked on land, the scientists said, has a moveable thigh bone that is involved in their motion – including humans, elephants, dogs, lizards and – in the ancient past – dinosaurs.

The implication, the researchers said, is that birds almost certainly did not descend from theropod dinosaurs, such as tyrannosaurus or allosaurus. The findings add to a growing body of evidence in the past two decades that challenge some of the most widely-held beliefs about animal evolution.

"For one thing, birds are found earlier in the fossil record than the dinosaurs they are supposed to have descended from," Ruben said. "That's a pretty serious problem, and there are other inconsistencies with the bird-from-dinosaur theories.

"But one of the primary reasons many scientists kept pointing to birds as having descended from dinosaurs was similarities in their lungs," Ruben said. "However, theropod dinosaurs had a moving femur and therefore could not have had a lung that worked like that in birds. Their abdominal air sac, if they had one, would have collapsed. That undercuts a critical piece of supporting evidence for the dinosaur-bird link.

"A velociraptor did not just sprout feathers at some point and fly off into the sunset," Ruben said.

The newest findings, the researchers said, are more consistent with birds having evolved separately from dinosaurs and developing their own unique characteristics, including feathers, wings and a unique lung and locomotion system.

There are some similarities between birds and dinosaurs, and it is possible, they said, that birds and dinosaurs may have shared a common ancestor, such as the small, reptilian "thecodonts," which may then have evolved on separate evolutionary paths into birds, crocodiles and dinosaurs. The lung structure and physiology of crocodiles, in fact, is much more similar to dinosaurs than it is to birds.

"We aren't suggesting that dinosaurs and birds may not have had a common ancestor somewhere in the distant past," Quick said. "That's quite possible and is routinely found in evolution. It just seems pretty clear now that birds were evolving all along on their own and did not descend directly from the theropod dinosaurs, which lived many millions of years later."

OSU research on avian biology and physiology was among the first in the nation to begin calling into question the dinosaur-bird link since the 1990s. Other findings have been made since then, at OSU and other institutions, which also raise doubts. But old theories die hard, Ruben said, especially when it comes to some of the most distinctive and romanticized animal species in world history.

"Frankly, there's a lot of museum politics involved in this, a lot of careers committed to a particular point of view even if new scientific evidence raises questions," Ruben said. In some museum displays, he said, the birds-descended-from-dinosaurs evolutionary theory has been portrayed as a largely accepted fact, with an asterisk pointing out in small type that "some scientists disagree."

"Our work at OSU used to be pretty much the only asterisk they were talking about," Ruben said. "But now there are more asterisks all the time. That's part of the process of science."

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In recent years Ruben and colleagues have made a career of publishing papers in which they assert that 'birds cannot be dinosaurs because of [whatever, blah blah blah]'. Quick & Ruben (2009) assert that non-avian theropods were fundamentally different in abdominal morphology from extant birds, and they hypothesise (note: hypothesise) that the sub-horizontal avian femur and its associated musculature might be required to prevent collapse of the lateral abdominal wall: non-avian theropods evidently moved their femora a lot during normal locomotion, and hence, say Quick & Ruben, could not have had abdominal air sacs. All of this is extremely questionable or just flat-out wrong (sternal movement etc. almost certainly was present in non-avian theropods, the 'mobile thigh inhibits abdominal air sacs' just doesn't make any sense, and the authors ignore evidence for abdominal pneumaticity in non-avian saurischians): if the authors have set out to demonstrate anything, it is that evolution cannot happen.

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Eberhard, W.G. (2009) Postcopulatory sexual selection: Darwin's omission and its consequences. PNAS, 106, 10025-10032.

In one of his few major oversights, Darwin failed to appreciate that male–male competition and sexual selection can continue even after copulation has begun. The postcopulatory equivalents of both direct male–male battles (sperm competition) and female choice (cryptic female choice) occur within the female's body. Recognition of this hidden, but intense, sexual competition provides new insights into a variety of fields. These include the hyperdiverse and paradoxically elaborate morphology of both sperm and male genitalia, the equally puzzling and elaborate morphology of nongenitalic male structures that are specialized to grasp and stimulate females, powerful manipulative effects of substances in male semen on female reproductive physiology, paradoxical male courtship behavior that occurs after copulation has already begun, variability in parental investments, and the puzzlingly complex and diverse interactions between sperm and female products that surround animal eggs and between male gametophytes and female tissues in flowering plants. Many bizarre traits are involved, including male genitalia that are designed to explode or fall apart during copulation leaving behind parts within the female, male genitalia that “sing” during copulation, potent seminal products that invade the female's body cavity and her nervous system to influence her behavior, and a virtual Kama Sutra of courtship behavior performed after rather than before genital coupling, including male–female dialogues during copulation.

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Key To Evolutionary Fitness: Cut The Calories

ScienceDaily (July 2, 2009) — Charles Darwin and his contemporaries postulated that food consumption in birds and mammals was limited by resource levels, that is, animals would eat as much as they could while food was plentiful and produce as many offspring as this would allow them to.

However, recent research has shown that, even when food is abundant, energy intake reaches a limit, even in animals with high nutrient demands, such as lactating females. Scientists at the Research Institute of Wildlife Ecology in Vienna suggest that this is due to active control of maternal investment in offspring in order to maintain long-term reproductive fitness.

The research, to be presented by Dr Teresa Valencak at the Society for Experimental Biology Annual Meeting in Glasgow has shown that, when their energy reserves are low or when their offspring are kept in cooler temperatures, Brown hares are able to increase their energy turnover and rate of milk production above that normally observed. This indicates that, ordinarily, the hares are operating at below their maximum capacity and shows that this is not due to any kind of physiological constraint, such as length of digestive tract or maximum capacity of mammary glands. Also, as the hares were provided with plentiful food, there could be no limitation of energy turnover due to food availability.

The way that females regulated their energy expenditure according to pup demand and their own fat reserves but did not exceed certain levels fitted with the group's theory that using energy at close to the maximum rate has costs for animals which may compromise their ability to successfully reproduce in the future. If a hare puts most of its energy into a litter of pups then it will have little left over for growth and body repairs for example, which may shorten its life or make it less able to produce or care for young in the future. By actively limiting the rate of energy turnover, a mother can prevent this and maintain a higher level of reproductive success over her lifetime

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Op maandag 6 juli 2009 15:02 schreef SpecialK het volgende:
Dit is dus met Hazen maar dat geldt zeker niet voor alle diersoorten. Ik dacht dat honden bijvoorbeeld zichzelf gewoon echt dood kunnen vreten.

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Darwin’s Mystery Of Appearance Of Flowering Plants Explained

ScienceDaily (July 14, 2009) — The appearance of many species of flowering plants on Earth, and especially their relatively rapid dissemination during the Cretaceous (approximately 100 million years ago) can be attributed to their capacity to transform the world to their own needs.

In an article in Ecology Letters, Wageningen ecologists Frank Berendse and Marten Scheffer postulate that flowering plants changed the conditions during the Cretaceous period to suit themselves. The researchers have consequently provided an entirely new explanation for what Charles Darwin considered to be one of the greatest mysteries with which he was confronted.

During the Cretaceous, the Earth's surface underwent one of its greatest changes in vegetation composition, a change which also took place with unprecedented speed. Frank Berendse (Professor of Nature Conservation and Plant Ecology), and Marten Scheffer, (Professor of Aquatic Ecology), both at Wageningen University, wanted to understand how this happened. They looked for the explanation in a totally unconventional direction.

Before the early Cretaceous, the vegetation consisted primarily of gymnosperms and ferns. These plants were largely replaced by an entirely new group of plants: the angiosperms (flowering plants). During the early Cretaceous – approximately 125 million years ago – the first flowering plants evolved. Soon thereafter, the gymnosperms in the tropics were replaced almost entirely by the angiosperms. And by the end of the Cretaceous (65 million years ago), the empire of the flowering plants had become definitively established in much of the rest of the world. The gymnosperms continued to exist only in the far north – which is the case even today.

The rapid increase in the fantastic diversity of flowering plants – linked to their rapid conquest of the Earth – was one of the greatest puzzles faced by Charles Darwin. In a letter to Joseph Hooker dated 22 July 1879, he referred to an "abominable mystery". The great diversity of fossil flowering plants from the late Cretaceous, while there were virtually no fossils known from the early Cretaceous, appeared to be completely in conflict with his vision that the emergence of new species could only take place very gradually.

The big question was how this massive change could have taken place with such unprecedented speed. Was it because – just before the Cretaceous – that the big Sauropods were forced out by the much smaller Ornithischian dinosaurs, which then systematically ate all the seedlings of the gymnosperms? Or was it because the flowering plants could evolve simultaneously with many insect species that could pollinate their flowers?

According to Berendse and Scheffer, we must think in a totally different direction. They postulate that the flowering plants were able to change the world to suit their own needs. They grew more rapidly and therefore required more nutrients. In a world that was poor in nutrients and was entirely dominated by the gymnosperms, that kept the soil poor - with their poorly degradable litter - flowering plants had great difficulties to establish. But at some locations where the gymnosperms had temporarily disappeared, for example due to floods, fires or storms, the angiosperms could increase so that they were capable of improving their own conditions with their easily degradable litter.

According to the theory of Berendse and Scheffer, this led to positive feedback; as a result, the flowering plants could increase even more rapidly and were capable of replacing the angiosperms in much of the world. Ultimately, the improved edibility of the leaves and fruits of the flowering plants led to a tremendous increase in the number of plant eaters on the Earth, which opened the way to the rapid evolution of mammals, and finally to the appearance of humans.

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How evolution acts to bridge the chasm between two discrete physiological states is a question that's long puzzled scientists. Most evolutionary changes, after all, happen in tiny increments: an elephant grows a little larger, a giraffe's neck a little longer. If those tiny changes prove advantageous, there's a better chance of passing them to the next generation, which might then add its own mutations. And so on, and so on, until you have a huge pachyderm or the characteristic stretched neck of a giraffe.

But when it comes to traits like the number of wings on an insect, or limbs on a primate, there is no middle ground. How are these sorts of large evolutionary leaps made?

According to a team led by scientists at the California Institute of Technology (Caltech), in close collaboration with Patrick Piggot and colleagues from the Temple University School of Medicine, such changes may at least sometimes be the result of random fluctuations, or noise (nongenetic variations), working alongside a phenomenon known as partial penetrance. Their findings were recently published online in the journal Nature.

"Our work shows how partial penetrance can play a role in evolution by allowing a species to gradually evolve from producing 100 percent of one form to developing 100 percent of another, qualitatively different, form," says Michael Elowitz, the Caltech assistant professor of biology and applied physics, Bren Scholar, and Howard Hughes Medical Institute investigator who led the team. "The intermediate states that occur along the way are not intermediate forms, but rather changes in the fraction of individuals that develop one way or the other."

Partial penetrance is the name given by evolutionary biologists to the degree to which a single genetic mutation may have different effects on different organisms in a population.

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Eldar, A. et al. (2009) Partial penetrance facilitates developmental evolution in bacteria. Nature, advance online.

Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fates of individual organisms differently1, 2, 3, 4. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve5, 6, 7, 8. Here we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an intercompartmental signalling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable 'twin' spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we can systematically tune the penetrance of each mutant fate. Furthermore, signalling and replication perturbations synergize to significantly increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum shows a strong resemblance to twin sporulation in these B. subtilis mutants9, 10. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.

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Parasites May Have Had Role In Evolution Of Sex

ScienceDaily (July 31, 2009) — What's so great about sex? From an evolutionary perspective, the answer is not as obvious as one might think. An article published in the July issue of the American Naturalist suggests that sex may have evolved in part as a defense against parasites.

Despite its central role in biology, sex is a bit of an evolutionary mystery. Reproducing without sex—like microbes, some plants and even a few reptiles—would seem like a better way to go. Every individual in an asexual species has the ability to reproduce on its own. But in sexual species, two individuals have to combine in order to reproduce one offspring. That gives each generation of asexuals twice the reproductive capacity of sexuals. Why then is sex the dominant strategy when the do-it-yourself approach is so much more efficient?

One hypothesis is that parasites keep asexual organisms from getting too plentiful. When an asexual creature reproduces, it makes clones—exact genetic copies of itself. Since each clone has the same genes, each has the same genetic vulnerabilities to parasites. If a parasite emerges that can exploit those vulnerabilities, it can wipe out the whole population. On the other hand, sexual offspring are genetically unique, often with different parasite vulnerabilities. So a parasite that can destroy some can't necessarily destroy all. That, in theory, should help sexual populations maintain stability, while asexual populations face extinction at the hands of parasites.

The scenario works on mathematical models, but there have been few attempts to see if it holds in nature.

Enter Potamopyrgus antipodarum, a snail common in fresh water lakes in New Zealand. What makes these snails interesting is that there are sexual and asexual versions. They provide scientists with an opportunity to compare the two versions side-by-side in nature.

Jukka Jokela of the Swiss Federal Institute of Aquatic Science and Technology, Mark Dybdahl of the University of Washington and Curtis Lively of Indian University, Bloomington began observing several populations of these snails for ten years starting in 1994. They monitored the number of sexuals, the number asexuals, and the rates of parasite infection for both.

The team found that clones that were plentiful at the beginning of the study became more susceptible to parasites over time. As parasite infections increased, the once plentiful clones dwindled dramatically in number. Some clonal types disappeared entirely. Meanwhile, sexual snail populations remained much more stable over time. This, the authors say, is exactly the pattern predicted by the parasite hypothesis.

"The rise and fall of these female-only lineages was surprisingly fast and consistent with the prediction of the parasite hypothesis for sex," Jokela said. "These results suggest that sexual reproduction provides an evolutionary advantage in parasite rich environments."

So we may well have to thank parasites—in spite of their nasty reputation—for the joy of sex.

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Researchers force bacteria to evolve for life in a fuel cell

While a recent report from the National Academies of the Sciences concluded that conservation is the short-term key to many energy issues, work continues on alternative energy production techniques like wind, solar, biomass, and fuel cells. For mobile applications, fuel cells have quickly become the technological leader because they offer high energy density (relative to other green technologies), low weight, and generally high mechanical durability. In this month's Biosensors and Bioelectronics, a research team from University of Massachusetts Amherst describes their work on microbial fuel cells enhanced by directed evolution.

A wide array of fuel cell technologies exist, but most fall into two catagories: solid oxide fuel cells (SOFCs) or polymer electrolyte membrane fuel cells (PEMFCs). SOFCs conduct O2- across ceramic membranes and produce high current densities with little degradation over time. Unfortunately, the ionic conduction mechanism requires high operating temperatures—usually several hundred degrees centigrade. PEMFCs conduct either protons or hydroxyls, but suffer from low current densities and significant degredation over time. While these systems show substantial promise, there is no clear leader for most mobile applications and there is room in several niche markets for other types of fuel cells.

To produce ATP, bacteria generate charge gradients when metabolizing nutrients, and these could theoretically be harvested. In the early 1990's, proof-of-concept microbial fuel cells (MFCs) were developed using bacterial electrolytes. These systems fed simple sugars to bacteria in anaerobic conditions and with an applied field. Electrons produced during digestion move to the anode while protons diffuse to the cathode, where they can recombine with any electrons that have conducted across a load circuit.

In order to produce electricity, it is imperative that MFC's bacteria conduct electrons to the cathode. The researchers at UMass Amherst realized that there has never been any natural selective pressure that would enhance electronic conduction in bacteria, so they used directed evolution to produce highly conducting bacteria.

G. sulfurreducens bacteria were cultured on a graphite electrode under a 400 mV applied bias. The goal was to force the bacteria to adapt to conditions inside the MFC with the hope that they would evolve greater functionality in the process. Several colonies were isolated after five months in the MFC environment and re-cultured under normal conditions. When placed in an MFC cell, the specially cultured bacteria grew much more rapidly—current saturated after 50 hours as opposed to 400 hours—and they provided twice the current density of normally cultured bacteria.

Analysis of the enhanced bacteria showed that there were two primary adaptions. First, pili, fine, thread-like structures that connect neighboring cells, dramatically increased in the new bacteria. These structures are thought to be responsible for electronic conduction in bacterial films. Also, unlike their precursors, the enhanced bacteria all had flagella that allowed both motility and enhanced attachment to anode surfaces. It is unclear which adaptation is primarily responsible for the enhanced performance.

MFCs must show significant improvement (orders of magnitude) in order to match SOFCs and PEMFCs; simply doubling performance will not make them viable for most applications. However, by harnessing evolution, it may be possible to rapidly accelerate development of reasonably performing systems. As a member of the ceramic research community with vested interests in SOFC development, I am not quite ready to salute my new bacterial overlords, but this is a fascinating area of research that has real potential in many niche applications.

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Khila, A. et al. (2009) Evolution of a Novel Appendage Ground Plan in Water Striders Is Driven by Changes in the Hox Gene Ultrabithorax.

Water striders, a group of semi-aquatic bugs adapted to life on the water surface, have evolved mid-legs (L2) that are long relative to their hind-legs (L3). This novel appendage ground plan is a derived feature among insects, where L2 function as oars and L3 as rudders. The Hox gene Ultrabithorax (Ubx) is known to increase appendage size in a variety of insects. Using gene expression and RNAi analysis, we discovered that Ubx is expressed in both L2 and L3, but Ubx functions to elongate L2 and to shorten L3 in the water strider Gerris buenoi. Therefore, within hemimetabolous insects, Ubx has evolved a new expression domain but maintained its ancestral elongating function in L2, whereas Ubx has maintained its ancestral expression domain but evolved a new shortening function in L3. These changes in Ubx expression and function may have been a key event in the evolution of the distinct appendage ground plan in water striders.

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Op dinsdag 1 september 2009 10:47 schreef Triggershot het volgende:
Racisten, eet je hart uit.
[..]

http://www.nu.nl/wetensch(...)0-jaar-geleden-.html

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Genes That Make Us Human

Finding genes that have evolved in humans among our genome's 3 billion bases is no easy feat. But now, a team has pinpointed three genes that arose from noncoding DNA and may help make our species unique.

Most genes have deep histories, with ancestors that reach down into the tree of life, sometimes all the way back to bacteria. The gradual increase from the few thousand genes in a bacterium to the tens of thousands of genes in a person came primarily through genome- and gene-duplication events, which created extra sets of genes free to evolve new sequences and new functions. Much of this duplication happened long before humans evolved, though some duplications occurred in the human lineage to create exclusively human twins of existing genes.

But in 2006, geneticists showed for the first time that they could identify truly novel genes. In fruit flies, they came across five young genes that were derived from "noncoding" DNA between existing genes and not from preexisting genes. As a result, other researchers started looking for novel genes in other species.

Meanwhile, while looking for gene duplications in humans, geneticists Aoife McLysaght and David Knowles of Trinity College Dublin kept coming across genes that seemed to have no counterparts in other primates, suggesting that new genes arose in us as well. To determine which of these genes with no counterparts were de novo genes, McLysaght and Knowles first used a computer to compare the human, chimp, and other genomes. They eliminated all but three of the 644 candidates because their sequence in the database was not complete--or they had equivalents in other species.

Next, they searched the chimp genome for signs of each gene's birth. "We strove hard to identify the noncoding DNA that gave rise to the gene," McLysaght says. Only by finding that DNA could they be sure that the gene wasn't already present in the chimp genome but was somehow unrecognizable to gene-finding programs. At three locations where the chimp and human genomes were almost identical, telltale mutations indicated that it was impossible to get a viable protein from the chimp DNA sequence. In contrast, the human version of each sequence had mutations that made it a working gene, the researchers report online tomorrow in Genome Research.

The researchers were able to verify that the genes worked by checking messenger RNA databases and protein surveys done by other scientists. They are now using antibodies to find out where in the cells these proteins are active and are trying to disable the genes in cells to tease out their functions.

The researchers analyzed only a subset of the human genome. Extrapolating to the full genome, they think humans have evolved at least 18 new genes. That's a small number compared to our total of 24,000 but nonetheless an important one. "The distinction between humans and other apes must lie somewhere in the small genetic differences between the species," says McLysaght.

Unlike duplicated genes, these are genes that "they really knew are human-specific," says Laurent Duret, a molecular evolutionary biologist at the University of Lyon in France. When he first heard about this project, he was skeptical, but not anymore. "It's the first convincing evidence of a real innovation in humans."

These three young genes join several hundred other uniquely human genomic features, including gene duplications, that provide tantalizing hints of what makes us human. But, says evolutionary biologist Gregory Wray of Duke University in Durham, North Carolina, researchers still have no clue what most of these genes do.

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Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?

A major challenge in ecology is forecasting the effects of species' extinctions, a pressing problem given current human impacts on the planet. Consequences of species losses such as secondary extinctions are difficult to forecast because species are not isolated, but interact instead in a complex network of ecological relationships. Because of their mutual dependence, the loss of a single species can cascade in multiple coextinctions. Here we show that an algorithm adapted from the one Google uses to rank web-pages can order species according to their importance for coextinctions, providing the sequence of losses that results in the fastest collapse of the network. Moreover, we use the algorithm to bridge the gap between qualitative (who eats whom) and quantitative (at what rate) descriptions of food webs. We show that our simple algorithm finds the best possible solution for the problem of assigning importance from the perspective of secondary extinctions in all analyzed networks. Our approach relies on network structure, but applies regardless of the specific dynamical model of species' interactions, because it identifies the subset of coextinctions common to all possible models, those that will happen with certainty given the complete loss of prey of a given predator. Results show that previous measures of importance based on the concept of “hubs” or number of connections, as well as centrality measures, do not identify the most effective extinction sequence. The proposed algorithm provides a basis for further developments in the analysis of extinction risk in ecosystems.

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Rapid Evolution of Functional Complexity in a Domain Family

Multicellular organisms rely on complex, fine-tuned protein networks to respond to environmental changes. We used in vitro evolution to explore the role of domain mutation and expansion in the evolution of network complexity. Using random mutagenesis to facilitate family expansion, we asked how versatile and robust the binding site must be to produce the rich functional diversity of the natural PDZ domain family. From a combinatorial protein library, we analyzed several hundred structured domain variants and found that one-quarter were functional for carboxyl-terminal ligand recognition and that our variant repertoire was as specific and diverse as the natural family. Our results show that ligand binding is hardwired in the PDZ fold and suggest that this flexibility may facilitate the rapid evolution of complex protein interaction networks.

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Time always marches forward — and so does evolution, according to a new study showing that protein changes that happened over the course of tens of millions of years can prevent molecular turnarounds and render evolution irreversible.

"This backwards pathway is not accessible to selection," says study author Joe Thornton, a molecular evolutionary biologist at the University of Oregon in Eugene. "It's very strongly supported evidence for the view that contingency plays a major role in evolution."

More than a century ago, the French–born Belgian palaeontologist Louis Dollo proposed that evolution cannot retrace its steps to restore a lost trait — an idea that has remained controversial. Dubbed Dollo's law, this proposition had a certain appeal to many evolutionary biologists. Whales and snakes never regained legs, for example; birds did not reacquire teeth. But more recently, studies have shown that silenced genes and dormant developmental programs can be reactivated, leading many researchers to believe that evolution can indeed double back on itself.

Evolution's arrow

Thornton and his colleagues decided to test Dollo's law at the molecular level. They focused on the glucocorticoid receptor (GR), a protein that binds the hormone cortisol to regulate the stress response and other functions in humans and other vertebrates. Thornton's team had previously showed that the first GR protein evolved more than 400 million years ago from an ancestral receptor that was activated by a trio of hormones: cortisol, aldosterone and deoxycorticosterone1. Over the course of 40 million years, the ancestral protein acquired 37 amino-acid alterations, cortisol binding to produce the 'modern' GR protein2.

The researchers reverse-engineered the protein to undo all seven mutations that affected cortisol binding, but the resulting receptor was non-functional and did not bind any hormone. To determine whether other mutations might be having an effect on receptor function, the team looked at the three-dimensional structure of the protein and pinpointed five additional mutations. These extra mutations did not affect the cortisol-binding specificity of the receptor but they did prevent it from doing its job properly. When the researchers reversed these mutations as well, the protein was transformed back into its ancestral functional state and could bind all three hormones.

Although it is technically possible for the molecular changes to backtrack, admits Thornton, such a shift couldn't be driven by natural selection. Undoing the five extra mutations in the absence of the other seven changes had negative or neutral consequences on protein function, and so would not be favoured by evolution, the researchers report in Nature3. "The chances of reversibility ever happening are vanishingly small," Thornton says. "It's virtually impossible."

Traces of time

The study reveals how interdependencies between amino acids can limit the scope of evolution, says Günter Wagner, an evolutionary developmental biologist at Yale University. "Because [the additional mutations] are only enabling but not themselves selective, they can mutate away, effectively burning the bridge you went over," he says.

Michael Rose, an evolutionary biologist at the University of California, Irvine, says that the experimental demonstration of irreversibility was "impressive" but not all that surprising. "That this phenomenon would apply on this timescale is what every evolutionary biologist would expect," he says. But in the short term, selection often goes back to its old ways. For example, earlier this year, Rose and his colleagues showed that fruit flies that had diverged over decades of selection in the lab returned to their ancestral state after just two years of reverse selection4. Thornton's study, by contrast, "is way, way macro in time frame," Rose says, adding, "It illustrates the importance of historicity in evolutionary biology."

But Fyodor Kondrashov, an evolutionary geneticist at the Centre for Genomic Regulation in Barcelona, Spain, disagrees. "There's absolutely nothing impossible about reversing everything that has happened," he says. Rather than focusing on the authors' "spin of reversibility", Kondrashov says, the paper highlights how the likelihood of particular evolutionary trajectories is contingent on a protein's genetics and structure. "We really need these kinds of examples", he adds.

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The city-size rock that impacted Earth sixty-five million years ago, in what is now Mexico's Yucatán Peninsula at a site known as Chicxulub, may not have been the main cause of the great extinction event that wiped out the dinosaurs and as much as 80 percent of the rest of life on the planet.

Instead, a 25-mile-wide meteorite, as much as five times the size of the one that struck Chicxulub, could have slammed into Earth where India is today, vaporizing the planet's crust and leaving the largest multi-ringed crater the world has ever seen.

Texas Tech University scientists think they have pieced together the geological evidence for this impact, and they will present their theory to the annual general meeting of the Geological Society of America (GSA), in Portland, oregon, this coming weekend.

"A mysterious basin off the coast of India could be the largest, multi-ringed impact crater the world has ever seen. And if a new study is right, it may have been responsible for killing the dinosaurs off 65 million years ago," GSA said in a statement about the research, released today.

"Sankar Chatterjee of Texas Tech University and a team of researchers took a close look at the massive Shiva basin, a submerged depression west of India that is intensely mined for its oil and gas resources. Some complex craters are among the most productive hydrocarbon sites on the planet," GSA said.

Chatterjee will present the research at the GSA meeting on Sunday.

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India was ground zero for two catastrophic events, the Shiva impact and Deccan volcanism at the KT boundary that have been linked to the dinosaur extinction. The buried and multiringed Shiva crater (~500 km diameter) on the western shelf of India is the remnant of a giant meteorite impact that left high-resolution stratigraphic signals in the sedimentary and volcanic rocks such as shocked quartz, iridium anomaly, nickel-rich spinels, sanidine spherules, magnetic nanoparticles, high pressure fullerenes, megatsunami deposits, and melt lavas. The Shiva crater is the largest hydrocarbon reserve in India, where the central uplift, the Bombay High, and the associated brecciated bodies and peripheral strata form ideal structural traps for oil and gas. The Shiva bolide (~40 km diameter) would generate lethal amount of kinetic energy of 1.45 x 1025 joules. The impact was so powerful that it led to several geodynamic anomalies: it fragmented, sheared, and deformed the lithosphere mantle across the western Indian margin and contributed to major plate reorganization in the Indian Ocean. It initiated rifting between India and Seychelles in the west and created the Laxmi Ridge; it shattered the Indian plate easterly along the Narmada-Son Rift extending 1500 km across, dividing the Indian shield into a southern peninsular block and a northern foreland block. Because of topographic barrier of the Western Ghat Mountain range, the impact-triggered tsunami was restricted along the Narmada-Son Rift at the KT boundary. The relationships between large meteoritic impact, hotspot, flood basalt volcanism, plate tectonics, geodynamic anomalies, and sudden environmental catastrophe on Earth may open up a new field of unified investigation. Although the Reunion hotspot responsible for Deccan eruption was close to the Shiva crater in time and space, impact probably triggered a component of the Deccan Trap: the iridium-rich alkaline igneous complex rocks that were emplaced asymmetrically as a fluid ejecta at the KT boundary along the NE downrange direction of the bolide trajectory outside the crater ring. Two large impacts such as Shiva and Chicxulub in quick succession on the antipodal position, in concert with Deccan eruptions, would have devastating effects globally leading to climatic and environmental catastrophes that wiped out dinosaurs and many other organisms at the KT boundary.

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Barrick, J.E. et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, advance online.

The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.

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Genome re-sequencing in the context of experimental evolution provides new opportunities for quantifying evolutionary dynamics. We observed discordance between the rates of genomic change and fitness improvement during a 20-year experiment with E. coli in two respects. First, mutations accumulated at a near-constant rate even as fitness gains decelerated over the first 20,000 generations. Second, the rate of genomic evolution accelerated markedly when a mutator lineage became established later. The fluid and complex coupling observed between the rates of genomic evolution and adaptation even in this simple system cautions against categorical interpretations about rates of genomic evolution in nature without specific knowledge of molecular and population-genetic processes. Our results also call attention to new opportunities for population-genetic models to explore the long-term dynamic coupling between genome evolution and adaptation, including the effects of clonal interference, compensatory adaptation, and changing mutation rates.

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Moral in Tooth and Claw
Animals are "in." This might well be called the decade of the animal. Research on animal behavior has never been more vibrant and more revealing of the amazing cognitive, emotional, and moral capacities of a broad range of animals. That is particularly true of research into social behavior—how groups of animals form, how and why individuals live harmoniously together, and the underlying emotional bases for social living. It's becoming clear that animals have both emotional and moral intelligences.

Philosophical and scientific convention, of course, has pulled toward a more conservative account of morality: Morality is a capacity unique to human beings. But the more we study the behavior of animals, the more we find that different groups of animals have their own moral codes. That raises both scientific and philosophic questions.

Researchers like Frans de Waal (The Age of Empathy: Nature's Lessons for a Kinder Society), Elliott Sober, David Sloan Wilson (Unto Others: The Evolution and Psychology of Unselfish Behavior), and Kenneth M. Weiss and Anne V. Buchanan (The Mermaid's Tale: Four Billion Years of Cooperation in the Making of Living Things) have demonstrated that animals have social lives rich beyond our imagining, and that cooperation and caring have shaped the course of evolution every bit as much as competition and ruthlessness have. Individuals form intricate networks and have a large repertoire of behavior patterns that help them get along with one another and maintain close and generally peaceful relationships. Indeed, Robert W. Sussman, an anthropologist at Washington University in St. Louis, and his colleagues Paul A. Garber and Jim Cheverud reported in 2005 in The American Journal of Physical Anthropology that for many nonhuman primates, more than 90 percent of their social interactions are affiliative rather than competitive or divisive. Moreover, social animals live in groups structured by rules of engagement—there are "right" and "wrong" ways of behaving, depending on the situation.

While we all recognize rules of right and wrong behavior in our own human societies, we are not accustomed to looking for them among animals. But they're there, as are the "good" prosocial behaviors and emotions that underlie and help maintain those rules. Such behaviors include fairness, empathy, forgiveness, trust, altruism, social tolerance, integrity, and reciprocity—and they are not merely byproducts of conflict but rather extremely important in their own right.

If we associate such behaviors with morality in human beings, why not in animals? Morality, as we define it in our recent book Wild Justice: The Moral Lives of Animals, is a suite of interrelated, other-regarding behaviors that cultivate and regulate social interactions. Those patterns have evolved in many animals, perhaps even in birds.

One of the clearest places to see how specific social rules apply is in animal play. Play has been extensively studied in social canids (members of the dog family) like wolves, coyotes, and domestic dogs, so it is a good example to use to examine the mechanisms of fair play.

Although play is fun, it's also serious business. When animals play, they are constantly working to understand and follow the rules and to communicate their intentions to play fairly. They fine-tune their behavior on the run, carefully monitoring the behavior of their play partners and paying close attention to infractions of the agreed-upon rules. Four basic aspects of fair play in animals are: Ask first, be honest, follow the rules, and admit you're wrong. When the rules of play are violated, and when fairness breaks down, so does play.

Detailed research on social play in infant domestic dogs and their wild relatives, coyotes and gray wolves, shows how just how important the rules are. Pains taking analyses of videos of individuals at play by one of us, Marc, and his students reveal that these youngsters carefully negotiate social play and use specific signals and rules so that play doesn't escalate into fighting.

When dogs—and other animals—play, they use actions like biting, mounting, and body-slamming one another, which are also used in other contexts, like fighting or mating. Because those actions can be easily misinterpreted, it's important for animals to clearly state what they want and what they expect.

In canids an action called a "bow" is used to ask others to play. When performing a bow, an animal crouches on his or her forelimbs. He or she will sometimes bark, wag the tail wildly, and have an eager look. So that the invitation to play isn't confusing, bows are highly stereotyped and show little variation. Marc and his students' detailed study of the form and duration of hundreds of bows showed surprisingly little variability in form (how much an animal crouched scaled to body size) and almost no difference between bows used at the beginning of sequences and during bouts of play. Bows are also swift, lasting only about 0.3 seconds. Over all, a threatening action—bared teeth and growls—preceded by a bow resulted in submission or avoidance by another animal only 17 percent of the time. Young coyotes are more aggressive than young dogs or wolves, and they try even harder to keep play fair. Their bows are more stereotyped than those of their relatives.

Play bows are honest signals, a sign of trust. Research shows that animals who violate that trust are often ostracized, suggesting that violation of the rules of play is maladaptive and can disrupt the efficient functioning of the group. For example, among dogs, coyotes, and wolves, individuals who don't play fairly find that their invitations to play are ignored or that they're simply avoided by other group members. Marc's long-term field research on coyotes living in the Grand Teton National Park, near Jackson, Wyo., shows that coyotes who don't play fairly often leave their pack because they don't form strong social bonds. Such loners suffer higher mortality than those who remain with others.

Animals engage in two activities that help create an equal and fair playing field: self-handicapping and role-reversing. Self-handicapping (or "play inhibition") occurs when individuals perform behavior patterns that might compromise them outside of play. For example, coyotes will inhibit the intensity of their bites, thus abiding by the rules and helping to maintain the play mood. The fur of young coyotes is very thin, and intense bites are painful and cause high-pitched squeals. In adult wolves, a bite can generate as much as 1,500 pounds of pressure per square inch, so there's a good reason to inhibit its force. Role-reversing happens when a dominant animal performs an action during play that wouldn't normally occur during real aggression. For example, a dominant wolf wouldn't roll over on his back during fighting, making himself more vulnerable to attack, but would do so while playing.

Play can sometimes get out of hand for animals, just as it does for human beings. When play gets too rough, canids keep things under control by using bows to apologize. For example, a bow might communicate something like, "Sorry I bit you so hard—I didn't mean it, so let's continue playing." For play to continue, it's important for individuals to forgive the animal who violated the rules. Once again there are species differences among young canids. Highly aggressive young coyotes bow significantly more frequently than dogs or wolves before and after delivering bites that could be misinterpreted.

The social dynamics of play require that players agree to play and not to eat one another or fight or try to mate. When there's a violation of those expectations, others react to the lack of fairness. For example, young coyotes and wolves react negatively to unfair play by ending the encounter or avoiding those who ask them to play and then don't follow the rules. Cheaters have a harder time finding play partners.

It's just a step from play to morality. Researchers who study child's play, like Ernst Fehr, of the University of Zurich, and Anthony D. Pellegrini, of the University of Minnesota-Twin Cities, have discovered that basic rules of fairness guide play, and that egalitarian instincts emerge very early in childhood. Indeed, while playing, children learn, as do other young animals, that there are right and wrong ways to play, and that transgressions of fairness have social consequences, like being ostracized. The lessons children learn—particularly about fairness—are also the foundation of fairness among adults.

When children agree, often after considerable negotiation, on the rules of a game, they implicitly consent not to arbitrarily change the rules during the heat of the game. During play, children learn the give and take of successful reciprocal exchanges (you go first this time; I get to go first next time), the importance of verbal contracts (no one can cross the white line), and the social consequences of failing to play by the rules (you're a cheater). As adults we are also constantly negotiating with others about matters of give and take, we rely daily on verbal contracts with others, and most of us, most of the time, follow myriad socially constructed rules of fairness during our daily lives.

The parallels between human and animal play, and the shared capacity to understand and behave according to rules of right and wrong conduct, are striking. They lead us to believe that animals are morally intelligent. Morality has evolved in many species, and unique features of human morality, like the use of language to articulate and enforce social norms, are simply modifications of broadly evolved behavioral patterns specific to our species.

Philosophical and scientific tradition, however, holds that although prosocial behaviors in animals may reveal the evolutionary roots of human morality, animals themselves do not and cannot have morality, because they lack the capacities that are essential constituents of moral behavior—especially the capacity for critical self-reflection upon values. Human morality is distinguished from animal "morality" by the greater generality of human moral norms, and by the greater rational self-awareness and choice that it requires. Indeed, the human prefrontal cortex, the area of the brain responsible for judgment and rational thought, is larger and more highly developed in human beings than in other animals.

That traditional view of morality is beginning to show signs of wear and tear. The fact that human morality is different from animal morality—and perhaps more highly developed in some respects—simply does not support the broader claim that animals lack morality; it merely supports the rather banal claim that human beings are different from other animals. Even if there are bona fide differences between morality in human beings and morality in other animals, there are also significant areas of overlap. Unique human adaptations might be understood as the outer skins of an onion; the inner layers represent a much broader, deeper, and evolutionarily more ancient set of moral capacities shared by many social mammals, and perhaps by other animals and birds as well.

Furthermore, recent research in cognitive neuroscience and moral psychology suggests that human morality may be much more "animalistic" than Western philosophy has generally assumed. The work of Antonio R. Damasio (Descartes' Error: Emotion, Reason, and the Human Brain), Michael S. Gazzaniga (The Ethical Brain), and Daniel M. Wegner (The Illusion of Conscious Will), among others, suggests that the vast majority of human moral behavior takes place "below the radar" of consciousness, and that rational judgment and self-reflection actually play very small roles in social interactions.

The study of animal play thus offers an invitation to move beyond philosophical and scientific dogma and to take seriously the possibility that morality exists in many animal societies. A broad and expanding study of animal morality will allow us to learn more about the social behaviors that make animal societies so successful and so fascinating, and it will also encourage us to re-examine assumptions about human moral behavior. That study is in its infancy, but we hope to see ethologists, neuroscientists, biologists, philosophers, and theologians work together to explore the implications of this new science. Already, research on animal morality is blossoming, and if we can break free of theoretical prejudice, we may come to better understand ourselves and the other animals with whom we share this planet.

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The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the tree of life as we knew it but also another central tenet of the modern synthesis inherited from Darwin, namely gradualism. In a world dominated by HGT, gene duplication, gene loss and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.

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1. Random (undirected), heritable variation is the principal material for natural selection.
YES. But the relevant random changes are extremely diverse: - nucleotide substitution, insertion and deletion; - duplication of genes, genome regions and whole genomes; - loss of genes and, generally, genetic material; - HGT including massive gene flux after endosymbiosis; and -invasion and transposition of mobile selfish elements and recruitment of sequences from these elements. Moreover, the wide spread of stress-induced mutagenesis and related phenomena suggests the possibility of quasi-Lamarckian variation (a part of Darwin's concept purged by the modern synthesis) [22].

2. Fixation of beneficial changes by natural selection is the main driving force of evolution that tends to generate increasingly complex adaptations; hence, progress as a general trend in evolution.
NO. Darwinian (positive) selection is important but is only one of several fundamental forces of evolution, and not necessarily the dominant one. Neutral processes constrained by purifying selection dominate evolution. Genomic complexity is not intrinsically adaptive and probably evolves as a ‘genomic syndrome’ in populations with small effective size and accordingly weak purifying selection. There is no consistent trend towards increasing complexity and no progress in evolution.

3. Natural selection operates on ‘infinitesimally small’ variations, so evolution never makes leaps – the principle of gradualism.
NO. Even duplication and HGT of single genes are not ‘infinitesimally small’ genomic changes let alone the deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication and, of course, endosymbiosis. Evolutionary (or even revolutionary) leaps are possible, especially during population bottlenecks, and are crucial for major evolutionary transitions.

4. Evolutionary processes were, largely, the same throughout the evolution of life – the principle of uniformitarianism borrowed by Darwin from geology.
YES and NO. The principal factors of evolution, diverse as they are, were all probably in operation throughout history. However, the earliest stages of evolution antedating the emergence of the three domains of cellular life should have involved processes distinct from ‘normal’ evolution. Furthermore, a major transition in evolution, such as eukaryogenesis, occurred through unique events (e.g. endosymbiosis).

5. Species is a central unit of evolution, and speciation a key evolutionary process.
NO. Species can be meaningfully defined only for organisms that engage in regular sex, ensuring reproductive isolation, but not promiscuous HGT. In general, the species concept does not apply to prokaryotes and is of dubious validity for unicellular eukaryotes as well [10].

6. The entire evolution of life can be depicted as a single ‘big tree’ that reflects the evolutionary relationships between organisms and species (species tree).
NO and YES. The discovery of the key roles of HGT and mobile genetic elements in genome evolution deal a death knell to the traditional tree of life concept. Still, trees remain natural templates to represent the evolution of individual genes and many intervals of evolution in groups of relatively close organisms [15].

7. All existing life forms descend from a single ancestral form, the last universal common ancestor (LUCA).
YES. But comparative genomics leaves no doubt of the common ancestry of all cellular life. However, there are strong indications that LUCA would have been quite different from modern cells [23].

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Are there any glimpses of a new synthesis on the horizon? At the distinct risk of overestimating the promise of the current advances, I will mention two candidates. The first is the population–genetic theory of the evolution of genomic architecture, according to which evolving complexity is a side product of non-adaptive evolutionary processes occurring in small populations where the constraints of purifying selection are weak [16]. The second area with a potential for major unification could be the study of universal patterns of evolution such as the distribution of evolutionary rates of orthologous genes, which is nearly the same in organisms from bacteria to mammals [20] or the equally universal anticorrelation between the rate of evolution and the expression level of a gene [21]. The existence of these universals suggests that simple theory of the kind used in statistical physics might explain some crucial aspects of evolution.

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Aubret, F. and Shine, R. (2009) Genetic Assimilation and the Postcolonization Erosion of Phenotypic Plasticity in Island Tiger Snakes. Current Biology, advance online.

In 1942, C.H. Waddington [1] suggested that colonizing populations could initially succeed by flexibly altering their characteristics (phenotypic plasticity; [2], [3] and [4]) in fitness-inducing traits, but selective forces would rapidly eliminate that plasticity to result in a canalized trait [1], [5] and [6]. Waddington termed this process “genetic assimilation” [1] and [7]. Despite the potential importance of genetic assimilation to evolutionary changes in founder populations [8], [9] and [10], empirical evidence on this topic is rare, possibly because it happens on short timescales and is therefore difficult to detect except under unusual circumstances [11] and [12]. We exploited a mosaic of snake populations isolated (or introduced) on islands from less than 30 years ago to more than 9000 years ago and exposed to selection for increased head size (i.e., ability to ingest large prey [13], [14], [15] and [16]). Here we show that a larger head size is achieved by plasticity in “young” populations and by genetic canalization in “older” populations. Island tiger snakes (Notechis scutatus) thus show clear empirical evidence of genetic assimilation, with the elaboration of an adaptive trait shifting from phenotypically plastic expression through to canalization within a few thousand years.

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Tiger snakes from newly colonized areas had relatively small heads at birth, but these increased rapidly in size (relative to body length) if the young snakes were offered large prey items. In contrast, snakes from “older” (long-colonized) islands had large heads at birth, but the head size of these animals displayed little phenotypic plasticity: the relative sizes of the snakes' heads were unaffected by the size of prey they encountered. Thus, the scenario accords well with Waddington's hypothesis [1] and [7] as well as many predictions of recent models [10]. As the animals colonized a novel type of habitat, the optimal values for major phenotypic traits (in this case, head size and body size) were different from those experienced in the ancestral (mainland) population. That challenge initially was solved by phenotypic plasticity (phenotypes were induced by local conditions, in this case prey size). Remarkably, such plasticity evolved or was selected for very quickly (in under 40 years; see above and [10], [17] and [18]) from undetectable levels of plasticity (this aspect is not predicted by current evolutionary models [10]). Over time (over thousands of years), this plasticity was eroded and replaced by genes coding for canalized expression of the same phenotypic trait (a large head size) that in earlier times had been generated by plasticity.

In a scenario where plasticity is eroded, we would expect to see a progressive increase in mean body size and head size at birth, as a function of time since population isolation. That is, tiger snakes in newly colonized areas should have relatively small heads at birth, whereas conspecifics from “older” populations should have larger head sizes. In keeping with this prediction, a gradient in size at birth was evident between the “old” population on Williams Island (large neonates) and mainland snakes with no exposure to larger prey items (Joondalup Lake, small neonates). Neonate sizes were intermediate in the sites with intermediate ages since colonization (Christmas and New Year islands).

Comparisons between the two most recently colonized sites, Carnac Island (less than 90 years since snake introduction) and Trefoil Island (40 years), are of particular interest. Snakes from both of these “young” populations are highly plastic in rates of jaw growth, but Carnac Island neonates also are born with larger jaws than their putative mainland ancestors (Joondalup Lake), whereas the Trefoil Island snakes do not differ from their putative (Tasmanian) ancestors in mean body or head sizes at birth. Therefore, genetic assimilation may occur rapidly (over a few decades), even in relatively long-lived, late-maturing animals such as tiger snakes (2 to 3 years old at maturation [13] and [18]). If such rapid change is common, then genetic assimilation will only be observed in studies specifically focused on the years immediately postcolonization. Future studies could usefully (1) assess and measure the putative costs of phenotypic plasticity in island tiger snakes and (2) explore plasticity during the postcolonization phase in other species to see whether Waddington's long-neglected concept of genetic assimilation may provide important insights into the process by which organisms adapt to novel environmental challenges.

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Springman, R. et al. (2009) Evolution at a High Imposed Mutation Rate: Adaptation Obscures the Load in Phage T7. Genetics, advance online.

Evolution at high mutation rates is expected to reduce population fitness deterministically by the accumulation of deleterious mutations. A high enough rate should even cause extinction (lethal mutagenesis), a principle motivating the clinical use of mutagenic drugs to treat viral infections. The impact of a high mutation rate on long-term viral fitness was tested here. A large population of the DNA bacteriophage T7 was grown with a mutagen, producing a genomic rate of 4 non-lethal mutations per generation, 2-3 orders of magnitude above the baseline rate. Fitness - viral growth rate in the mutagenic environment - was predicted to decline substantially; after 200 generations, fitness had increased, rejecting the model. A high mutation load was nonetheless evident from ( i) many low- to moderate-frequency mutations in the population (averaging 245 per genome), and (ii) an 80% drop in average burst size. Twenty eight mutations reached high frequency and were thus presumably adaptive, clustered mostly in DNA metabolism genes, chiefly DNA polymerase. Yet blocking DNA polymerase evolution failed to yield a fitness decrease after 100 generations. Although mutagenic drugs have caused viral extinction in vitro under some conditions, this study is the first to match theory and fitness evolution at a high mutation rate. Failure of the theory challenges the quantitative basis of lethal mutagenesis and highlights the potential for adaptive evolution at high mutation rates.

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The evolutionary consequences of a high mutation rate are mysterious. It is widely considered that mutations are essential for adaptation, but that the rate maximizing adaptation is far below what can be tolerated (e.g., Trobner and Piechocki 1984; Sniegowski 1997, 2001). In this 'twilight zone' of higher-than-optimal mutation rates, the population experiences unique challenges. In one process, the 'error catastrophe,' the best genotype is driven out of the population deterministically because the onslaught of viable, mutant genotypes simply overwhelms it (Eigen et al. 1988). With Muller's ratchet, a phenomenon of finite asexual populations, high mutation rates and genetic drift combine to cause loss of the wild-type genome, and the absence of recombination blocks its recreation (Muller 1964); fitness gradually decays as mutations continue their stochastic accumulation. Yet another high mutation rate process is the straightforward, deterministic decline in population fitness as deleterious mutations accumulate (Kimura and Maruyama 1966), leading to extinction if fecundity is too low to compensate (Maynard Smith 1978; Bull et al. 2007).

The problem with our understanding of evolution at high mutation rate is that it is piecemeal. We don't yet know how to combine these different processes nor do we know their relative importances. For example, the fitness loss at high mutation rate can be offset both by adaptation and by the error catastrophe, but for realistic models, there is no formal basis for predicting the magnitude of adaptation nor even for recognizing an error catastrophe (Bull et al. 2007, 2005). Empirical studies are needed. Several studies of viruses have explored extinction through elevated mutation rate (lethal mutagenesis; Anderson et al. 2004; Domingo et al. 2001, also see Discussion), but they have not been tied to any quantitative model. The practical value of such work is that mutagenic drugs are sometimes used to treat viral infections, yet we do not know how the elevated mutation rate is impacting the virus.

Here we develop an empirical system to enforce viral evolution at high mutation rate and test theory developed for lethal mutagenesis. A mutagen is applied to the culture in which the DNA bacteriophage T7 is grown, the mutation input per generation is measured on a genome-wide scale, and the system is used to observe both molecular and fitness evolution. Comparison of data and theory provides new insights to the process that underlies lethal mutagenesis. However, existing theory must also be modified to address some empirical properties of the system.

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How Did Flowering Plants Evolve to Dominate Earth?

ScienceDaily (Dec. 1, 2009) — To Charles Darwin it was an 'abominable mystery' and it is a question which has continued to vex evolutionists to this day: when did flowering plants evolve and how did they come to dominate plant life on earth? A new study in Ecology Letters reveals the evolutionary trigger which led to early flowering plants gaining a major competitive advantage over rival species, leading to their subsequent boom and abundance.

The study, by Dr Tim Brodribb and Dr Taylor Field of the University of Tasmania and University of Tennessee, used plant physiology to reveal how flowering plants, including crops, were able to dominate land by evolving more efficient hydraulics, or 'leaf plumbing', to increase rates of photosynthesis.

"Flowering plants are the most abundant and ecologically successful group of plants on earth," said Brodribb. "One reason for this dominance is the relatively high photosynthetic capacity of their leaves, but when and how this increased photosynthetic capacity evolved has been a mystery."

Using measurements of leaf vein density and a linked hydraulic-photosynthesis model, Brodribb and Field reconstructed the evolution of leaf hydraulic capacity in seed plants. Their results revealed that an evolutionary transformation in the plumbing of angiosperm leaves pushed photosynthetic capacity to new heights.

The reason for the success of this evolutionary step is that under relatively low atmospheric C02 conditions, like those existing at present, water transport efficiency and photosynthetic performance are tightly linked. Therefore adaptations that increase water transport will enhance maximum photosynthesis, exerting substantial evolutionary leverage over competing species.

The evolution of dense leaf venation in flowering plants, around 140-100 million years ago, was an event with profound significance for the continued evolution of flowering plants. This step provided a 'cretaceous productivity stimulus package' which reverberated across the biosphere and led to these plants playing the fundamental role in the biological and atmospheric functions of the earth.

"Without this hydraulic system we predict leaf photosynthesis would be two-fold lower then present," concludes Brodribb. "So it is significant to note that without this evolutionary step land plants would not have the physical capacity to drive the high productivity that underpins modern terrestrial biology and human civilisation."

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Brodribb, T.J. and Felid, T.S. (2009) Leaf hydraulic evolution led a surge in leaf photosynthetic capacity during early angiosperm diversification. Ecology Letters, advance online.

Angiosperm evolution transformed global ecology, and much of this impact derives from the unrivalled vegetative productivity of dominant angiosperm clades. However, the origins of high photosynthetic capacity in angiosperms remain unknown. In this study, we describe the steep trajectory of leaf vein density (Dv) evolution in angiosperms, and predict that this leaf plumbing innovation enabled a major shift in the capacity of leaves to assimilate CO2. Reconstructing leaf vein evolution from an examination of 504 angiosperm species we found a rapid three- to fourfold increase in Dv occurred during the early evolution of angiosperms. We demonstrate how this major shift in leaf vein architecture potentially allowed the maximum photosynthetic capacity in angiosperms to rise above competing groups 140–100 Ma. Our data suggest that early terrestrial angiosperms produced leaves with low photosynthetic rates, but that subsequent angiosperm success is linked to a surge in photosynthetic capacity during their early diversification.

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The fundamental role played by angiosperms in the biological and atmospheric function of earth provides a major impetus for research into the adaptive processes responsible for early angiosperm diversification. Until recently most inquiry has focused on reproductive functions and plant–animal interactions as the engines of today's biodiversity (Crepet 2008; Williams 2008). To the extent that high leaf Pc is linked to canopy productivity (Bonan 2008), our results suggest that the Early to mid-Cretaceous transition in leaf architecture was an event of profound significance in the functional evolution and modernization of terrestrial vegetation. We posit that angiosperm leaves, by virtue of their veins, provided a Cretaceous productivity stimulus package that reverberated throughout the biosphere. Elevated Pc and the linked high rates of transpiration are likely to have enhanced the flows of energy, water and nutrients through the biosphere, which cascaded into new opportunities for diverse organisms in geologically young, angiosperm-dominated ecosystems (Berendse & Scheffer 2009; Boyce et al. 2009).

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Op woensdag 30 december 2009 19:29 schreef zakjapannertje het volgende:

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http://knack.rnews.be/nie(...)45-article44376.html