[Centraal] Evolutie in het nieuws

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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.