[Centraal] Evolutie in het nieuws

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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

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Genome Study Provides a Census of Early Humans

From the composition of just two human genomes, geneticists have computed the size of the human population 1.2 million years ago from which everyone in the world is descended.

They put the number at 18,500 people, but this refers only to breeding individuals, the “effective” population. The actual population would have been about three times as large, or 55,500.

Comparable estimates for other primates then are 21,000 for chimpanzees and 25,000 for gorillas. In biological terms, it seems, humans were not a very successful species, and the strategy of investing in larger brains than those of their fellow apes had not yet produced any big payoff. Human population numbers did not reach high levels until after the advent of agriculture.

Geneticists have long known that the ancestors of modern humans numbered as few as 10,000 at some time in the last 100,000 years. The critically low number suggested that some catastrophe, like disease or climate change induced by a volcano, had brought humans close to the brink of extinction.

If the new estimate is correct, however, human population size has been small and fairly constant throughout most of the last million years, ruling out the need to look for a catastrophe.

The estimate, reported in the issue on Tuesday of The Proceedings of the National Academy of Sciences, was made by a team of population geneticists at the University of Utah led by Chad D. Huff and Lynn B. Jorde.

The human population a million years ago was represented by archaic species like Homo ergaster in Africa and Homo erectus in East Asia. The Utah team says its estimate of 18,500 implies “an unusually small population for a species spread across the entire Old World.”

But that estimate would apply to the worldwide population only if there were inbreeding between the humans on the different continents. If not, and if modern humans are descended from just one of these populations, like Homo ergaster in Africa, then the estimate would apply only to that.

Richard G. Klein, a paleoanthropologist at Stanford, said it was hard to believe the population from which modern humans are descended was as small as 18,500 “unless they were geographically restricted to Africa or a small part of it.”

There is no independent way of assessing a genetics-based estimate of population size at this period, Dr. Klein said, although archaeologists have developed ways of assessing ancient populations of more recent times.

The Utah team based its estimate on the genetic variation present in two complete human genomes, one prepared by the government’s human genome project and the other by J. Craig Venter, the genome sequencing pioneer. The government decoded a single copy of a mosaic genome derived from a medley of people, apparently of European and Asian origin. Dr. Venter decoded both copies of his own genome, the one inherited from his father and the one from his mother.

The Utah team thus had three genomes to work with and looked at ancient elements known as Alu insertions, the youngest class of which appeared in the human genome around a million years ago. The amount of variation seen in the DNA immediately surrounding the Alu insertions gave a measure of the size of human population at that time.

Their estimate agrees almost exactly with an earlier one, also based on Alu insertions but with sparser data. The insertions tag ancient regions of the genome that are unaffected by the recent growth in population, Dr. Huff said.

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Draghi, J.A. et al. (2010) Mutational robustness can facilitate adaptation. Nature, 463, 463, 353-355.

Robustness seems to be the opposite of evolvability. If phenotypes are robust against mutation, we might expect that a population will have difficulty adapting to an environmental change, as several studies have suggested1, 2, 3, 4. However, other studies contend that robust organisms are more adaptable5, 6, 7, 8. A quantitative understanding of the relationship between robustness and evolvability will help resolve these conflicting reports and will clarify outstanding problems in molecular and experimental evolution, evolutionary developmental biology and protein engineering. Here we demonstrate, using a general population genetics model, that mutational robustness can either impede or facilitate adaptation, depending on the population size, the mutation rate and the structure of the fitness landscape. In particular, neutral diversity in a robust population can accelerate adaptation as long as the number of phenotypes accessible to an individual by mutation is smaller than the total number of phenotypes in the fitness landscape. These results provide a quantitative resolution to a significant ambiguity in evolutionary theory.

[..]

The relationship between robustness and evolvability is complex because robust populations harbour a large diversity of neutral genotypes that may be important in adaptation9, 10, 11. Although neutral mutations do not change an organism’s phenotype, they may nevertheless have epistatic consequences for the phenotypic effects of subsequent mutations12, 13, 14, 15, 16, 17, 18. In particular, a neutral mutation can alter an individual’s ‘phenotypic neighbourhood’, that is, the set of distinct phenotypes that the individual can access through a further mutation. Pioneering studies based on RNA folding and network dynamics suggest that genotypes expressing a particular phenotype are often linked by neutral mutations into a large neutral network, and that members of a neutral network differ widely in their phenotypic neighbourhoods1, 19, 20, 21. Numerous studies have documented the importance of neutral variation in allowing a population to access adaptive phenotypes5, 17, 18, 22, 23, 24, and neutral networks have consequently been proposed to facilitate adaptation9, 10, 11.

Here we analyse the relationship between robustness and evolvability using a population genetics model that specifies statistical properties of the fitness landscape.

[..]

Our results reveal a complex relationship between robustness and evolvability. In some situations, increasing robustness will decrease evolvability, whereas in other situations it will accelerate adaptation. The latter phenomenon can occur only when the number of phenotypes accessible to an individual, K, is smaller than the total number of alternative phenotypes in the landscape, P.

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Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection

Ever since Cicero's De Natura Deorum ii.34., humans have been intrigued by the origin and mechanisms underlying complexity in nature. Darwin suggested that adaptation and complexity could evolve by natural selection acting successively on numerous small, heritable modifications. But is this enough? Here, we describe selected studies of experimental evolution with robots to illustrate how the process of natural selection can lead to the evolution of complex traits such as adaptive behaviours. Just a few hundred generations of selection are sufficient to allow robots to evolve collision-free movement, homing, sophisticated predator versus prey strategies, coadaptation of brains and bodies, cooperation, and even altruism. In all cases this occurred via selection in robots controlled by a simple neural network, which mutated randomly.

Genes do not specify behaviours directly but rather encode molecular products that lead to the development of brains and bodies through which behaviour is expressed. An important task is therefore to understand how adaptive behaviours can evolve by the mere process of natural selection acting on genes that do not directly code for behaviours. A spectacular demonstration of the power of natural selection comes from experiments in the field of evolutionary robotics [1],[2], where scientists have conducted experimental evolution with robots. Evolutionary robotics has also been advocated as a method to automatically generate control systems that are comparatively simpler or more efficient than those engineered with other design methods because the space of solutions explored by evolution can be larger and less constrained than that explored by conventional engineering methods [3]. In this essay we will examine key experiments that illustrate how, for example, robots whose genes are translated into simple neural networks can evolve the ability to navigate, escape predators, coadapt brains and body morphologies, and cooperate. We present mostly—but not only—experimental results performed in our laboratory, which satisfy the following criteria. First, the experiments were at least partly carried out with real robots, allowing us to present a video showing the behaviours of the evolved robots. Second, the robot's neural networks had a simple architecture with no synaptic plasticity, no ontogenetic development, and no detailed modelling of ion channels and spike transmission. Third, the genomes were directly mapped into the neural network (i.e., no gene-to-gene interaction, time-dependent dynamics, or ontogenetic plasticity). By limiting our analysis to these studies we are able to highlight the strength of the process of Darwinian selection in comparable simple systems exposed to different environmental conditions. There have been numerous other studies of experimental evolution performed with computer simulations of behavioural systems. Reviews of these studies can be found in [4]–[6]. Furthermore, artificial evolution has also been applied to disembodied digital organisms living in computer ecosystems, such as Tierra [7] and Avida [8], to address questions related to gene interactions [9], evolution of complexity [10], and mutation rates [11],[12].

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Seven habits of highly successful toads

Toads are an evolutionary success story. In a relatively short span of time, they diversified into around 500 species and spread to every continent except Antarctica. Now, Ines van Bocxlaer from Vrije University has uncovered the secrets of their success. By comparing the most home-bound toads with the most invasive ones, she has outlined seven qualities that enabled these amphibians to conquer the world. In a common ancestor, these seven traits came together to create an eighth - a pioneer's skill are colonising new habitats.

Some, like the harlequin toads, are restricted to such narrow tracts of land that they are vulnerable to extinction. Others, like the infamous cane toads, are highly invasive and notoriously resistant to extinction despite the best efforts of Australians and their sporting equipment. This diversity of lifestyles allowed Bocxlaer to search for characteristics shared by the most pioneering of toad species.

She compared over 228 species, representing just under half of all the known toads, and constructed a family tree that charts their relationships. She showed, as others before have suggested, that the family's fortunes kicked off in South America, around 35-40 million years ago. This was the start of their global invasion.

Seven qualities make for wide-ranging toads. For a start, the adults don't have the typical amphibian dependency on constant water or humidity. They have skins that can cope with the drier side of life, giving them a chance to seek out new habitats away from the safety net of moist environments. Secondly, they tend to have fat deposits near their groin, which act as a back-up energy source when food is scarce. Thirdly, they tend to be larger (meaning at least 5 centimetres in length), which also helps to conserve water. Larger animals have larger bladders so they retain more water, and they lose less of it because they have small surface areas for their size.

Fourthly, the most wide-ranging species have parotid glands, large sacs that are usually armed with poisons called bufotoxins. Those of the cane toads have claimed the lives of many would-be predators, and even some humans. The defensive benefits are obvious but they also help toads to, once again, break their water habit. The glands secrete molecules that are extremely attracted to water, allowing the animals to store large amounts in the dry season.

The final three traits all affect the toads' reproductive life. Some species have to lay their eggs in very specific locations. But the widest-ranging ones opportunistically lay in all sorts of environments as long as there is some water, such as the brief puddles that form during sporadic rainfall. Pioneering species also tend to have tadpoles that get their food from their environment, rather than from yolk or other food sources packaged by their parents. Finally, toads with the largest egg clutches (up to 45,000 in the great plains toad) are more widely distributed than those that lay few eggs, like the flathead toads that only lay five.

By their powers combined, these seven attributes make a toad optimally poised to expand its range. By mapping the presence of these traits across the toad family tree, Bocxlaer showed that they slowly accumulated in the earliest toads. The point where all seven had been checked off the list coincided with the dramatic expansion of the dynasty out of South America and into other continents.

As these ancestral species hopped across the world, so they diversified into new forms. As the toads reached new continents and colonised new niches, they rapidly gave rise to new species. In the Old World, several lineages independently lost their ancestors' globe-trotting abilities, in favour of being more specialised and locally adapted.

But many retained the pioneering qualities. Today, many toads still have all seven traits to the extent that even distantly related species look very similar. They're relatively large, land-living animals with fat deposits and parotid glands, and they opportunistically lay large clutches of eggs that hatch into independent tadpoles. That's certainly a fair description of the cane toad. Bocxlaer's study shows that this pest's remarkable skill at invading Australia was rooted deep in its ancestry, a "remnant of the period when toads colonised the world".

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Changes in Hox genes’ structure and function during the evolution of the squamate body plan

Hox genes are central to the specification of structures along the anterior–posterior body axis1, 2, and modifications in their expression have paralleled the emergence of diversity in vertebrate body plans3, 4. Here we describe the genomic organization of Hox clusters in different reptiles and show that squamates have accumulated unusually large numbers of transposable elements at these loci5, reflecting extensive genomic rearrangements of coding and non-coding regulatory regions. Comparative expression analyses between two species showing different axial skeletons, the corn snake and the whiptail lizard, revealed major alterations in Hox13 and Hox10 expression features during snake somitogenesis, in line with the expansion of both caudal and thoracic regions. Variations in both protein sequences and regulatory modalities of posterior Hox genes suggest how this genetic system has dealt with its intrinsic collinear constraint to accompany the substantial morphological radiation observed in this group.