Wednesday, 9 December 2020

Evolution News - Another 'Non-Existent' Observed Instance of Evolution in Progress

E. coli are common in the gut – and in scientific experiments.

Credit: Maurizio de Angelis/Science Photo Library/Getty Images
UZH - Natural Selection also Increases the Adaptability of Organism
Not that it will bother them because truth is the least of their concerns, but from today, Creationists who claim there are no observed instances of evolution in progress, are either knowingly lying or repeating lies they have been fooled with, because here we have another instance of as clear and unambiguous an example of it as you could wish for.

Amusingly, Creationists have already tried hard to dismiss it with typically childish responses such as:
Aha! But can you prove it will become a horse? Didn't think so.
This discovery was a real surprise because it showed that selection for fitness didn't conflict with selection for robustness, which contrasts with previous work. While most mutations that proteins encounter harm their stability or ability to assume their correct spatial form, the robustness-improving mutations actually mitigate such deleterious effects. Robust proteins have a higher chance to function and thus evolve new traits.

Jia Zheng, first author
Univerity of Zurich
Although it's not clear that this is not a parody of creationism. It is almost always impossible to tell a parody of Creationism because there is no lower level to the credulity, gullibility and dishonesty of a Creationist.

It is, of course, the case of the evolving E. coli bacteria, reported by a Swiss team led by Andreas Wagner of the University of Zurich as announced in a Zurich University press release, entitled, Natural Selection also Increases the Adaptability of Organism and published in the journal Science a few days ago.

As the press release explains:
The green fluorescent protein originally comes from a jellyfish. If the protein is excited with blue or UV light, it fluoresces green.
Credit: istock.com/hanohiki
Natural selection causes organisms to adapt continuously. Researchers at the University of Zurich now show for the first time that proteins in bacteria develop a new property more rapidly when the selection pressure is high. Natural selection can thus also increase the evolutionary capacity itself.
Everywhere we look in the natural world, there’s evidence of natural selection: the resin armor of a lodgepole pine cone evolved to defend against seed-hungry birds and squirrels, or the long neck of a giraffe was evolutionarily favored for reaching high vegetation that the competition can't touch. It is known that natural selection shapes how animals, plants, and other organisms evolve and adapt. But does natural selection also influence an organism’s very capacity to evolve? And if so, to what degree?

The group under strong selection won the "evolution race"
A new study, published in Science, hints at some surprising answers to that question. A team of researchers led by Andreas Wagner of the University of Zurich (UZH) and the Santa Fe Institute, subjected populations of a yellow fluorescent protein from a marine invertebrate that was transferred into the enterobacteria E. coli to weak and strong selection pressure to find out which one enhances evolvability more effectively. The evolutionary goal of the experiment was to get protein populations to evolve from yellow to green fluorescence. The results showed that the group under strong selection won the "evolution race", because those populations underwent mutations that made them more robust – and therefore better able to evolve.

[...]

No need for controversy Wagner hopes that the results will help to settle the long-standing controversy over whether an organism’s evolvability itself can evolve. "So far some scientists thought that natural selection on evolvability must not be very direct — it must be overridden by selection on fitness,” he says. “But now we have an example where both go hand in hand. In other words: there is no need for this controversy.”
Details of the teams findings were publishe in Science:

Structured Abstract


INTRODUCTION


Natural selection plays a central role in adaptive evolution, but we still know little about its role in changing evolvability—the ability to bring forth new and adaptive phenotypes. Different kinds of selection may increase evolvability by different means. Weak purifying selection may enhance evolvability by promoting the accumulation of neutral or slightly deleterious mutations that can serve as stepping stones toward new phenotypes. By contrast, strong directional selection may enhance evolvability by favoring the accumulation of beneficial mutations that can enhance both fitness and evolvability, such as mutations that increase a protein’s thermodynamic stability or its robustness to mutations.

RATIONALE


To find out how the strength of selection affects protein evolvability, we subjected populations of yellow fluorescent proteins to multiple rounds of directed evolution in Escherichia coli. To control the strength of selection with precision, we used high-throughput phenotypic screening via fluorescence-activated cell sorting. During a first phase of our experiment (phase I), we subjected our populations to either strong selection, weak selection, or no selection on the ancestral phenotype of yellow fluorescence. During the second phase (phase II), we evolved all populations under the same selection pressure toward the new phenotype of green fluorescence. We subsequently used high-throughput phenotypic screening to study how phenotypes evolved in all our populations. In every generation, we also studied genotypic evolution with single-molecule real-time sequencing. We then engineered key adaptive mutants and determined their phenotype and thermodynamic stability. In addition, we determined the robustness of their phenotype to DNA mutations. Furthermore, we quantified the foldability of these mutants by unfolding them and observing their refolding kinetics.

RESULTS


We found that populations under strong selection for the ancestral yellow fluorescent phenotype during phase I subsequently evolved the new green fluorescent phenotype most rapidly during phase II. Compared to populations under weak or no selection, they reached higher green fluorescence during each generation of phase II and evolved a green emission peak more rapidly. Strong selection promoted both the elimination of deleterious mutations and the accumulation of foldability-improving mutations. As a result, proteins under strong selection evolved higher efficiency of protein folding (foldability) and, to an even greater extent, higher robustness to mutations than proteins under weak or no selection. Their robustness and foldability accelerated the selective sweeps of neofunctionalizing mutations that are necessary to evolve a new phenotype. By contrast, proteins under weak selection accrued more deleterious mutations that slowed down the fixation of neofunctionalizing mutations during the evolution of the new phenotype, even though neofunctionalizing mutations had initially risen to higher frequencies under weak selection.

CONCLUSION


Strong directional selection enhances the evolvability of a new phenotype to a greater extent than weak purifying selection. The responsible mutations enhance tolerance to mutations, improve protein foldability, and thus increase accessibility of a protein’s native state. In doing so, they promote the formation of correctly folded states that can display new functions after incorporating neofunctionalizing mutations. Although “first order” selection of fitness-enhancing mutations can be in conflict with “second-order” selection of evolvability-enhancing mutations, our experiments demonstrate a class of mutations that avoid this conflict, because the mutations they reveal enhance both fitness and evolvability. In the context of an adaptive landscape (see figure), they do so by circumnavigating rather than traversing adaptive valleys, passing through flat regions of such a landscape, and thus allowing an evolving population to climb a new adaptive peak more rapidly. More generally, our experiments prove that natural selection itself can create the conditions under which Darwinian evolution can succeed.

Selection can drive evolvability.

Evolutionary theory holds that Darwinian evolution takes place on adaptive landscapes of fitness, which can be visualized as topological maps of high-fitness peaks and low-fitness valleys. This hypothetical landscape illustrates how mutations can increase evolvability by enhancing both fitness and mutational robustness. Favored by strong selection because they enhance fitness, such mutations move an evolving population into a region of low curvature and high robustness (red arrow), from which the population can bypass rather than traverse (blue arrow) an adaptive valley on its way to an adaptive peak.

Abstract


Natural selection can promote or hinder a population’s evolvability—the ability to evolve new and adaptive phenotypes—but the underlying mechanisms are poorly understood. To examine how the strength of selection affects evolvability, we subjected populations of yellow fluorescent protein to directed evolution under different selection regimes and then evolved them toward the new phenotype of green fluorescence. Populations under strong selection for the yellow phenotype evolved the green phenotype most rapidly. They did so by accumulating mutations that increase both robustness to mutations and foldability. Under weak selection, neofunctionalizing mutations rose to higher frequency at first, but more frequent deleterious mutations undermined their eventual success. Our experiments show how selection can enhance evolvability by enhancing robustness and create the conditions necessary for evolutionary success.

The delicious irony here is that E. coli is the favourite organism of leading Creationist, Michael J. Behe who famously misrepresented the know science of the evolution of the bacterial flagellum, using E. coli, to the universal delight and aclaim of Creationists and the universal derision of biologists, and so almost single-handedly invented the intelligent [sic] design hoax on behalf of the Discovery Institute, and here we have a very clear example of something that Creationists spend a great deal of time and effort over to persuade their dupes doen't happen.









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