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ZEN: Eco-evolutionary Software

13 Février 2017,

Publié par Bioécologie


Figure 1
Deployment of polymorphism in a population subjected to asymmetric competition
(ZEN simulation, model from Kisdi & Geritz 2001).
The distribution of phenotypes is shown along evolutionary time in ordinates.


Ecological models with an evolutionary component allow to study several biological phenomena: host-pathogens interactions, coevolution of plants and pollinisators, mimicry, development of the immune system, evolution of cooperation, evolution of life history traits, and more generally biodiversity and speciation.

What is simulated by ZEN ? The evolution of populations under the mutation-selection process 

ZEN uses an individual-based (in fact ‘phenotype-based’) approach with 3 components:

  • Stochastic equations in discrete time describing the dynamics of finite populations
  • Adaptive traits and their mutations (mutation rates and distributions)
  •  Ecological interactions between phenotypes

During the ZEN simulation, mutant phenotypes created by the triggering of mutations interact with resident phenotypes. They persist or go extinct, possibly leading to evolutionary branching and polymorphism (Figs. 1, 2).

How does ZEN work ?

Models are described in a text file using a reduced declaration language, and studied by means of a simple interface with convenient graphics. The ZEN kernel is a symbolic evaluator handling ‘polymorphic’ variables.

More information here

Scientists Seek to Update Evolution

23 Novembre 2016,

Publié par Bioécologie

Recent discoveries have led some researchers to argue that the modern evolutionary synthesis needs to be amended.

Kevin Laland looked out across the meeting room at a couple hundred people gathered for a conference on the future of evolutionary biology. A colleague sidled up next to him and asked how he thought things were going.

“I think it’s going quite well,” Laland said. “It hasn’t gone to fisticuffs yet.”

Laland is an evolutionary biologist who works at the University of St. Andrews in Scotland. On a chilly gray November day, he came down to London to co-host a meeting at the Royal Society called “New Trends in Evolutionary Biology.” A motley crew of biologists, anthropologists, doctors, computer scientists, and self-appointed visionaries packed the room. The Royal Society is housed in a stately building overlooking St. James’s Park. Today the only thing for Laland to see out of the tall meeting-room windows was scaffolding and gauzy tarps set up for renovation work. Inside, Laland hoped, another kind of renovation would be taking place.

In the mid-1900s, biologists updated Darwin’s theory of evolution with new insights from genetics and other fields. The result is often called the Modern Synthesis, and it has guided evolutionary biology for over 50 years. But in that time, scientists have learned a tremendous amount about how life works. They can sequence entire genomes. They can watch genes turn on and off in developing embryos. They can observe how animals and plants respond to changes in the environment.

As a result, Laland and a like-minded group of biologists argue that the Modern Synthesis needs an overhaul. It has to be recast as a new vision of evolution, which they’ve dubbed the Extended Evolutionary Synthesis. Other biologists have pushed back hard, saying there is little evidence that such a paradigm shift is warranted.

This meeting at the Royal Society was the first public conference where Laland and his colleagues could present their vision. But Laland had no interest in merely preaching to the converted, and so he and his fellow organizers also invited prominent evolutionary biologists who are skeptical about the Extended Evolutionary Synthesis.

Both sides offered their arguments and critiques in a civil way, but sometimes you could sense the tension in the room — the punctuations of tsk-tsks, eye-rolling, and partisan bursts of applause.

But no fisticuffs. At least not yet.

Making Evolution as We Know It

Every science passes through times of revolution and of business as usual. After Galileo and Newton dragged physics out of its ancient errors in the 1600s, it rolled forward from one modest advance to the next until the early 1900s. Then Einstein and other scientists established quantum physics, relativity and other new ways of understanding the universe. None of them claimed that Newton was wrong. But it turns out there’s much more to the universe than matter in motion.

Read more here


Scientists Seek to Update Evolution

Entre gènes et environnements

9 Mai 2016,

Publié par Bioécologie

A écouter. Une émission radio par Jean-Claude Ameisen.

"L’intérieur et l’extérieur s’interpénètrent et un être vivant est à la fois le produit et le lieu de cette interaction.
Richard Lewontin. La triple hélice. Les gènes, l’organisme, l’environnement."

Why do some fish thrive in oil-polluted water?

3 Février 2016,

Publié par Bioécologie

Scientists thought guppies in Northern Trinidad could be a rare example of adaptation to crude oil pollution. But they found something else.

By Melody Enguix (26 JAN 2016):

When scientists from McGill University learned that some fish were proliferating in rivers and ponds polluted by oil extraction in Southern Trinidad, it caught their attention. They thought they had found a rare example of a species able to adapt to crude oil pollution.

At a time when humans are imposing an unprecedented burden on the world's ecosystems, studying how organisms can tolerate pollutants is crucial to understanding the impact of human activities – and to helping to mitigate it in the future.

Led by Dr. Gregor Rolshausen, then a postdoctoral researcher at McGill working with Prof. Andrew Hendry, the team went to study the guppy fish living in polluted areas, comparing their morphology and genetic makeup to those of similar guppies from non-polluted parts of Trinidad.

More here

La médecine darwinienne, un autre regard sur la santé

12 Janvier 2015,

Publié par Bioécologie

La médecine darwinienne, un autre regard sur la santé

Un article de Laure Cailloce paru dans Le Journal du CNRS, le 5 mars 2014

L’homme, comme la plupart des espèces, s’est adapté à son environnement pour maximiser sa reproduction. Cette réalité amène des scientifiques à considérer les problèmes de santé à la lumière des lois de l’évolution et à porter un nouveau regard sur des maladies comme le cancer, les maladies auto-immunes ou les allergies.

« Les antibiotiques, c’est pas automatique ! » La rengaine serinée depuis plusieurs années par les autorités de santé est dans toutes les têtes. Destinés à éradiquer les infections d’origine microbienne, ces médicaments, largement prescrits contre des infections d’origine virale notamment, ont eu pour effet de sélectionner les souches microbiennes les plus résistantes. Un cas d’école dela théorie darwinienne de l’évolution appliquée à la santé ! « Les microbes qui possédaient une mutation génétique leur conférant une meilleure résistance aux antibiotiques ont bénéficié d’un avantage pour se reproduire, tandis que les autres souches succombaient au traitement », explique Frédéric Thomas, chercheur en biologie évolutive au Mivegec1, à Montpellier, laboratoire spécialisé dans les maladies infectieuses.

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Florida lizards evolve rapidly, within 15 years and 20 generations

29 Octobre 2014,

Publié par Bioécologie

Stuart, Y.E., T.S. Campbell, P.A. Hohenlohe, R.G. Reynolds, L.J. Revell, and J.B. Losos. 2014. Rapid evolution of a native species following invasion by a congener. Science, 346: 463-466. DOI: 10.1126/science.1257008. [link, pdf]

Native green anoles (left) have evolved better gripping feet in response to an invasion of brown anoles (right) on islands in Florida. Credit: Todd Campbell and Adam Algar.

Native green anoles (left) have evolved better gripping feet in response to an invasion of brown anoles (right) on islands in Florida. Credit: Todd Campbell and Adam Algar.