Saturday, 20 June 2015

Watching Evolution As It Happens

Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli | bioRxiv

The world's longest running evolutionary experiment has just produced another embarrassing result; embarrassing for creationists that is. The result is, of course, exactly what the Theory of Evolution predicts.

This experiment, Richard Lenski's Long-term Experimental Evolution Project, has been running since 1988 when Lenski set up 12 cultures of a single strain of E. coli. Every day since then a sample of each culture has been taken and used to seed a new culture. Every 75 days a sample of each cultural line is frozen so any future change can be backtracked. The main nutrient in the culture was glucose.

The experiment has now been running for over 60,000 generations. The biggest evolutionary change occurred at about generation 31,500 when one line evolve the ability to use another component of the nutrient medium, citrate. The originals of this strain of E. coli lacked the ability to use citrate as a nutrient because they were unable to import it across their cell membrane. The citrate utilising E. coli overcame this by producing a protein which enables them to take citrate into their cells. But there was a cost. The trade off was that they needed to export malate, succinate and fumarate which are useful molecules, but less so than citrate.

This mutation was so successful that the citrate utilising E.coli soon came to dominate in their culture line, replacing all but one non-citrate utilising strain which in turn evolved to exploit the changed environment, which now contained the free malate, succinate and fumarate exported by the citrate-utilising E. coli. There was a cost involved but this was low compared to the benefit gained from the imported molecules

But the change didn't stop there. There was now also an advantage to the citrate-utilising E. coli to evolve the same ability as the non-citrate utilising strain to recover some of the exported molecules.

This experiment demonstrates the principle that evolution doesn't occur in isolation. Any evolutionary change in one organism is an environmental change for the others in the ecosystem so ecosystems themselves evolve as the organisms within them change.

Abstract

Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following evolution of a novel function in the long-term evolution experiment (LTEE) with Escherichia coli. A characteristic feature of E. coli is its inability to consume citrate aerobically. However, that ability evolved in one of the LTEE populations. In this population, citrate-utilizing bacteria (Cit+) coexisted stably with another clade of bacteria that lacked the capacity to utilize citrate (Cit−). This coexistence was shaped by the evolution of a cross-feeding relationship in which Cit+ cells released the dicarboxylic acids succinate, fumarate, and malate into the medium, and Cit− cells evolved improved growth on these carbon sources, as did the Cit+ cells. Thus, the evolution of citrate consumption led to a flask-based ecosystem that went from a single limiting resource, glucose, to one with five resources either shared or partitioned between two coexisting clades. Our findings show how evolutionary novelties can change environmental conditions, thereby facilitating diversity and altering both the structure of an ecosystem and the evolutionary trajectories of coexisting organisms.


The disturbing thing for creationists, who can always dismiss all this as the actions of their magic invisible creator friend, is that it shows no sign of any intelligence and every sign of mindless utilitarianism. As the authors point out, the simplest way to make use of the citrate in their medium would have been to evolve a mechanism which didn't involve exporting three other valuable molecules, then evolving the ability to re-import them later at a cost.

This would have been an intelligently designed solution but, as is usual with evolution, the test isn't whether the solution is optimal but whether it works well enough. The net gain was positive so there was an advantage in going with it. This advantage led to a big increase in the frequency of the allele which enabled it. The environment then changed as a result of this evolution so there was now an advantage in evolving the ability to re-import the exported molecules. Each step conveyed an advantage in the prevailing environment so came to predominate but what this strain of E. coli ended up with was a mechanism which worked but was far from optimal.

The end result is the equivalent of going to the greengrocers for some potatoes and leaving a cabbage in payment, then going back to the greengrocers and swapping the cabbage for some runner beans. It doesn't take a genius to come up with a better plan than that.

And again science has shown that evolution works, it can be observed in detail and there is no sign of any intelligence or any planning in the process. No wonder creationist get so upset when this long-running experiment is mentioned and quickly redefine evolution.


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