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Study: Darwinian fitness does not overcome mutational decay during tens of thousands of bacteria generations

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E. coli 1000x/USDA

With comments by Michael Behe.

The finding is a setback for origin of life theories that depend on conservation of favorable mutations. Creation-Evolution Headlines draws our attention to a very recent paper on the Lenski long-term evolution experiment (LTEE) which shows that, contrary to hopes, Darwinian fitness did not overcome mutational decay: “Here, we document the rapid genome decay of hypermutable bacteria even during tens of thousands of generations of sustained adaptation to a laboratory environment.”

Abstract: Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolutionary biology, despite long-standing debate about the relative importance of natural selection, mutation, and random drift. A potentially important confounding factor is the variation in mutation rates between lineages and over evolutionary history, which has been documented in several species. Mutation accumulation experiments have shown that hypermutability can erode genomes over short timescales. These results, however, were obtained under conditions of extremely weak selection, casting doubt on their general relevance. Here, we circumvent this limitation by analyzing genomes from mutator populations that arose during a long-term experiment with Escherichia coli, in which populations have been adaptively evolving for >50,000 generations. We develop an analytical framework to quantify the relative contributions of mutation and selection in shaping genomic characteristics, and we validate it using genomes evolved under regimes of high mutation rates with weak selection (mutation accumulation experiments) and low mutation rates with strong selection (natural isolates). Our results show that, despite sustained adaptive evolution in the long-term experiment, the signature of selection is much weaker than that of mutational biases in mutator genomes. This finding suggests that relatively brief periods of hypermutability can play an outsized role in shaping extant bacterial genomes. Overall, these results highlight the importance of genomic draft, in which strong linkage limits the ability of selection to purge deleterious mutations. These insights are also relevant to other biological systems evolving under strong linkage and high mutation rates, including viruses and cancer cells. (paywall) – Alejandro Couce, Larissa Viraphong Caudwell, Christoph Feinauer, Thomas Hindré, Jean-Paul Feugeas, Martin Weigt, Richard E. Lenski, Dominique Schneider, and Olivier Tenaillon, Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria, PNAS

Michael Behe, who studied the question in Edge of Evolution, (and came to similar conclusions about the limitations of Darwinian evolution) says,

This article actually goes very well with the new Lenski article. The Lenski article shows that “mutator” strains of E. coli constantly degrade, even under selective conditions. Now, the “mutator” strains aren’t that bad. They have DNA repair rates about 100-fold greater than normal. However, “normal” is about 1 mutation per 10exp10 nucleotides. That means the “mutator” rate is about 1 mutation per 10exp8. Since E. coli’s genome is only about 4 million base pairs, that means only one new mutation occurs for every 25 E. coli cell divisions — far above the “error catastrophe” limit of 1 or more mutations per cell division.

That’s really a very impressive repair apparatus. Nonetheless, Lenski’s new work shows that even that would not be sufficient to allow life to succeed. Thus, in origin-of-life scenarios, one couldn’t expect repair mechanisms to evolve gradually. They would have to be astoundingly good from the beginning.

Incidentally, a cancer researcher wrote us to say that, actually, Darwinian evolution can promote lack of fitness, as follows:

Impairment in DNA repair is one of the chief risk factors for cancer development. BRCA1 and BRCA2 are prime examples. I like to say cancer is a great example of Darwinian evolution as it is well accepted that the best adapted cells survive and propagate to ultimately become an aggressive tumor. But cancer represents a loss of functions – the ability of a cell to regulate itself properly. While cancer does follow Darwinian principles well, it always tends towards a condition that is disadvantageous to the host.

See also: Are blind cave fish breaking the laws of evolution? We know that the ducts need cleaning in the evolutionary biology building when people think there are laws of evolution, in a strict sense, and that the Big Worry is that if a claim for Darwinism is better explained by epigenetics, the proponents of epigenetics will sneak in religious ideas…

and

From Biology Direct: Darwinism, now thoroughly detached from its historical roots as a falsifiable theory, “must be abandoned” (The author sounds serious.)

4 Replies to “Study: Darwinian fitness does not overcome mutational decay during tens of thousands of bacteria generations

  1. 1
    Bob O'H says:

    Yes, this show that selection can’t overcome mutational decay. But is shows it in hypermutable bacteria. In other words, their genomes are being degraded faster than selection can work to remove the mutations from the gene pool. But with a lower mutation rate, there will be less mutational pressure, so it will be easier for selection to overcome mutational decay.

  2. 2
    ET says:

    Well Bob, until proof-reading and error-correction “evolved” (as if it could without intelligent direction), hypermutable bacteria is all you would have. And it looks like from that you wouldn’t get much further up the tree of life.

  3. 3
    PaV says:

    Bob O’H:

    So, NS slows down “mutational decay.” How does that get you 20 plus phyla showing up in the Cambrian?

    I’m reading Nei’s latest book, and obviously NS is being abandoned. I’m not at that part yet; but, you can see it coming.

    Now I know the kind of “evolutionary biologist” wd400 is. He’s completely aligned to genetic drift.

    But, of course, this means that the “theory of evolution”–which is a FACT!–has become unhinged from NS. So, Darwin’s theory no longer applies. What would “evolutionary biologists” like to replace it with?

  4. 4
    gpuccio says:

    Bob O’H:

    “But is shows it in hypermutable bacteria.”

    I would say that it shows it in hypermutable bacteria and extreme environmentals selective pressure in the lab.

    Where is all the past enthusiasm for Lenski’s experiment as a model for evolution?

    From the paper:

    Significance

    Bacterial genomes are extremely diverse in size and composition. Biologists have long sought to explain such variability based on present-day selective and mutational forces. However, mutation rates can change dramatically over time, and experiments with hypermutable bacteria show that their genomes rapidly decay when propagated under the near absence of selection. Whether selection can prevent this decay is unclear. Here, we document the rapid genome decay of hypermutable bacteria even during tens of thousands of generations of sustained adaptation to a laboratory environment. These findings suggest the need to reexamine current ideas about the evolution of bacterial genomes, and they have implications for other hypermutable systems such as viruses and cancer cells.

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