Major new analysis of the LTEE published today


(Stephen Matheson) #1

A big new paper was published in today’s issue of Nature, reporting extremely in-depth details on the 12 populations that have been evolving in the LTEE for almost 30 years. I just did a quick read and have read the accompanying News & Views piece by Josh Plotkin. There are some very interesting new findings in the paper, and there’s an emphasis on ecology that might seem unexpected (given that the experiment involves nothing more than bacteria in liquid broth swirling in a flask) and that should bring a smile to some faces around here. (I’m looking at you, @Relates.)

The paper (“The dynamics of molecular evolution over 60,000 generations”):

Plotkin commentary (“Molecular evolution: No escape from the tangled bank”):

Here is the abstract of the paper:

The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population. Interactions between ecological and evolutionary processes play an important role, as long-term quasi-stable coexistence arises spontaneously in most populations, and evolution continues within each clade. We also present evidence that the targets of natural selection change over time, as epistasis and historical contingency alter the strength of selection on different genes. Together, these results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed.

Their final paragraph:

Together, our results demonstrate that long-term adaptation to a fixed environment can be characterized by a rich and dynamic set of population genetic processes, in stark contrast to the evolutionary desert expected near a fitness optimum. Rather than relying only on standard models of neutral mutation accumulation and mutation–selection balance in well-adapted populations, these more complex dynamical processes should also be considered and included more broadly when interpreting natural genetic variation.

This is the first paragraph of Plotkin’s piece:

At the end of On the Origin of Species, Charles Darwin describes a tangled bank — an ecosystem of plants, birds and insects whose evolution is inextricably linked by their dependence on one another for survival. Researchers who study evolution in the wild must contend with the tangled bank. Controlled laboratory experiments provide an alternative approach that may avoid the complexities of ecological interactions. But in a paper online in Nature, Good et al. analyse evolution in laboratory populations of bacteria and make a surprising discovery: ecological interactions emerge spontaneously and sustain evolution by natural selection for tens of thousands of generations.

One thing that jumped out at me on my first reading of the paper: they saw strong evidence of clonal interference and hitchhiking, through the whole (long) history of the experiment. They describe the model of molecular evolution they see in the LTEE as “quasi-neutral,” with fixation probabilities far lower than expected under simple selection. (It was a quick reading…I think I have that right…maybe @T_aquaticus and/or @agauger can jump in to comment on the findings.)

I don’t think either the paper or the News & Views piece are open access. I can help you get a copy of either or both on request.


(Ann Gauger) #2

Thanks. I’ll try to take a look.


#3

There is a lot to unpack from that paper, and I wish they had more specifics about the genes that were mutated, how those genes relate to one another, and specifics on gene losses and gains. As Ann’s own work has shown there can be conditions where selection drives gene loss, so it would have been cool to see what their findings were. I quickly looked up the asterisked genes from Fig 6, which are genes that showed significant numbers of mutations in parallel populations. They seem to be genes involved in metabolism and heat shock response. Adaptations involved in digesting food and stabilizing other proteins seems to be two pathways that were taken by more than one population.

Population genetics isn’t my strong suit, but from what I can understand there were expected and unexpected results. If you are using the fitness landscape analogy, as you get closer to the most fit phenotype there will be fewer and fewer changes that improve fitness. This seems to play out in their experiment where increases in fitness slowed down through time. However, beneficial mutations seemed to sweep through the population just as quickly in later generations meaning that the difference between fitter and less fit was still significant enough to drive selection.

Overall, it is a pretty cool paper that takes a macroview of the evolution of these unique populations. Kudos to Lenski for having the foresight to keep this experiment going through all of those years.


(Roger A. Sawtelle) #4

@sfmatheson

Stephen,

This does appear to vindicate my understanding of ecology and evolution.

Thank you for the heads up and thinking of me…


(Steve Schaffner) #5

We’ve got a small evolutionary reading group that meets every other week. I think I’ll schedule this paper for a meeting soon.


(system) #6

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