Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

Matthew D. Herron and Michael Doebeli. PLoS Biology 11(2): e1001490. DOI:10.1371/journal.pbio.1001490. Parallel evolutionary dynamics of adaptive diversification in Escherichia coli.

Below, we give our first impressions of this article. Please comment below, or tweet Will or Lynsey (maybe use #pegejc). Think of this as a journal club discussion group!

Will Pearse

Will Pearse

This is another article that pushed me outside of my comfort zone; I know nothing about bacterial ecology, and probably even less about bacterial evolution. However, this is a very neat demonstration of how bacterial approaches can shed light on questions biologists have been asking for decades: what would happen if we turned back the clock and started evolution afresh?

According to this paper, very similar things. The authors find that bacteria exposed to the same conditions evolved the same kinds of responses, and split into the same kinds of species. Us big-bodied ecologists know that things like this can happen in species like Anolis lizards, but we don’t have the ability to turn back the clock, do the whole thing again, and sequence the genomes of everything while it’s happening. Indeed, while Anolis lizards have radiated into similar niches, I’m not sure there’s evidence that they underwent mutations at exactly the same loci. To be precise, these mutations happened in the same genes, and in the same order, but were not at the exact same points in the genes. This is still amazing, and I guess makes it less likely that we’re just picking up mutations that were previously at too low a frequency to be sequenced.

I wonder what effect gene transfer has on all of this. I’m happy to admit that these are distinct ecotypes, but I’d be surprised if the bacteria weren’t able to share genes. Thus it seems that this is the perfect example of reinforcement driving the generation of these ecotypes – becoming half of one ecotype and half of the other must be maladaptive, and this is something that could be experimentally tested. Thus despite the ability to rapidly ‘hybridise’ and share genes, the bacteria don’t, or rather those that do die out. I imagine it’s the frequency-dependent ‘clonal niche construction’ mechanisms the authors discuss that help this get going to begin with – otherwise the first variant to evolve would dominate the entire assemblage. I wonder to what extent such dynamics are a consequence of constant environmental conditions that allow these biotic interactions to play out.

Lynsey McInnes

Lynsey McInnes

I have a soft spot for experimental evolution. I think it’s because I know, and like, simulation studies and experimental evolution seems like the elusive next step. Elegant, tractable and yet also more ‘valid’ than the clinical world of simulations where, some might say, you get out what you put in. One day, perhaps, I’ll have the guts to team up with these people and step out of my simulated world.

The beauty in these setups include the opportunity to have multiple replicate ‘runs’, for evolution to occur relatively fast and with the possibility to take samples during the run to monitor the trajectory of diversification, to manipulate the ‘environment’ of each run while minimising variation from the outside the system. Mmmm…

Anyways, I digress.

This paper builds on previous work from the Doebeli lab and I think provides a neat addition, capitalizing on advances in sequencing technology to really get at how parallel the dynamics of adaptive diversification can be. I found the conclusions – that the dynamics of diversification follow the same trajectory across populations and that this sometimes involves parallel mutations, sometimes not, really quite cool. That different mutations at the genetic level can lead to the same derived phenotype was also a very neat finding. The authors also make a convincing case that the patterns observed are due to frequency-dependent ecological interactions rather than genetic drift or clonal interference.

The introduction touches upon sympatric speciation and how frequency-dependent selection can cause it; the authors seem to shy away from this still controversial topic in their discussion. This is perhaps fair enough, they make their case briefly and then stick to the study in hand, although the implicit message throughout is that this study is providing further evidence for the feasibility of sympatric diversification.

My following of the literature on sympatric speciation is a bit patchy (although I know Doebeli has made some major contributions) although I have had countless relatively uninformed discussions on its prevalence in macroscopic speciation, me spouting that there is probably some kind of microallopatry going on, my opponent countering that such a setup might still be considered sympatric. Anyways, this paper was one of the first to effectively explain how frequency-dependent selection might lead to ‘sympatric’ speciation. My mind is now whirring as to how this mechanism translates up out of this microcosm setup.


About will.pearse
Ecology / evolutionary biologist

2 Responses to Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

  1. ellie says:

    I had to comment on this one because I was so excited to see you reviewing this paper! It’s one that I’ve been gradually reading over the last week as we’re thinking of looking closer at some of our experiments in this way, so it’s really interesting to see it through a macro-lens.

    There has been a lot of excitement around applying whole genome resequencing to experimental evolution and this is one of neatest examples I’ve seen so far. It’s actually kind of amazing how we talk so much about selection and adaptation but we’re only really able to delve into the anatomy of it now. For example, I’m used to thinking of sweeps in these homogenous environments as being complete, so you get a progression of trendy new mutants replacing crapper ones. But in this paper you see stable coexistance of, not only different the niche specialists, but also several lineages using the same niche – which is the bit I find more surprising. I guess this is more driven by clonal interference, though of course they could also be exploiting some other unidentified niche

    Will, I liked your ponderings on gene transfer. I doubt it would feature hugely in this experiment (from what I can tell the strain didn’t contain any of the drivers of gene transfer – plasmids, phages etc – and E. coli are a bit pants at doing it themselves), but I think the question of whether the inclusion of those mechanisms would help or hinder this type of diversification is super interesting!

    • will.pearse says:

      Well, just goes to show what I know about bacteria 😦 However, I guess they wouldn’t have to do it that often for it to be an issue, right? Most models of large-animals only require a small amount of outbreeding to create trouble…

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