Field of Science

What happens to bacterial communities under selection?

When one gene comes under a new selection pressure, a population can respond by increasing the frequency of the better alleles. This can involve directional selection, whereby the population shifts towards the new optimum, and/or it can entail stabilizing selection, where the genetic diversity of the population decreases. In both cases allele frequencies change, and this is what (biological) evolution is.

This is all fairly straightforward. However, when there are many populations that are distinct species, and they all come under the same new selection pressure, then what is that? If we can detect selection between these distinct populations, is that still evolution? It is not evolution in the traditional sense, which center its attention on what happen within a population. So if we’re not looking at what happens within one population, can we even say that we are studying evolution?

In a previous post I explained how we have used metagenomics to retrieve DNA sequences of a specific gene called nitrite reductase (nirK) that soil bacteria use to obtain energy from fertilizer. When sequencing the soil only a limited set of sequences are discovered. Imagine then that some species are more abundant in the soil than others. Because it is random with respect to which species they come from, we are then clearly more likely to retrieve sequences from the most abundant species. There are many bacterial species that has a copy of nirK, and we are limited in how many sequences we can obtain. Many species will therefore not be represented in our sample.

Now, comparing these sequences is done using the formalism of dN/dS, which measures the ratio between non-synonymous nucleotide substitutions and synonymous substitutions (substitutions that change an amino acid vs. those that do not). dN/dS (also designated by ω) is measured between species, so it is perfect for the sequences we have. The analysis showed that ω is very low, indicating purifying selection – there are more synonymous nucleotide changes compared to non-synonymous changes than expected if both were equally likely. That means that nirK is being constrained and optimized, presumably because the gene carries out an important function for the bacteria. Changes to the resulting protein are not tolerated, though a little variation in the amino acid sequence between the species does exist.

Furthermore, different environments were compared. In one environment, deciduous forest (DF), the soil is not fertilized. In another environment used for standard agriculture (AG), the soil is fertilized. The analysis showed that the sequences in AG are under stronger purifying selection than sequences in DF (figure 1). Presumably this is because the conditions in AG make it more favorable and more important to have a really good copy of nirK that can help the bacteria to obtain energy from the nitrate in the fertilizer.

Figure 1. dN/dS is smaller in Ag than in DF, indicating that there is stronger purifying selection in AG compare to DF. ES and SF are environments that have not been used for agriculture for about 20 and 40 years, respectively.

So far, so good. Now here is my question. Given that the bacteria experience purifying selection, do we really know what is happening to the community of species? Take a look at the following figure.

Figure 2. An artist’s representation of different populations in two-dimensional amino acid space. Click to enlarge.

The farther sequences are from each other, the fewer amino acids they have in common. In (A) several species of bacteria can be seen, each represented by a Gaussian distribution, where the darkest points are the more abundant sequences. The red cross represents the optimal sequence (need there be only one?), but because bacteria in DF get most of their energy from oxygen, nirK is of relatively little consequence. In (B) and (C), AG has been loaded with fertilizer, so now there is ample opportunity to get energy from that. Therefore the species experience a pull towards the optimal sequence. In (B) this results in each of the population shifting their distribution towards to optimum, while in (C) they do not shift, but instead the species that are already closer to the optimum experience an increases in carrying capacity, such that they become more abundant compared to species that are farther away from the optimum.

dN/dS basically measures this distance in amino acid space, and clearly this distance is on average diminished in (B). However, because we are more likely to retrieve sequences from the more abundant species, the average distance between sequences is also diminished in (C). In other words, both models are consistent with dN/dS being lower in AG, and we therefore cannot say what is really going on in the soil. Is there a way to distinguish between the two models? Could we take some bacteria to the lab and grow them under DF and AG like conditions, and then figure this out? Is there a third model that can explain the data as well?

And then the question of evolution – is this even evolution? Some biologists simply call this species sorting, and dismiss that it is evolution. However, I argue that it is evolution, because what we are observing is the effect of natural selection, which in (B) causes a change in allele frequencies within each population, and in (C) because it changes abundance that can lead to long-term changes in community structure.

Evolution or not? What do you think? Cross-posted on BEACON's blog.


Some times very technical papers are published that would be very good for me to read. Papers that on title don't look very sexy (to me). On the details of psedogenization, for example, whereby a functional gene becomes unexpressed, meaning it does not produce a protein anymore. Who knows if I will get around to it.

But then there are papers like this one, which I will get around to read: Environmental change exposes beneficial epistatic interactions in a catalytic RNA. That should be a good read about the impact of dynamic fitness landscapes (when fitness is not a static function of genotype or phenotype, but changes as the environment changes.

  • Genomic consequences of multiple speciation processes in a stick insect 
  • The Nearly Neutral and Selection Theories of Molecular Evolution Under the Fisher Geometrical Framework: Substitution Rate, Population Size, and Complexity 
  • Estimating the Strength of Selective Sweeps from Deep Population Diversity Data Biology of the sauropod dinosaurs: the evolution of gigantism 
  • The role of gene flow asymmetry along an environmental gradient in constraining local adaptation and range expansion 
  • Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation 
  • Specific inactivation of two immunomodulatory SIGLEC genes during human evolution 
  • Cast adrift on an island: introduced populations experience an altered balance between selection and drift 
  • Environmental change exposes beneficial epistatic interactions in a catalytic RNA 
  • Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae)

Oh, and no new creationist science paper published since last week.

CoE poster for Ottawa

BEACON has a booth at Evolution 2012 in Ottawa, and they have invited me to put up a poster about Carnival of Evolution.

Here's a draft. Let me know what you think, plz. (Click image for larger version.)

China is a dictatorship

The fact that Hu Jintao refuses to talk to the Danish press as he visits Denmark next week. Apparently he never has in China either, in the almost ten years that he has been General Secretary, President, etc. etc.

Right now, as I search Google news, all articles fail to mention that the Danes are very skeptical towards a state leader that won't meet the press, and who leads a country whose politics oppresses its own people (no freedom of speech, no democracy, massive violations of human rights), but it is all over the Danish news (in Danish, sorry). He runs a dictatorship, basically. Thanks to Mao.

Hu Jintao, with slight editing.


This is only a fraction of the new papers on research in evolutionary biology from the last week or so. How many creationist papers have been published in the same time-span?

  • The Evolution of Patch Selection in Stochastic Environments
  • Local Adaptation along Smooth Ecological Gradients Causes Phylogeographic Breaks and Phenotypic Clustering
  • Tradeoffs limit the evolution of male traits that are attractive to females
  • Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli
We may, as evolutionists (a term that I take to mean those who believe in evolution*) be frustrated with creationists, because they so incessantly refuse to give up dogma and take the evidence from nature at face value.

However, some years ago I realized how much more frustrating it must be for the creationists that the experts all but a few loonies believe in evolution, that all the evolution research in universities confirms evolution, and that nearly everyone who aren't a creationist because of their religious beliefs believe in evolution. The creationists (at least the ones who aren't ignorant and boneheaded) know that the evidence is on our side, and that must be excruciatingly frustrating.


 * You may refuse to use the word believe in this context, and insist that we say "accept evolution", but then you don't read enough dictionaries.

Kreativ Blogger {award}

I've been chosen for the Kreativ Blogger award chain letter*. I'll play along.

Rules: link to the blog who nominated you, say seven things about yourself that readers may not know, list seven other blogs that you feel deserve the award chain letter and let them know, and include the Kreativ Blogger logo. Here goes:

Dear friends, I wish to send my heartfelt thanks to my (new) dearest friend, Gunnar De Winter of The Beast, the Bard and the Bot for thinking of Pleiotropy (it is an important concept in genetics). I would not be here without him.

And friends, you probably didn't know about me that I
  1. don't believe in free will, 
  2. am an optimist-pessimist-optimist, 
  3. want to try to be homeless, 
  4. want to try to be pregnant, 
  5. have eaten cod uterus, 
  6. taught myself to play guitar and piano,
  7. currently have a Klout score of 44
Lastly, here are six blogs that warms my heart:

* Today, about 870,000 results Googling "Kreativ Blogger award", and about 324,000 results in Google images.

Carnival of Evolution on Pharyngula

The June edition of Carnival of Evolution is now live on Pharyngula: Carnival of Evolution #48: The Icelandic Saga!

There are nearly 50 posts written by some amazing science bloggers. I seriously wonder when CoE is going to reach that tipping point where close to all evolutionary biologists know about it, and looks forward to some more or less light reading about diverse topics in evolution every month.

Follow CoE on Twitter @CarnyEvolution
Like CoE on Facebook


Wondering, with all the time in the world, would we even do all the things we say we would if we had all the time in the world?

How does that even work? By saying all the time int he world, do we mean that time will stand still at our command, while we can do what we want in the "meantime"? Or does it mean to live forever, in which case I don't think I would use my immortality to read these papers?

  • Density-dependent fitness benefits in quorum-sensing bacterial populations 
  • On the Evolution of Personalities via Frequency-Dependent Selection 
  • Fitness conferred by replaced amino acids declines with time ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli 
  • Species Interactions Alter Evolutionary Responses to a Novel Environment 
  • Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution 
  • Metopic suture of Taung (Australopithecus africanus) and its implications for hominin brain evolution