Today marked the first day of the Qbio course!

Kicked off with Paul Rainey giving a talk about microbial ecology. He started off talking about a system of Pseudomonas with three different types: wrinkly, smooth, and fuzzy. They have some non-trivial frequency dependent selection where each one can invade the other, and he described some experiments to characterize them.

He then talked about an experiment which may be one of the ones I get a chance to work on, involving soil bacteria. They took some samples from compost, and put them in minimal media with some paper (cellulose) as the main carbon source. One set of 10 lines was passaged with serial dilution (and new paper) every two weeks. Another set was passaged similarly, but with filtered “phage juice” added as well. The “juice” was made from liquid from all 10 lines mixed and filtered down to virus/dna particle sizes. The idea here was that one set of lines had the possibility for “migration” of genes - no individual bacteria making it through, but genomic elements getting to migrate between populations.

The hope was that if an adaptive mutation/beneficial gene rose to high levels in one population it would be sent to others, and then incorporated via horizontal gene transfer. They have whole genome sequences for some individuals at the last timepoint, and then compared shotgun metagenome reads to these whole genome sequences to see if they lineup. They claim that there are large “gaps” whose emergence can be tracked through time (and between lines in the case of the second experimental condition), which suggest a large amount of horizontal gene transfer. It’s a cool experimental idea, and I would be curious how strong that evidence of horizontal gene transfer actually is, and to try to falsify different scenarios. Would also be cool to see if one can back out things about the evolutionary dynamics, and maybe even the incorporation rates of horizontal gene transfer from those data.

The third section of his talk was quite interesting - talking about the possibility of selection on the level of the community. The question was: how can you get emergent behavior where selection/heritability occur on the level of some collection of types rather than just a few? A toy example given was a model of growth with spatial structure - where there were patchy resources, and organisms had to travel from patch to patch. There was a tension between fast growth at short timescales (growing to take over your patch), and surviving long enough to transmit yourself to another patch. You could find regimes where guys who grew more slowly would, in the long term, win out. With a similar setup you could also, in the right parameter regime evolve a steady frequency of “altruistic” types which were sterile, but conferred a fitness benefit to their downstream offspring.

This was a pretty interesting idea - that a multi-step growth dynamic with separation of timescales could lead to stabilization of diversity in some way, and lead to types being generated/surviving which wouldn’t get a chance to in simpler environments. In some sense this goes against the notion of “fitness” that can be used to simply quantify evolutionary outcomes; in another way it just says that what we call fitness might have to be coarse grained over the appropriate scale, and depend on certain higher order moments/spatial averages of the system (ie frequency dependent selection). I wonder if this sort of idea could be deployed to explain the existence of other cheater systems. I also wonder what consequences this has for the role of stochasticity/differences in local population structure. Could this stuff be tied into Michael (Pearce)’s spatial structure models? This also reminds me of classic antagonistic pleiotropy stuff, like how flies may make themselves more mortal in order to have more early life growth.

He then talked about experimental setups where one could select “at the community level” by explicitly selecting for mixed populations. In simulation you can do this in the right regime. I found this one a lot more artificial and a lot less compelling; it reminds me of ecology models where the niches are “put in by hand”. I’ll have to think more about the original example, and what that might say about what sorts of models/scenarios might be interesting to think about.

We also had the project presentations. I think I’ll talk about them more in subsequent posts, since I’ll be working on one or two of them in the following weeks. Needless to say I think there are a few exciting ones that hopefully I’ll get to do some cool stuff with. Stay tuned!