Posted by: Jeremy Fox | July 8, 2012

Evolution 2012: Saturday notes (UPDATED)

Greetings from Evolution 2012 in delightfully summery Ottawa. My hometown of Calgary experienced an intense hailstorm centered on my house the day before I left for the meeting. I took this as an indication that it was a good time to get out of town for a few days.

The conference center is only about a year old and it’s great. Beautiful views of the canal and Parliament Hill. Just the right size for the meeting. Very easy to get back and forth between different rooms. Many of the seminar rooms are down short little hallways and so don’t open directly onto the main gathering spaces, which is good because it minimizes the noise from conversations outside the rooms.

And there are free boxed lunches! I didn’t know lunch was included. That was like the culinary equivalent of finding money in your pocket that you didn’t know you had. 😉

p.s. In light of my deranged post about the chimes, I suppose you’re all wondering what I think of them. The answer is I don’t mind them as much as I thought I would, but I do mind them a little bit. I’d probably mind them less if they were having the intended effect more consistently. The first few talks I saw were very careful about using the chimes to time the talks as intended. But later in the day I saw many talks where one talk ended early, and so the next speaker started early, thereby defeating the purpose of the chimes. The presiders are presumably supposed to prevent this, but I think many presiders were just relying on the chimes and so not stepping in when speakers ignored the chimes. And as I expected, even when the chimes are adhered to, people are still coming in and out of the rooms while the talks are beginning and ending, simply because it takes more than 60 seconds to walk between even closely-spaced rooms. Please don’t get me wrong, I’m really enjoying the meeting, the chimes aren’t a big deal, and my opinion about the chimes is just my personal opinion. I’m sure many attendees think the chimes are great and many others don’t mind them at all.

Here are some highlights from what I saw today:

My colleague Sean Rogers did a great job summarizing his work on the genomics of ecological speciation in fishes. Very clear and very deft, compact and dense in a good way, without needing to resort to genomics jargon.

Tristan Long gave a great talk on a really clever experiment, selecting for fruit flies that can count. Yes, you can do this, apparently. You basically select for flies that, in response to an adverse stimulus, move towards a sequence of two light flashes rather than three, or three rather than four. And you have to be very careful about randomizing the properties of your flash sequences, to make sure the flies are “counting” the flashes rather than going by the total amount of time the lights are on, or the time between flashes, or the total time of the flash sequences. I envision a future in which math classes will be taught by highly evolved flies.

Anita Melnyk presented a nice series of experiments showing that Pseudomonas bacteria adapting to growth on xylose experience a more “rugged” fitness landscape than when adapting to growth on glucose. Which, as she noted briefly in the questions, is exactly the opposite of what you might have expected, given that these bacteria can metabolize glucose via two distinct biochemical pathways, but can metabolize xylose by only one. Predicting genotype-phenotype maps is hard, even for simple, well-known organisms; I’m curious if that’s something people will try to have a go at more frequently in the future.

Melanie Mueller talked about a very simple and elegant system using microbial colonizes growing on plates as a model system for studying selective sweeps in the context of populations undergoing spatial spread. Basically, it involves inoculating mixtures of different colored bacteria at a single point, and the resulting colony exhibits pretty, well-defined colored bands that change in size in predictable ways depending on the relative fitnesses of the different bacteria. Indeed, I actually wonder if the system is a little bittoo elegant, to the point of being too simple to really teach us anything new. It almost came off as engineering rather than science.

Andrew Furness talked about adaptive plasticity and bet-hedging in a really cool system, annual killifish that live in temporary ponds that dry every year. The timing of pond filling and drying is somewhat predictable (there’s a wet season, associated with reliable temperature and light cues), but somewhat unpredictable. And so as you’d expect, the fish lay diapausing eggs that initiate (and even pause!) development in response to cues, but that also develop and hatch somewhat randomly (thereby hedging their bets, rather than going “all in” in response to a possibly-unreliable cue).

Noah Ribeck explained how we’ve all been incorrectly estimating the strength of frequency-dependent selection (whoops!) The standard way to do it is to vary the initial relative frequencies of two different genotypes, then after some period of time measure their relative abundances again, and from that calculate what the selection coefficient was as a function of initial relative abundance. Which of course isn’t quite right, because you’re assuming that selection at any given initial frequency is constant over time, which it can’t possibly be in a system with frequency dependence (by definition, frequency-dependent selection coefficients change as relative abundances change). Noah derived the correct way to calculate selection coefficients for this sort of experiment, and showed that the resulting estimates differ substantially from those estimated via the usual method when frequency dependence is strong (so that relative abundances change a lot during the experiment).

Pedro Gomez did a nice poster asking how Pseudomonas fluorescens diversifies when grown under semi-natural conditions. In highly artificial lab conditions (unshaken, 6 ml batch cultures), P. fluourescens is a model system for adaptive radiation: it repeatedly diversifies into ecologically-distinct morphotypes, the two main ones being “wrinkly spreaders” and “smooths”, named for their colony morphologies when plated on agar. In nature, P. fluorescens lives in soil. And if you culture it in soil…wait for it!…it diversifies into the same frickin’ morphotypes as it does in batch cultures! Which is kind of amazing because the very specific spatial structure of batch cultures is thought to be what drives the repeatable diversification into these particular morphotypes, which occupy distinct spatial locations in batch cultures. Apparently this organism is a one trick pony! The match between the batch culture and soil diversifications is actually even tighter than that. In batch cultures you typically see a couple of different subtypes of smooths, and three or four subtypes of wrinklies–and you see all the same subtypes when you do the experment in soil! Now, it’s worth noting that in batch cultures you actually need rather specific culture conditions (e.g., specific growth medium) for the radiation to happen. And apparently those specific batch culture conditions are actually a really good analogue for this organism’s natural habitat! Who says laboratory microcosms are unrealistic?

Other notes:

“Eco-evolutionary dynamics” is hot. That kind of surprised me. I of course knew that it was hot in ecology, but I had thought that the proper evolutionary biologists would kind of dismiss it, since a fair bit of work by ecologists on “eco-evolutionary dynamics” treats the evolutionary side in kind of a weak way (a lot of it doesn’t, of course). But I’ve already seen a number of talks by people from proper evolutionary labs that sound just like the sorts of talks I’ve been seeing at the ESA meeting. Indeed, there’s a symposium on eco-evolutionary dynamics tomorrow that includes several speakers from a symposium on the same topic at the ESA meeting last year. I’m not complaining or criticizing this at all, it’s just something that surprised me a little.

Paralellism and convergence is hot. Under what circumstances is convergent evolution at the phenotypic level underpinned by the same mutations, or mutations at the same loci? But people mostly seem to be taking a case study approach to this. Maybe it’s just the brevity of the talks, but I haven’t seen any so far that have tried to place their results on this in a larger comparative or theoretical context. I don’t know, maybe we don’t yet have enough data or theory to make that worthwhile?

I saw a couple of talks on experimental bacterial evolution that pretty much came down to cross feeding (bacteria evolving to live off the metabolic waste products of other bacteria). That cross feeding evolves easily under certain culture conditions has been well-known for a long time, both experimentally and theoretically. I think it would’ve been nice to see recent work placed in the context of that literature–I wasn’t clear on if we’d learned anything really new about cross-feeding that we didn’t know before.

UPDATE: Post title corrected; it was late at night when I wrote it and for some reason I slipped into thinking I was at the ESA, where the first day of talks is always Monday.

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