This Week in Evolution

I always enjoy Olivia Judson's columns in the New York Times, but today's post on evolution "failing" left out an important point. She referred to a paper published last year from Richard Lenski's long-term evolution experiment, showing that a bacterial population took 31,000 generations to evolve the ability to use citrate. Furthermore, although she didn't mention this, this trait has only evolved, so far, in one of their twelve replicate populations. If evolution is too slow to keep up with the changes we humans are making in the environment, then species that might evolve and survive if changes were slower will instead go extinct.

I agree that this is a significant problem, but I wouldn't assume that it would take polar bears, for example, 31,000 generations to evolve adaptations to warmer temperatures. The bacteria that Lenski's group studies don't have sex. So if one cell has a mutation that would allow it to use citrate, but only in combination with a second mutation found in another cell, they don't have any way to combine the two mutations in one citrate-using individual. If cells with only one mutation or the other have no advantage over cells with neither, then lineages with the first mutation will usually die out before acquiring the second mutation. A lineage could die out, for example, because the next mutation is gets is one of the many lethal ones, rather than one of the few beneficial ones.

Bacterial populations can sometimes evolve rapidly (with significant changes in only a few days) because their generation times are so short and because their large population sizes include many mutants. Evolution requiring a series of steps isn't a problem so long as each step is an improvement. But when a mutation is neutral or negative, except in the context of a second mutation, sexual species can evolve faster. Not necessarily fast enough to save the polar bears, though.

Posted by R. Ford Denison at 5:08 PM | Permalink | Comments (2)

Guest blogger: Will Ratcliff

This week's paper, "Experimental evolution of bet hedging" by Hubertus Beaumont, Jenna Gallie, Christian Kost, Gayle Ferguson and Paul Rainey, published in Nature, shows that a trait that initially evolves for non bet hedging purposes can be maintained in the population through bet hedging.

The theory of bet hedging was first mathematically developed by Daniel Bernoulli (yes, the Bernoulli we all learned about in high school physics) in 1738. Because the basic idea is so simple - uncertain future conditions make conservative strategies beneficial - it is likely that folk wisdom advising bet hedging long predates Bernoulli's maths. The phrase "Don't put all your eggs in one basket" is one example of a widespread but anachronistic reminder to spread risk. Before we dive into this week's paper, I want to briefly cover the theory of bet hedging.

Like investing in the stock market, evolution is a multiplicative process, not an additive one. Steve Stearns (2000) illustrates this well....

Continue reading "Experimental evolution of bet hedging" »

Posted by R. Ford Denison at 7:42 PM | Permalink | Comments (7)

Richard Lenski and colleagues have been monitoring evolution of the bacterium Escherichia coli in his laboratory for 40,000 generations. Their latest paper, "Genome evolution and adaptation in a long-term experiment with Escherichia coli" was recently published in Nature.

One nice thing about E. coli is that they can freeze samples of their evolving populations every few thousand generations, for later analysis. So they were able to compare the fitness of different generations by competing each against a thawed ancestor. They also found the complete DNA sequence for many of these strains....

Continue reading "Experimental evolution meets genomics" »

Posted by R. Ford Denison at 9:37 PM | Permalink | Comments (0)

"I show that a similar cost of sex exists when asexual mutants arise... but not when the species is a self-fertile hermaphrodite.... Although individual fitness (expected reproductive success) is assumed to be equal for sexual and asexual females, the heritability of fitness is... twice as high in asexual females" -- Richard Michod, Darwinian Dynamics

I should be working on my book, but a paper that just came out in Nature got me thinking about sex. A population with half males and half females will grow only half as fast as one consisting only of females that self-fertilize or clone themselves. So, many people have asked why sex evolved.

That's an interesting question, but I'm not sure about the rationale. As noted by Michod, a population of self-fertilizing hermaphrodites doesn't have any intrinsic growth advantage over a population of hermaphrodites that mostly cross-fertilizes. So is the problem sex, or males?

Evolutionary changes in gene frequency over generations depend on whether individuals with a given gene survive and reproduce more than other members of their population, not on the consequences for overall population growth. (Individuals can move between populations.) So we really have two related questions:
1) why do genes for producing male offspring persist? and
2) why do genes for cross-fertilization persist in species that can self-fertilize?

From an individual perspective, it's not apparent that producing male offspring is always a bad idea. Do couples with two sons have fewer descendants than those with two daughters? It can depend on the sex ratio in the population. If a human couple produces one offspring of whichever sex is in the minority, their offspring may have an easier time finding a mate.

But what about cross-fertilization? If a female cloned herself, her offspring would have all of her genes, rather than just half of them. So the frequency of genes for self-fertilization would tend to increase, unless individuals resulting from cross-fertilization were more likely to survive and reproduce. An offspring with half as many of one's genes, but a 2.1-fold better chance of survival (maybe because a sexual partner contributes different disease-resistance genes) gives a greater increase in fitness. So, one key to understanding the evolution of sex (cross-fertilization) is to measure the survival of individuals with one parent versus two, under conditions that plausibly occurred at critical points in a species ancestry.

This week's paper, "Mutation load and rapid adaptation favour outcrossing over self-fertilization", set out to "recapitulate the evolutionary process under the specific conditions predicted to favour either selfing or outcrossing." Levi Morran, Michelle Parmenter, and Patrick Phillips used the nematode, C. elegans, which consists of males and hermaphrodites. (This mix, and the lack of pure females, suggests there can be individual benefits to maleness, whatever the consequences for the population as a whole.) They used genetic manipulation to make populations that only self-fertilized or never self-fertilized, exposed them to high mutation rates or to a bacterial pathogen, and let them evolve.

Continue reading "Experimental evolution of sex (revised)" »

Posted by R. Ford Denison at 7:29 PM | Permalink | Comments (4)

Experimental populations of hermaphroditic plants evolved a significant increase in male function in only three generations.

Many plant species are hermaphrodites, with each individual producing both pollen and seeds. Others species have separate sexes, as mammals and birds do, while still others have mixtures of unisexuals and hermaphrodites. Based on the distribution of these traits in the family tree of life, evolutionary transitions among these "lifestyles" appear to have been fairly common. This week's paper shows how hermaphrodites can evolve to be more female or, in this case, more male. Hermaphroditic Sex Allocation Evolves When Mating Opportunities Change was just published in Current Biology by Marcel Dorken and John Pannell.

Continue reading "How fast can sexual traits evolve?" »

Posted by R. Ford Denison at 3:24 AM | Permalink | Comments (0)

How did the first life on Earth arise? We may never know for sure, but can we at least demonstrate one or more mechanisms that could have led to life as we know it? Not yet, but this week’s paper seems like a significant step towards that goal. “Self-sustained replication of an RNA enzyme” was published in Science by Tracey Lincoln and Gerald Joyce.

Most species have protein-based enzymes (running the biochemical reactions needed for growth and reproduction) and DNA-based heredity (passing genetic information to the next generation), with RNA serving various other functions. Under the “RNA-world” hypothesis, however, RNA molecules once served both as enzymes and for heredity. Some viruses use RNA as their hereditary material and some RNA molecules still act as enzymes, with a key role in protein synthesis, for example.

Can we recreate the early RNA world in a laboratory? What is the simplest system that could evolve by natural selection, eventually leading to something that would be universally recognized as alive?

Continue reading "Experimental evolution of an RNA world" »

Posted by R. Ford Denison at 8:04 PM | Permalink | Comments (0)

Fossils and DNA-sequence comparisons among species are like fingerprints and other clues found at crime scenes. We can often draw reliable conclusions about past events (evolutionary or criminal) from such physical evidence, but some people prefer eyewitness accounts. So evolutionary biologists are increasingly doing experiments that let us see evolution in action. Evolution is a change over generations, so the short generation times of microbes make them especially useful for experimental evolution.

Two recent examples, both published in Proceedings of the Royal Society, are "Experimental evolution of a microbial predator's ability to find prey", by Kristina Hillesland, Greg Velicer, and Richard Lenski, and "Experimental evolution of a sexually selected display in yeast", by David Rogers and Duncan Grieg.

Continue reading "Experimental evolution of predation and sexual attractiveness" »

Posted by R. Ford Denison at 8:18 PM | Permalink | Comments (0)

I’m done with two grant proposals, revising a book chapter, and checking the final version of a review article. I still have a pile of interesting reading and writing to do before I can get back into the lab – actually, I did help Ryoko set up an experiment yesterday – but no more looming deadlines for awhile. So, here are two more summaries of talks from Evolution 2008.

Do I know you?

The ability to tell other individuals apart by their faces is presumably maintained by natural selection, so you can recognize and avoid bad guys. But is there also selection for looking different enough to be recognizable? Or is it better to blend in with the crowd, so you can get away with stuff?

Michael Sheehan and Elizabeth Tibbetts are studying individual recognition in wasps (Tibbetts and Dale, 2007). Their hypothesis is that distinctive-looking individuals benefit, because they get in fewer fights over dominance.

Continue reading "More talks from Evolution 2008" »

Posted by R. Ford Denison at 9:37 PM | Permalink | Comments (0)

About 1500 scientists attended Evolution 2008 here last week. The four-day meeting was filled with 15-minute talks (usually ten at once, in different rooms), plus two evening poster sessions (like a science fair, for grownups, with discussions rather than judging), scenically located on a pedestrian bridge over the Mississippi. Reports that “scientists are abandoning evolution�? appear to be exaggerated.

Here are summaries of some of the talks I enjoyed.

Continue reading "Evolution 2008: sexy plants, battling bacteria, durable cooperation" »

Posted by R. Ford Denison at 8:36 PM | Permalink | Comments (3)

This week’s paper is Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae published in Nature by Lorenzo Santorelli and colleagues at Rice University and Baylor College of Medicine, both in Texas.

The evolution of cooperation is a central problem in the history of life. Darwin explained how sophisticated adaptations -- “the structure of the beetle which dives through the water… the plumed seed which is wafted by the gentlest breeze�? -- can evolve in a series of small improvements over generations. But some of the major transitions in evolution are harder to explain, because It seems that they should have been opposed, rather than supported, by natural selection. The origin of multicellular life is a good example. It’s not that hard to imagine independent cells working together in loose groups for mutual benefit – huddling together for defense, say – but why would a cell give up the ability to reproduce, as most of the cells in our bodies have done?

Continue reading "Knowing when not to cheat" »

Posted by R. Ford Denison at 9:41 PM | Permalink | Comments (0)

There are enough examples of ‘‘cheating’’ in bacteria ... that mindless obedience to such [quorum-sensing] chemical signals cannot be assumed. Mindlessness can be assumed, but not obedience. -- Denison et al. (2003) Ecology 84:838-845

Quorum sensing, an exchange of chemical signals among bacteria, can solve the coordination problem. But this week's paper Cooperation and conflict in quorum-sensing bacterial populations shows that quorum sensing doesn't automatically solve the problem of cheaters. The paper is by Stephen Diggle, Ashleigh Griffin, Genevieve Campbell, and Stuart West and published in Nature.

Continue reading "Communication doesn't automatically prevent cheating" »

Posted by R. Ford Denison at 11:08 PM | Permalink | Comments (0)

Two papers on cooperation this week. If you were trying to help someone, but end up causing problems for them, were you being cooperative? I have no idea, so I like to study cooperation in microbes. Microbes don't have brains, so "intent" isn't a factor. And the only definition of "benefit" that makes sense is an increase in Darwinian fitness or reproductive success, which is often easy to measure in microbes; just count them.
I like these definitions:

Cooperation: a behaviour which provides a benefit to another individual (recipient), and which is selected for because of its beneficial effect on the recipient. [Exhaling CO2 isn't cooperation; it evolved as a side-effect of breathing oxygen, not to benefit plants.]
Cheaters: individuals who do not cooperate (or cooperate less than their fair share), but are potentially able to gain the benefit of others cooperating. ["Equal share" might be less ambiguous.]

Continue reading "Cooperation and cheating in microbes: quorum sensing and persisters" »

Posted by R. Ford Denison at 5:27 PM | Permalink | Comments (0)

Yesterday, my wife asked, "why are there so many theoretical papers in evolutionary biology?" I suggested one reason may be that evolutionary theory is better developed, in the sense of making accurate predictions, than theory in much of biology. This week's paper, comparing results from an evolution experiment to predictions of a mathematical model, is a good example.

The paper is about the evolution of cooperation. This is a hot topic and also my own area of research. Humans enforce cooperation, to varying extents. For example, we often punish cheaters, those who try to benefit from cooperative activities of others without contributing anything themselves. Human cheaters are mostly pretty stupid -- don't even think about plagiarizing this blog for a term paper! -- but what about cheaters with no brains at all?

Continue reading "How disturbed are most cheaters, really?" »

Posted by R. Ford Denison at 10:16 PM | Permalink | Comments (4)

A reader asked an interesting question about the difficulty of coordinated evolution of groups of genes. Although I welcome comments and questions, I won't usually have time for detailed responses. and I'd already discussed one paper this week. But then Huxley brought in a recent issue of Nature he'd been chewing on, and there it was: "Empirical fitness landscapes reveal accessible evolutionary paths" (Nature 445: 383-386). So I guess I should take this dog-given opportunity to talk about the evolution of multiple interacting genes. The Nature paper is a review article with no original data, so isn't eligible for my regular weekly paper discussion, but maybe it's OK as a bonus paper, especially since the most interesting papers it discusses were published within the last year and they do contain original data.

The exciting thing about these papers is that people are starting to use molecular methods in experiments that solve "you can't get there from here" problems in evolutionary biology.

Continue reading "Experiments with "fitness landscapes" explain evolution of interacting genes" »

Posted by R. Ford Denison at 3:57 PM | Permalink | Comments (9)

Last week's paper discussed trade-offs between seed size and seed number. Many such trade-offs (growth vs. reproduction, more seeds vs. taller stem, etc.) follow directly from conservation of matter or energy, but what about other sorts of trade-offs? It has been suggested, for example, that there is a trade-off between competitiveness and dispersal ability. Why should this be? For seeds, at least, a larger seed gives the seedling a head-start against competitors, but smaller seeds travel farther on the wind.

This week's paper proposes another trade-off, for which the mechanism is less obvious. "Drop or fly? Negative genetic correlation between death-feigning ability and flying ability as alternative anti-predator strategies", was written by Tatunori Ohno and Takahisa Miyatake and published in Proceedings of the Royal Society B (vol. 274, p. 555-560).

Continue reading "Experimental evolution: play dead or fly away?" »

Posted by R. Ford Denison at 7:05 PM | Permalink | Comments (3)