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March 1, 2013

Copying in birds, dolphins, and viruses; evolution & environmental change; evolution of mutation rate

Learning and signal copying facilitate communication among bird species "where only two species regularly interact, one species' [alarm] calls incorporate the call of the other."

Vocal copying of individually distinctive signature whistles in bottlenose dolphins "Copying occurred almost exclusively between close associates such as mother-calf pairs and male alliances during separation... copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it... no evidence for the use of copying in aggression or deception."

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity "the only documented bacterial adaptive immune system is the CRISPR/Cas... a phage-encoded CRISPR/Cas system is used to counteract a phage inhibitory chromosomal island of the bacterial host. "

Evolutionary rescue from extinction is contingent on a lower rate of environmental change" "By assessing fitness of these engineered [E. coli] strains across a range of drug concentrations, we show that certain genotypes are evolutionarily inaccessible under rapid environmental change."

Fossil evidence for a hyperdiverse sclerophyll flora under a non-Mediterranean-type climate "sclerophyll hyperdiversity has developed in distinctly non-Mediterranean climates... likely a response to long-term climate stability."

A trade-off between oxidative stress resistance and DNA repair plays a role in the evolution of elevated mutation rates in bacteria "The dominant paradigm for the evolution of mutator alleles in bacterial populations is that they spread by indirect selection for linked beneficial mutations when bacteria are poorly adapted... [but] hydrogen peroxide, generates direct selection for an elevated mutation rate in the pathogenic bacterium Pseudomonas aeruginosa as a consequence of a trade-off between the fidelity of DNA repair and hydrogen peroxide resistance."


January 18, 2013

Modular mice, experimental evolution, Bayesian enzymes, environmental extinction

Here are some papers that look interesting this week:

Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice
"In burrows built by first-generation backcross mice, entrance-tunnel length and the presence of an escape tunnel can be uncoupled... a classic 'extended phenotype' can evolve through multiple genetic changes each affecting distinct behaviour modules"

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections
"We developed a biofilm model enabling long-term selection for daily adherence to and dispersal from a plastic bead in a test tube... experimental evolution may illuminate the ecology and selective dynamics of chronic infections and improve treatment strategies."

Navigating the protein fitness landscape with Gaussian processes
"sequence design algorithms motivated by Bayesian decision theory.... allowed us to engineer active P450 enzymes that are more thermostable than any previously made"

Evolution: A history of give and take
"deep-sea sediment cores show that environmental change correlates closely with extinction but not with speciation"

December 27, 2012

Antibiotic resistance, camouflage, exinction...

Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance "Using experimental evolution and deep sequencing to monitor the allelic frequencies of the seven most biochemically efficient TetX2 mutants in 10 independently evolving populations, we showed that the model correctly predicted the success of the two most beneficial variants"

Early evolution and ecology of camouflage in insects Lacewings were carrying "trash" (parts of ferns) as camouflage 110 million years ago.

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species "Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type."

Mass extinction of lizards and snakes at the Cretaceous-Paleogene boundary "The recovery was prolonged; diversity did not approach Cretaceous levels until 10 My after the extinction"

Equatorial decline of reef corals during the last Pleistocene interglacial "poleward range expansions of reef corals occurring with intensified global warming today may soon be followed by equatorial range retractions. "

January 17, 2012

Experimental evolution of multicellularity: the movies

In case you missed the news coverage by Carl Zimmer in the New York Times, Jeff Akst in The Scientist, and Ed Yong on Nature's news site, among others, our paper on experimental evolution of multicellularity has just been published in Proceedings of the National Academy of Sciences. It's open access, so you can read all the details yourself.

In nature, multicellularity has only evolved a few about 25 times, and it took billions of years. But Mike Travisano (a fellow faculty member in Ecology Evolution and Behavior) and postdoc Will Ratcliff (who earned a PhD with me recently) came up with a simple and repeatable way to speed the process enough to study under lab conditions: selection for rapid settling in liquid media, starting with unicellular yeast. They kindly invited Mark Borrello and me to participate in this exciting project, which also depended on hard work by undergrads Kristin Jacobsen, Mitch Hoverman, and Amanda Muehlbauer and funding from the National Science Foundation. We have also had some support for preliminary genetic analysis (in progress) from the College of Biological Sciences at the University of Minnesota.

The best collection of links related to this work is at the Microbial Population Biology (Micropop) website, which brings together people and projects from the laboratories of Mike Travisano, Tony Dean, and me. I particularly recommend the videos showing reproduction of snowflake-like multicellular yeast via smaller multicellular propagules -- think of plants reproducing from fragments, rather than seeds -- and genetic stability of the multicellular trait, shown by regrowth of multicellular clusters from enzymatically isolated single cells.

I gave some background for this work in an earlier post, when Elizabeth Pennisi wrote about it for Science.

Update: two scientists criticize some of our claims, and Will Ratcliff responds, on Carl Zimmer's blog, here.

November 28, 2011

Experimental evolution of metabolism, sex, and multicellularity

Update: links to our open-access Proceedings of the National Academy of Sciences paper on experimental evolution of multicellularity, including PDF and great videos, can be found at the Microbial Population Biology (Micropop) website.

The Nov. 18 issue of Science has a news feature by Elizabeth Pennisi on recent research using experimental evolution, including some work on the evolution of multicellularity, led by Mike Travisano and Will Ratcliff, in which I've been involved.

Two interesting experimental evolution projects are underway in Canada. In Montreal, Graham Bell has been evolving algae that get their energy from a simple organic molecule, acetate, instead of from light. At first, the algae could barely survive without light, but after five years (still a fraction of the time that Richard Lenski has been evolving E. coli) he has hundreds of independent lines that have evolved a variety of ways to grow on acetate in the dark.

In Toronto, Aneil Agrawal is subjecting the sex life of rotifers to experimental evolution. Like aphids, Daphnia, and some other species, rotifers normally reproduce asexually, resorting to sex only under stress. Populations consisting of females, producing other females asexually, grow twice as fast as populations that are half male. (In my forthcoming book, Darwinian Agriculture, I discuss how reindeer herders increase production by harvesting mostly male calves for meat, so that most adults are females producing more calves, rather than males fighting over females.) But sexual reproduction shuffles genomes in ways that may be beneficial under different conditions. Agrawal and his postdoc Lutz Becks found that the balance between sexual and asexual reproduction evolved in response to environmental conditions. In stable environments, sex eventually disappeared. Once you've evolved the perfect genotype for some particular stable environment, why scramble that genotype through sex?

Meanwhile, we've been exploring the transition to multicellularity.
ClusterShowingDifferentiation.jpg
Cellular differentiation in multicellular clusters evolved from unicellular yeast (photo by Will Ratcliff).

Unicellular life apparently had the earth to itself for over a billion years before even simple multicellular life evolved. So you might think that this major evolutionary transition requires some complicated series of genetic changes that would only happen rarely. Alternatively, maybe the first simple multicellular organisms weren't that different, genetically, from their unicellular ancestors -- they just couldn't out-compete their unicellular parents until conditions were right.

Individual cells would have greater access to nutrients in their environment than cells in the middle of a cluster, but what advantages might clusters have, under what conditions?

Continue reading "Experimental evolution of metabolism, sex, and multicellularity" »

June 22, 2011

This is not a press release

Major journals often ask scientists to limit interactions with the press before their work is published. I agree with this policy, which prevents the public disillusionment with science that can happen when a scientist makes claims (like cold fusion) that don't stand up to subsequent peer review. But presentations at scientific meetings (where the audience can critique exaggerated claims) are allowed. Members of the press can attend those meetings, report on what they hear, and ask other scientists for their reactions.

That's what happened this week, when Will Ratcliff (my recent PhD student, now doing a postdoc with Mike Travisano, Mark Borrello and me) talked about experimental evolution of multicellularity in yeast, at the Evolution meetings. His PhD was recent enough that he was eligible for and won the (William) Hamilton Prize for "Best Student Presentation." Our interactions with the press are constrained, for now, by the journal that's considering our paper on this work, but I look forward to blogging about it once it's published.

Meanwhile, see my earlier posts on Will's theoretical work on the evolution of aging, commentary on multiple roles for antibiotics in interactions among bacteria, and the discovery of a new form of bet-hedging in bacteria. This work was made possible by support from the US National Science Foundation.

April 8, 2011

This week's picks

Workers influence royal reproduction
"worker aggressive and non-aggressive behaviour towards queens predicted which queen monopolized reproduction. In contrast, among-queen interactions were rare and did not predict queen reproduction. Furthermore, parentage analysis showed workers favoured their mother when present"
[Maybe "inclusive fitness" is useful after all!]

Updated chronology for the Miocene hominoid radiation in Western Eurasia
"Eurasian pongines [orangutans and extinct relatives] and African hominines [humans, chimps, bonobos, and extinct relatives] might have independently evolved in their respective continents from similar kenyapithecin ancestors [apes living 14 million years ago], resulting from an early Middle Miocene [5-23 MYA] intercontinental range extension followed by vicariance [geographic separation, reducing or eliminating interbreeding so allowing evolutionary divergence]. "

Ribozyme-Catalyzed Transcription of an Active Ribozyme "we recombined traits evolved separately in different ribozyme [catalytic enzyme made of RNA rather than protein] lineages. This yielded a more general polymerase ribozyme that was able to synthesize a wider spectrum of RNA sequences, as we demonstrate by the accurate synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme. "

An evolutionary process that assembles phenotypes through space rather than through time "assortative mating between fast-dispersing individuals at the invasion front results in an evolutionary increase in dispersal rates in successive generations"

Fork-tailed drongos use deceptive mimicked alarm calls to steal food
"false alarm calls when watching target species handling food, in response to which targets flee to cover abandoning their food"

Moving calls: a vocal mechanism underlying quorum decisions in cohesive groups
"a sharp increase in the probability of changing foraging patch when the number of group members joining the chorus increased from two up to three"

Differences in the temporal dynamics of phenotypic selection among fitness components in the wild "The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival."

Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias "Rickettsia sp. nr. bellii swept into a population of an invasive agricultural pest, the sweet potato whitefly, Bemisia tabaci, in just 6 years. Compared with uninfected whiteflies, Rickettsia-infected whiteflies produced more offspring, had higher survival to adulthood, developed faster, and produced a higher proportion of daughters. The symbiont thus functions as both mutualist and reproductive manipulator. "

The evolutionary biology of child health "cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes"

Tradeoffs associated with constitutive and induced plant resistance against herbivory "Across all 58 plant species, we demonstrate a tradeoff between constitutive and induced resistance, which was robust to accounting for phylogenetic history of the species. Moreover, the tradeoff was driven by wild species and was not evident for cultivated species."

Towards a quantitative understanding of the late Neoproterozoic carbon cycle
"all of the main features of the carbonate and organic carbon isotope record can be explained by the release of methane hydrates from an anoxic dissolved organic carbon-rich ocean into an atmosphere containing oxygen levels considerably less than today"

February 25, 2010

Evolution of symbiosis

This week's paper is "Experimental Evolution of a Plant Pathogen into a Legume Symbiont" published recently in PLoS Biology by Marta Marchetti and colleagues.

It's not hard to convert a highly beneficial rhizobium, which infects legume roots and provides them with nitrogen, into a slightly harmful one -- just knock out the nitrogen-fixation gene and you get a bacterium that has some cost to its host but provides no benefit in return. But how hard is it for a bacterium that causes disease to evolve into a beneficial bacterium?

One process that sometimes happens in nature is the wholesale "horizontal" transfer of a gene (or many linked genes) from one microbe to another. So the authors of this week's paper started by transferring the symbiotic plasmid (a loop of DNA with genes for infecting roots and then fixing nitrogen) into a plant pathogen.

Continue reading "Evolution of symbiosis" »

November 25, 2009

Not so fast!

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.

November 11, 2009

Experimental evolution of bet hedging

Will headshot.jpg
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" »

November 5, 2009

Experimental evolution meets genomics

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" »

October 23, 2009

Experimental evolution of sex (revised)

"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)" »

April 3, 2009

How fast can sexual traits evolve?

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?" »

March 14, 2009

Experimental evolution of an RNA world

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" »

October 10, 2008

Experimental evolution of predation and sexual attractiveness

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" »

July 17, 2008

More talks from Evolution 2008

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.
4fuscatus.jpg

Continue reading "More talks from Evolution 2008" »

June 29, 2008

Evolution 2008: sexy plants, battling bacteria, durable cooperation

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" »

March 1, 2008

Knowing when not to cheat

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" »

November 16, 2007

Communication doesn't automatically prevent cheating

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
Millions of cooperating cells can do things far beyond the ability of an individual cell. This is most obvious in multicellular organisms, whose cells cooperate because they are all genetically identical, or nearly so. Genetically diverse populations of cells could often benefit from cooperating, but do they? For example, the mixed bacteria populations associated with plant roots might benefit from keeping the plant healthy, so that it can continue to feed them with its root exudates. But for this to happen, they need some method of coordinating their plant-benefiting activities. Furthermore, cells whose genes lead to this form of cooperation must, on average, survive and reproduce more than "cheaters" who don't invest in cooperative activities. Otherwise, cooperative traits will disappear.

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" »

September 27, 2007

Cooperation and cheating in microbes: quorum sensing and persisters

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" »

May 6, 2007

How disturbed are most cheaters, really?

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?" »

March 8, 2007

Experiments with "fitness landscapes" explain evolution of interacting genes

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" »

February 28, 2007

Experimental evolution: play dead or fly away?

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?" »