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October 29, 2010

Join my lab?

I am mainly interested in the evolution of microbial cooperation, particularly by the symbiotic rhizobia that provide some crops and wild legumes with nitrogen. I have money in a current grant that could be used to support a new student working on legume symbiosis with "eusocial" rhizobia. Other student research and collaborations (especially with Mike Travisano) have extended from microbial bet-hedging and the evolution of aging and multicellularity (submitted) to applying ecology and evolution to improving agricultural productivity and sustainability.

This week's picks

Some recent papers that look interesting:

Crime and punishment in a roaming cleanerfish

Kin competition, natal dispersal and the moulding of senescence by natural selection

Learning in a game context: strategy choice by some keeps learning from evolving in others

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds

Fitness Correlates of Heritable Variation in Antibody Responsiveness in a Wild Mammal

Middle Pleistocene lower back and pelvis from an aged human individual from the Sima de los Huesos site, Spain

Diet and hormonal manipulation reveal cryptic genetic variation: implications for the evolution of novel feeding strategies

Biogeographic and evolutionary implications of a diverse paleobiota in amber from the early Eocene of India

Colonization, mouse-style

Ecosystem-specific selection pressures revealed through comparative population genomics

Q&A: H1N1 pandemic influenza - what's new?

October 26, 2010

Mutualisms in a changing world: an evolutionary perspective

That's the title of a review article recently published in Ecology Letters. Authors include Toby Kiers, who did a PhD with me a few years ago, and Judy Bronstein, who visited UC Davis when I was just starting to work on evolution of cooperation and told me about some key papers in the field.

"I use this term ["struggle for existence"] in a large and metaphorical sense including dependence of one being on another, and including (which is more important) not only the life of the individual, but success in leaving progeny" -- Darwin

Climate change, pollution, hunting, and introduced species can have direct effects on endangered species, but what about indirect effects? For example, a wild plant species, growing alone, might produce fewer seeds when exposed to higher temperatures. But if higher temperature hurts the plant's competitors or pests enough, the resulting indirect decreases in competition or pest damage might outweigh direct negative effects. On the other hand, a plant that depends on animals for seed dispersal could suffer more seed predation, as shown below, if climate change or over-hunting reduces disperser numbers, even if climate change and hunting have no direct effect on the plant itself.
Coleoptera larva attacks the fruit of Iriartea deltoidea in western Amazonia. Over-hunting of seed dispersers has resulted in huge caches of undispersed seeds at parental trees, vulnerable to attack by various pests. Photo: Patricia Alvarez.

This week's paper adds evolution to the already complex problem of mutualism (cooperation between species) in changing environments. For example, what if the timing of flowering and the emergence of a pollinating insect both depend on temperature, but in different ways? Then climatic change may reduce pollination, at least in the short run. Both species will continue to evolve, however, which could bring them back into sync -- unless the pollinators switch to a different host whose flowering time fits their new schedule!

Switching partners is one of three possible evolutionary responses discussed in this week's paper. The other two are abandonment of mutualism, which won't necessarily lead to the extinction of either partner, and good interactions going bad. Examples of mutualisms that have been abandoned include plants evolving to use wind pollination instead of insect pollinators, and plants that don't form symbioses with mycorrhizal fungi. These examples aren't all the result of human impacts on natural ecosystems, but they illustrate the potential for such changes.

Examples given of positive interactions becoming negative include fungi living inside leaves that were once apparently beneficial become harmful to trees weakened by drought. Mycorrhizal fungi, which provide their plant hosts with phosphorus, apparently become more costly or less beneficial with overuse of fertilizer. Ants that defend trees from herbivores have become harmful with changes in herbivore populations. In most of these cases, it is not clear whether these negative changes result from evolution (genetic changes with a species), ecological changes (different species interacting), phenotypic plasticity (different behavior without a genetic change), or (most likely), some combination of these. Out of 179 studies analyzed, only 15 looked at evolutionary aspects. Maybe this paper will encourage those studying changing mutualisms to pay more attention to evolution.

October 20, 2010

Grad school application deadlines in December

If you're thinking about grad school next year, it's time to get serious. Application deadlines for the two grad programs I'm associated with are both in December. You might want to read my thoughts on who should go to grad school first, though.

If that didn't scare you away, I still have some money left to support a student to work on the first of these two grants. Other topics are possible, but it's nice to work on something for which your major professor has a grant. You may be able to support yourself in grad school as a teaching assistant, but what about money for supplies?

Prospective grad students must apply to the grad program. In my case that would be:
Ecology Evolution and Behavior or else Plant Biology. If you want to be taken seriously by any grad program, you also need to identify specific professors you might want to work with and contact them individually -- after reading at least two of their recent papers. If the papers seem boring to you, you will probably hate working in that lab. Look elsewhere!

October 19, 2010

Applied Evolution Summit video (Heron Island)

Many evolutionary biologists do field work in exciting locations, like the Galapagos. I mostly work in the lab these days -- when I'm not at the computer writing or revising papers -- but I often get invited to speak at meetings in interesting places. For example, I'll be talking about Darwinian agriculture in Paris in December, at the EUCARPIA meeting on plant breeding for organic farming.

But it's hard to beat Heron Island, Australia, where I spoke at the Applied Evolution Summit in January. The scientific output from our discussions will be coming out in Evolutionary Applications, but if you like sea turtles, birds, and coral reefs with your science...

Here's a beautiful video about the meeting.

Casuarina, a tree that hosts nitrogen-fixing bacteria not closely related to those that form symbioses with legumes, frames a sea turtle laying eggs, on Heron Island. Photo by R. Ford Denison.

October 15, 2010

Bet-hedging in symbiotic rhizobia from alfalfa nodules

This week's paper is another recent one from my lab "Individual-level bet hedging in the bacterium Sinorhizobium meliloti", now on-line at Current Biology. Will Ratcliff did a guest post earlier, discussing a paper on the experimental evolution of bet hedging. This latest paper reports Will's own experiments.

S. meliloti is best known for its symbiosis with alfalfa. After infecting via root hairs, it reproduces inside developing root nodules.AlfalfaNodules2.jpg
Alfalfa nodules in our lab; copyright Inga Spence, used by permission.

When the nodules senesce, reproductive rhizobia escape into the soil, leaving the nonreproductive "workers" (bacteroids), which had been providing the plant with nitrogen, behind. A nodule may release millions of rhizobia -- we're not sure how many, actually -- each of which may have accumulated resources there, including high-energy PHB. So a single rhizobial cell that infects a root hair may end up with millions of well-endowed descendants, a few months later. But then what?

If there's another host root nearby, going back into symbiosis is probably the best way to get millions of grandchildren. But only a small fraction of the newly discharged rhizobia are likely to get a chance to re-enlist right away. The others may have to wait.

So Will took a bunch of high-PHB S. meliloti cells (a) and starved them for a month. As expected, many of the rhizobial cells apparently used up most of their PHB. (PHB per cell was measured using a flow cytometer, after staining with Nile red, which fluoresces in proportion to PHB per cell.) Low-PHB cells make up the higher of the two peaks in part (b) of the figure below.PHB.jpg
But, to our surprise, there were still many high-PHB cells (right peak in b), even after a month of starvation.

Part (c) of the figure shows what had happened. The two green images show an S. meliloti cell dividing. Green-fluorescent protein (GFP) ended up mostly in the daughter cell. But Nile red staining shows that the mother cell kept most of the PHB.

Why not divide resources equally? The two cells are genetically identical clonemates, so there's no evolutionary reason to be selfish.

This is where bet hedging comes in. Unequal division of resources increases the chance that at least one of the cells will survive long enough to find another host plant or another source of food. Of course, it also increases the chances that one of the cells will die before finding food. In bet hedging, you always give up the chance of a big win (e.g., two survivors) in order to reduce the chance of a big loss (no survivors).

But rhizobial bet hedging is actually more sophisticated than what I've just described. The high-PHB cell further enhances its chances of long-term survival by becoming at least somewhat dormant. This is apparent, for example, in the low growth rate of the high-PHB cells in competition with a labeled competitor, relative to the growth of the low-PHB cells with the same competitor. By not growing, however, the high-PHB cells conserve their resources, so that 70% of them were still alive after 528 days of starvation!

Similar bet hedging strategies are seen in many wild plants. They make some seeds that germinate the next year and others that stay dormant for a few years. If conditions next year are very favorable (for example, if most of their competitors are killed by a disease that doesn't kill them), then many of the nondormant seeds will grow into adult plants, each producing many more seeds. But if next year is terrible (drought, fire, too many competitors, etc.), then maybe the dormant seeds will have a better chance.

Previous examples of bet hedging in bacteria, however, have involved a small fraction of the cells in a large population switching, apparently at random, to some different state. In a large population of genetically identical clonemates, there may therefore be a few individual cells able to survive catastrophe. A small chance of random switching isn't likely to occur in a small population, however, so the variability needed to ensure survival may not be there. With the bet hedging strategy Will found in S. meliloti, on the other hand, even a single cell can bet hedge, producing one faster-growing offspring and one slow-growing offspring resistant to starvation. He also showed that the dormant cells are resistant to some antibiotics, but a reviewer wanted so many additional experiments on that part of the paper that we left it out.

This material is based upon work supported by the National Science Foundation under Grant No. NSF/DEB-0918897.

This week's picks

I'm going to write about another recent paper from my lab this week, but here are some other recent papers that look interesting:
Sex, drugs and moral goals: reproductive strategies and views about recreational drugs

Rapid Construction of Empirical RNA Fitness Landscapes

Advertised quality, caste and food availability influence the survival cost of juvenile hormone in paper wasps

Q&A: Antibiotic resistance: where does it come from and what can we do about it?

Phenotypic plasticity and population viability: the importance of environmental predictability

Selection at Linked Sites Shapes Heritable Phenotypic Variation in C. elegans

October 8, 2010

Why do leaves really track the sun?

This week I'll discuss one of my own papers, "Individual fitness versus whole-crop photosynthesis -- solar tracking tradeoffs in alfalfa", which was recently published in the Evolutionary Applications special issue on Agriculture.
The alfalfa leaf at the right is brightly illuminated because it is facing directly towards the sun, an orientation it maintains by turning slowly over the day. By tracking the sun, this leaf captures more sunlight, so it might be expected to photosynthesize more. On the other hand, the leaf is partly shaded by another leaf, which casts a bigger shadow because it, too, is tracking the sun. This increased shading of lower leaves by upper leaves would tend to reduce overall photosynthesis.

Does increased shading outweigh the photosynthetic benefits of tracking?

Jim Fedders, Barry Harter, and I decided to find out. We measured photosynthesis of a model community of alfalfa plants tracking the sun naturally, then turned them 90 degrees, to temporarily disrupt solar tracking.

(That's me at the left, but these experiments were done 20 years ago, when I was a USDA scientist in West Virginia. By now, I probably look more like my father, William Denison, who was visiting the day the picture was taken. The cloudless days needed for the turning experiment were rare, so I made him come to work and help with the experiment. He was a botanist/mycologist, known for his 1973 Scientific American article, "Life in Tall Trees", so I don't think he minded.)
Here are the results in which I have the most confidence. With a sparse leaf canopy, photosynthesis decreased about 2% when we disrupted solar tracking. (Leaf area index = 2 means there are 2 square centimeters of leaf per square centimeter of ground. Relative photosynthesis of 1.02 means photosynthesis with normal solar tracking is 1.02 times that with tracking disrupted by turning.) Beyond leaf area 4, however, photosynthesis actually increased when we disrupted solar tracking.

Why do leaves track the sun, when doing so decreases photosynthesis? Maybe because the leaves that get shaded are often those of neighboring competitors. We found that tracking reduces light levels near the ground to half what they were without tracking. So seedlings coming up under a solar tracking plant would photosynthesize and grow less, making them less of a competitive threat.

The curved line shows predicted effects of solar tracking on photosynthesis, based on simulations using the computer model, ALFALFA, which I developed around 1984, under the guidance of my postdoctoral mentor, Bob Loomis. The model predicts that solar tracking will have a negative effect on photosynthesis over a wider range of leaf areas than in our experiments. It's only a model, of course. But our artificial plant community is also a model system. One key difference between our small group of plants and an entire field of alfalfa is that lower leaves can get a lot of light from the side, if they're at the edge of a small group of plants. This "edge effect" would tend to reduce the negative effects of tracking on photosynthesis, because shading by upper leaves would have less effect on the total light available to lower leaves. So the computer model might actually be a better predictor of solar tracking effects in the field.

Especially if we believe the computer model, we might be able to increase the photosynthesis and growth of alfalfa by breeding varieties that don't track the sun. They would be less competitive with weeds, though.

A Nobel Prize -- congratulations!

Can you identify this Nobel prize winner? Too bad he can't receive the prize in person.

Updated 13 October 2010 -- in related news, a respected news source blocked in some countries reports that:

A group of 23 Communist Party elders... has written a letter calling for an end to the country's restrictions on freedom of speech...

They include a former personal secretary to the revolutionary leader Mao Zedong, and a former editor of the People's Daily, the official Communist Party newspaper.

The letter, addressed to ... parliament, makes a number of proposals for change.

Censorship should be ended; restrictions on book publishing abolished, they say.

Journalists should be given protection and support when they investigate official corruption and a new media law should be drawn up to ensure they do their job responsibly, it says.

Scientific progress is slower when students and young professors are afraid to argue with senior professors or administrators. And they may well be afraid, if broader discussions can trigger arbitrary punishment. So, even though this wasn't one of the science prizes, it could have been.

Scientists working in the US win a lot of Nobel prizes, but many of the winners moved here from other countries. Being able to discuss your ideas without going to jail may help attract top scientists here. There's plenty of room for improvement in the US, though. For example, keeping prisoners locked up in Guantanamo indefinitely, without bringing them to trial, is a violation of human rights right out of The Count of Monte Cristo:

"Have pity on me, then, and ask for me, not intelligence, but a trial; not pardon, but a verdict - a trial, sir, I ask only for a trial; that, surely, cannot be denied to one who is accused!"

Three organizations working on these issues are:
Center for Constitutional Rights
American Civil Liberties Union
Amnesty International

October 1, 2010

Also this week...

Other recent papers that looked interesting:
Kinship affects investment by helpers in a cooperatively breeding bird

The coming and going of Batesian mimicry in a Holarctic butterfly clade

Jaw biomechanics and the evolution of biting performance in theropod dinosaurs

An experimental study of the population and evolutionary dynamics of Vibrio cholerae