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October 4, 2013

Domestication effects on stomata, and kin competition in plants

There's probably some scientific connection between the two topics in this week's title, but I'm combining them because Ruben Milla has worked on both.

He and his colleagues just published a paper on "Shifts in stomatal traits following the domestication of plant species", comparing lots of crops with their wild relatives. Total abundance of stomata (leaf pores that let CO2 in and water vapor out) doesn't show a consistent increase or decrease with domestication, but there's a tendency for fewer of them to be on the lower side of the leaf.

In adding this paper to my database, I rediscovered one of Milla's earlier papers, on kin interactions in plants. Even though I'd blogged about it when it came out, I'd forgotten nearly all the details. I may be trying, unsuccessfully, to follow too many topics. Since some readers may have missed my earlier post, and since we are celebrating the 50th anniversary of Hamilton's and Maynard Smith's papers on inclusive fitness and kin selection, I am copying my 2009 post below.

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This week I will discuss two papers, both dealing with plants and competition, in the context of genetic relatedness that might be expected to moderate competition:
"Growing with siblings: a common ground for cooperation or for fiercer competition among plants?" by Ruben Milla and colleagues (Proceedings of the Royal Society), and
"Do plant parts compete for resources? An evolutionary viewpoint" by Victor Sadras and me (New Phytologist).

Earlier I discussed a paper by Susan Dudley and Amanda File showing that some plants grow less root when interacting with related than with unrelated neighbors. Spending less resources on roots could have freed resources for more seed production, but they didn't measure that. Now Milla and colleagues have.
They grow three lupine plants per pot, using either three seeds from the same plant, three seeds from different plants in the same area, or three seeds from different parts of Spain, and measured various aspects of plant growth and reproduction. In contrast to what I might have expected from Dudley and File's work, plants surrounded by siblings produced no more seeds than plants surrounded by strangers. In fact, one of their measures showed significantly more seed production from plants growing with plants from other regions.

They suggest two possible explanations. First, there was some tendency for plants to grow taller when growing with close kin, perhaps because they all germinated at the same time and thereby triggered an "arms race" to get above each other. The resulting over-investment in stem could leave less resources for seed production. Their other explanation is almost the opposite. What if closely related plants invest less in root, as Dudley and File found, and (under the conditions of Milla's experiment) this resulted in too little root for optimal uptake of water and nutrients?

When wild plants are grown in pots in a greenhouse, they may not allocate resources optimally, nor respond normally to environmental cues, including cues about the relatedness of their neighbors. But if hypothetical cooperation among closely related plants is weak enough to be undermined (even reversed) by growth conditions, the tendency to cooperate can't be very strong.

I discussed a paper by Victor Sadras in one of my first posts in This Week in Evolution, so I was intrigued when he invited me to collaborate on a paper reviewing the idea of "competition" among parts of the same plant. We argue that mechanisms that look like within-plant competition often act to maximize overall plant reproduction. A branch shaded by another branch may die, but this is more like suicide than murder. We know this because the same degree of shading isn't lethal when the whole tree is shaded equally. When only one branch is shaded, however, it can increase the frequency of its genes in the next generation by sending its nitrogen to better-lit branches, where the photosynthesis rate per unit nitrogen is greater. Seeds produced on those branches carry the same genes as those that the shaded branch could have produced itself. Selfish genes lead to unselfish branches.

Competition among seeds on the same plant is a different story. These seeds may have different fathers, whose pollen contained competing versions of various genes. Gene variants that help a seed take more than its share of resources from the mother plant will tend to increase over generations, unless countered. But mother plants have various counter-measures that tend to equalize resources among seeds. (This contrasts with birds that can only bring enough food to feed one chick. They may lay two eggs, but then let the stronger chick kill the weaker.)

We suggested that natural selection for equalizing resources among seeds has often set limits on how much seeds can grow, even when conditions turn out to be unusually favorable during seed-fill. This tradeoff may have been worth it for genetically diverse wild plants. In modern agriculture, however, whole fields may be almost identical, genetically. We might therefore be able to eliminate some of these ancestral seed-balancing mechanisms, letting seeds grow more when conditions are good.

Such tradeoffs between past natural selection and present human goals are a major theme of my forthcoming book, "Darwinian Agriculture: where does Nature's wisdom lie?"

July 19, 2013

Weed evolution in the New York Times

Carl Zimmer, author of several evolution-themed books and an interesting blog, published an article on weed evolution in Tuesday's New York Times. He used one of my favorite examples of rapid evolution of complex traits (flooding tolerance and crop mimicry in Echinochloa barnyardgrass/watergrass in <1000 years) to make the point that evolution of herbicide resistance (a much-simpler trait) in only a few years shouldn't have been a surprise.
Barrett1983.jpg
(Left) Under selection pressure imposed by farmers with hoes, Echinochloa watergrass evolved to resemble rice more than it resembles its own recent ancestor, barnyardgrass (Barrett, 1983). I discussed this example near the end of this lecture at the International Rice Research Institute.

Glyphosate-resistant weeds are becoming increasingly common, just before the expiration of Monsanto's patent on Roundup-Ready soybeans. What does the US Constitution say about patents?

"The Congress shall have Power To...promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries...."
If the original intent was to give inventors short-term monopolies, in exchange for long-term benefits to society, should the duration of patent protection be shorter for inventions whose useful life is likely to be limited by evolution? For example, 17 years with a really good resistance-management plan, 5 years with no resistance-management plan.... Of course, the Patent Office might need to hire an evolutionary biologist or two.

I agree with the statement from David Mortensen that adding another resistance gene to glyphosate-resistant crops, and spraying with both herbicides, will be only "a short-lived solution," although it might last long enough to be worth patenting. If they had put two different herbicide-resistant genes into soybean from the start, and if evolution of resistance requires two or more independent mutations -- this isn't always true -- and if farmers growing that herbicide-resistant crop were somehow required to use both herbicides (so that mutants resistant to just one of the herbicides wouldn't have increased in frequency), evolution of resistance might have taken much longer.

Zimnmer quoted me and mentioned my book on Darwinian Agriculture, depleting Amazon's stock, though they still have a few copies left. You could try your favorite independent bookstore or library.

June 14, 2013

Nursing Neanderthals, multisexual mutant mice, and the undead

Barium distributions in teeth reveal early-life dietary transitions in primates
"in a Middle Palaeolithic juvenile Neanderthal... exclusive breastfeeding for seven months, followed by seven months of supplementation.... [then] Ba levels in enamel returned to baseline prenatal levels, indicating an abrupt cessation of breastfeeding at 1.2 years of age"

Serotonin signaling in the brain of adult female mice is required for sexual preference
"male mutant mice lacking serotonin have lost sexual preference.... female mouse mutants lacking either central serotonergic neurons or serotonin... displayed increased female-female mounting"

Regeneration of Little Ice Age bryophytes emerging from a polar glacier with implications of totipotency in extreme environments "following 400 y of ice entombment... [bryophyte cells can ] dedifferentiate into a meristematic state (analogous to stem cells) and develop a new plant."

Quorum-sensing autoinducers resuscitate dormant Vibrio cholerae in environmental water samples
[I wonder if this would work with other "unculturable" microbes.]

May 31, 2013

This week's picks

Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size "areas deprived of large avian frugivores for several decades present smaller seeds than nondefaunated forests, with negative consequences for palm regeneration"

Molecular evolution of peptidergic signaling systems in bilaterians "phylogenetic reconstruction tools... show that a large fraction of human PSs [peptide-based signaling systems] were already present in the last common ancestor of flies, mollusks, urchins, and mammals"

Honey constituents up-regulate detoxification and immunity genes in the western honey bee Apis mellifera "apicultural use of honey substitutes, including high-fructose corn syrup, may thus compromise the ability of honey bees to cope with pesticides and pathogens and contribute to colony losses"

Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes" "the oldest known fossil 'ape', represented by a partial mandible... the oldest stem member of the Old World monkey clade, represented by a lower third molar... recovered from a precisely dated 25.2-Myr-old stratum in... the East African Rift in Tanzania."

Experimental evidence that evolutionarily diverse assemblages result in higher productivity "Species produced more biomass than predicted from their monocultures when they were in plots with distantly related species and produced the amount of biomass predicted from monoculture when sown with close relatives."

March 8, 2013

Cooperation, inducible defense, cancer, and more

Here are some papers that look interesting this week.

Prairie Dogs Disperse When All Close Kin Have Disappeared "cooperation among kin is more important than competition among kin for young prairie dogs"

Variants at serotonin transporter and 2A receptor genes predict cooperative behavior differentially according to presence of punishment "Participants with a variant at the serotonin transporter gene contribute more, leading to group-level differences in cooperation, but this effect dissipates in the presence of punishment."

Plant mating system transitions drive the macroevolution of defense strategies
the repeated, unidirectional transition from ancestral self-incompatibility (obligate outcrossing) to self-compatibility (increased inbreeding) leads to the evolution of an inducible (vs. constitutive) strategy of plant resistance to herbivores."

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics "we reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later events during cancer progression"

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality"
"natural selection against optimal codons to achieve adaptive responses to environmental changes"

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote "> 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally"

Recent land use change in the Western Corn Belt threatens grasslands and wetlands
"a recent doubling in commodity prices has created incentives for landowners to convert grassland to corn and soybean cropping... onto marginal lands characterized by high erosion risk and vulnerability to drought."

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."


February 22, 2013

Mimic defectors to keep them from winning... and more

Stabilization of cooperative virulence by the expression of an avirulent phenotype "host manipulation by S. typhimurium is a cooperative trait that is vulnerable to the rise of avirulent defectors; the expression of a phenotypically avirulent [but genetically identical] subpopulation that grows as fast as defectors slows down this process, and thereby promotes the evolutionary stability of virulence"

Evolution of a genetic polymorphism with climate change in a Mediterranean landscape "significant increase in the proportion of morphs that are sensitive to winter freezing... associated with relaxed selection (less extreme freezing events)"

Behavioural and genetic analyses of Nasonia shed light on the evolution of sex pheromones "male Nasonia vitripennis evolved an additional pheromone compound differing only in its stereochemistry from a pre-existing one... females responded neutrally to the new pheromone... new pheromone compounds can persist in a sender's population, without being selected against by the receiver and without the receiver having a pre-existing preference for the new pheromone phenotype, by initially remaining unperceived."

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly "Counterintuitively, selection for mRNA folding also impacts the nonsynonymous-to-synonymous nucleotide substitution rate ratio, requiring a revision of the current interpretation of this ratio as a measure of protein-level selection."

January 25, 2013

What's for dinner?

This week's picks all have something to do with food.

Tree climbing and human evolution "aspects of the hominin ankle associated with bipedalism remain compatible with vertical climbing [to collect fruit or honey]"

Earliest evidence for cheese making in the sixth millennium bc in northern Europe" "compelling evidence for the vessels having being used to separate fat-rich milk curds from the lactose-containing whey... in the manufacture of reduced-lactose milk products among lactose-intolerant prehistoric farming communities"

Anatomical enablers and the evolution of C4 photosynthesis in grasses
"when environmental changes promoted C4 evolution, suitable anatomy was present only in members of the PACMAD clade [which doesn't include rice] explaining the clustering of C4 origins in this lineage"

Macropredatory ichthyosaur from the Middle Triassic and the origin of modern trophic networks "recovery from Earth's most severe extinction event at the Permian-Triassic boundary... may have occurred faster [in oceans than on land]"

Sustainable bioenergy production from marginal lands in the US Midwest" "successional herbaceous vegetation, once well established, has a direct GHG emissions mitigation capacity that rivals that of purpose-grown crops "

Extracellular transmission of a DNA mycovirus and its use as a natural fungicide
"Our findings may prompt a reconsideration of the generalization that mycoviruses lack an extracellular phase in their life cycles and stimulate the search for other DNA mycoviruses with potential use as natural fungicides. "

January 11, 2013

Predictability, multiple fitness peaks, fungus-growing ants, pesticide resistance...

Predictability of evolution depends nonmonotonically on population size
"evolutionary predictability based on an experimentally measured eight-locus fitness landscape for the filamentous fungus Aspergillus niger.... entropies display an initial decrease and a subsequent increase with population size N"

Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild "We measured the adaptive landscape in a nascent adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas, and found multiple coexisting high-fitness regions driven by increased competition at high densities"

Laccase detoxification mediates the nutritional alliance between leaf-cutting ants and fungus-garden symbionts "laccase activity is highest where new leaf material enters the fungus garden [in ant feces], but where fungal mycelium is too sparse"

A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae "selection for the ability to mount a broad response to the diverse defense chemistry of plants predisposes the evolution of pesticide resistance in generalists"

See my Darwinian Agriculture Blog for links to videos of two of my talks.

September 26, 2012

Diversity of Opinions on Diversity

CedarCreekLowDiversity.jpg
Cedar Creek plots weeded to maintain low diversity have low plant cover, explaining their low productivity. But why does that space stay open?

Part two of the mostly positive review by Jeremy Cherfas, on the Agricultural Biodiversity blog, argues that my Darwinian Agriculture book understates the benefits of mixing varieties (e.g., with different disease-resistance genes) within a field.

I added a comment there, noting that I had included a comparison of this strategy to an alternative way of deploying the same amount of genetic diversity. But his overall point remains valid. I think I over-reacted to what I see as a tendency to think about crop diversity mainly at fine spatial scales, while ignoring diversity at larger spatial scales and over time.

While I'm on the subject of plant diversity, I talked to Dave Tilman about the suggestion in the book that the low plant cover (see above) in his low-diversity treatments could be an artifact from their weeding protocol. He apparently has data showing that seedlings of the one "resident" species in his monoculture plots do poorly, relative to seedlings of other species. I've seen the same mechanism as an explanation for high tree-species diversity in the tropics -- species X doesn't do well near species X, perhaps due to disease.

The fact remains, however, that photons hitting soil, rather than leaves, drive water loss without contributing to photosynthesis. So it's not surprising that low-cover plots have low productivity. Crop monocultures, however, usually achieve full cover, limiting the relevance of this work to agriculture.

If I get to do a second edition, I will try to correct these flaws. Meanwhile, I see thoughtful negative comments as positive, consistent with my goal of stimulating more-insightful discussion.

September 24, 2012

Comments on Forbes article on biomimicry

Steven Kotler, at Forbes, recently posted a story titled "Move Over Genetic-Engineering; Biomimicry Seems The Better Bet For Solving Global Hunger."

The Forbes site said I could comment using my Google identity, if they could just have access to my contact list. No thanks. I"m amazed it's even legal to ask, if it is.

So I'll comment here. Biomimicry is a major theme of my recently published book, Darwinian Agriculture -- but biomimicry of what?

The adaptations of individual plants, animals, and microbes have been improved (by the criterion of Darwinian fitness in past environments) through millions of years of competitive testing against alternatives. But larger-scale patterns we see in nature, such as the total number of species in a forest, or how trees are arranged, haven't been tested competitively. Trees compete against trees, but forests don't compete against forests.

If we copy individual adaptations of trees, we are copying the winners of many past rounds of competition. A forest may have persisted for thousands of years, so it's probably not too dysfunctional. But it hasn't been tested through repeated competition, so there's likely to be plenty of room for improvement.

I would have expected a writer at Forbes -- do they still call themselves "a capitalist tool?" -- to understand how competition is key to improvement, but apparently not.

Now, what about the specific examples in the Forbes post? Spiders compete against spiders and sharks compete against sharks, so it's not surprising that spider silk and shark skin are awesome.

But his "favorite" example is that wildlife corridors that mimic electric circuits work better. I'm not sure what point Kotler is trying to make here -- did he not notice that this is biomimicry in the opposite direction? Although caribou have competed against caribou, curved and straight wildlife migration corridors haven't competed against each other. (OK, maybe they have competed for caribou and their manure, sort of, but the winning corridors don't produce "offspring" with the same degree of curvature.) So this case calls for intelligent design by humans, not mimicry of large-scale patterns seen in nature.

And then there's the endophyte example. Some fungi that live inside plants can provide major benefits to those plants. We will be reading and discussing journal articles about this in a couple weeks, in our graduate seminar.

If there were only one fungus per plant, fungi that benefit their hosts would thereby benefit themselves. But mixed infections seems to be common. With mixed infection, a fungus that invests resources to benefit the host is like someone who pays taxes when nobody else does. Admirable, perhaps, but not likely to be very successful. It's a variation on the classic "tragedy of the commons."

One benefit often provided by endophytes is chemical defense against a plant's enemies. This case isn't too hard to understand. Maybe the various fungi make toxic chemicals to attack each other, since they're competing for the same plant resources, and those same toxins also protect against insects that might otherwise eat the plant.

But how and why do endophytes improve drought tolerance? Unlike mycorrhizal fungi, which extend out into the soil, most endophytes are entirely inside the plant. So it's not as if they can pull more water out of the soil. Sure, they can produce chemicals that mimic plant hormones, thereby manipulating the plant to make more (or fewer) roots or to open (or close) the stomata through which water evaporates from leaves.

But it's hard for me to believe that:
1) a fungus infecting a plant is a better judge of how many roots a plant needs than the plant is
2) that the fungus would put the plant's interests ahead of its own.

It's a mystery. But that's what science does: solve mysteries. Stay tuned.


July 8, 2012

Evolution of cooperation in Ottawa

MikeTravisanoMulticellularity.jpg
Mike Travisano discusses experimental evolution of multicellularity.

My talk here at the Evolution meetings inn Ottawa was taking 12 minutes in practice but I finished in 10. Nervous? Maybe, because I was arguing that most past measurements of fitness benefits to legumes from rhizobia are suspect, which would throw lots of results into question.

Typically, people who want to compare benefits from two different rhizobial strains inoculate host plants with each strain separately, then compare plant growth. But plants in the field are almost always nodulated by multiple strains. I showed that a plant inoculated with a slow-nodulating but highly efficient strain (which eventually provides lots of nitrogen, relative to its carbon cost) may provide no more growth than a less-efficient but faster nodulating strain, when each is inoculated alone. The problem is that plants with only the slow, efficient strain will be short of nitrogen at first, with compound-interest effects on growth. In the field, though, there will always be some fast-nodulating rhizobia. So it's not a matter of nodules vs. no nodules, but of how efficient those nodules are. So we inoculate plants with the two strains being compared, in different ratios, then measure plant growth as a function of the percent of nodules containing the focal strain. With this method, a computer model and actual data agree that an increase in growth with nodule occupancy by the focal strain indicates a more-efficient strain.

Maren Friesen suggested a similar method in a recent paper in New Phytologist. Unfortunately, her main conclusions were based on the old, one-strain-per-plant method.

Megan Frederickson gave a stimulating talk on cheating in symbionts. We have shown that soybean, alfalfa, and peas all impose fitness-reducing sanctions on rhizobia that fail to fix nitrogen, once established inside root nodules. Frederickson asked what maintains such sanctions? If they work, "cheaters" will be rare, so there will be only weak selection on legumes to maintain sanctions. She suggested that something else (such as a generalized response of sending more resources to parts of a root that supply more nitrogen) must select for the responses we call sanctions.

I agree that cheaters would be rare under consistent sanctions, which could relax selection to maintain sanctions. But sanctions may not be that consistent. See Toby Kiers' "measured sanctions" paper. And maybe only a fraction of less-beneficial rhizobia are cheaters, that is, strains that benefit from diverting resources from nitrogen fixation to their own reproduction. Many may be defective mutants, that fix less nitrogen but don't benefit thereby. Sanctions would keep any individual strain of defective mutant rare, but there could be many different strains.

Frederickson's talk stimulated a lot of useful discussion afterwards and I am looking forward to seeing her paper.

August 19, 2011

Reciprocity maintains cooperation between plants and mycorrhizal fungi

Mycorrhizal fungi attach to plant roots and trade phosphorus (and sometimes other benefits) for photosynthates. But is it really "trade"? In other words, if one partner defects, will the other continue its contribution? A recent paper in Science, by Toby Kiers and colleagues, shows that the term, "trade" is justified.(Kiers et al. 2011)

Earlier, as my first PhD student, Toby showed that symbiotic rhizobia, living inside soybean root nodules, can't stop supplying the plant with nitrogen without suffering a decrease in their own fitness.(Kiers et al. 2003) We called the plant response "sanctions", although this could be misinterpreted as an attempt by the plant to improve the behavior of the rhizobia. We assume that the behavior of a given rhizobial genotype is programmed by its DNA, but sanctions against less-beneficial strains will decrease their frequency in subsequent generations. More recently, Ryoko Oono demonstrated a subtler form of sanctions against potentially reproductive rhizobia when their nonreproductive clonemates stop fixing nitrogen.(Oono et al. 2011)

Different strains of rhizobia on the same plant are (mostly) segregated in different root nodules, so "shutting down" one nodule preferentially hurts a single strain of rhizobia. But multiple strains of mycorrhizal fungus typically infect the same root. Can plants preferentially allocate resources to the most-beneficial fungi? Jim Bever and colleagues showed that they can, when different strains are attached to different parts of the root, but apparently not when the strains are more mixed.(Bever et al. 2009) Results from Kiers' group, however, suggest that mixing is not a problem.

They grew Medicago truncatula (a model species related to alfalfa) with mixtures of mycorrhizal fungi that they classified as more- or less-beneficial. To track photosynthate allocation, they let plant photosynthesis take up carbon dioxide containing the heavier 13C isotope of carbon. To see which fungi got more of this carbon, they used a clever technique.

They extracted RNA from the fungi and separated it into lighter and heavier (more-recent-plant-carbon) fractions, using a centrifuge. Then they used difference in the RNA base sequences of their different fungi to measure their relative representation in the light and heavy fractions. Fungi with greater representation in the heavy fraction were getting more recently supplied carbon from the plant, so they were benefiting more from symbiosis. A more-beneficial fungal species got more carbon than either of two less-beneficial species. This result is consistent with host sanctions (or, since each fungus interacts with multiple plants, with a "biological market" where individuals trade more with those that offer the best deal).

It's hard to measure all of the benefits a mycorrhizal fungus provides, however, so they also manipulated the exchange of specific resources. The species they classified as more beneficial got more carbon when it had access to more phosphorus, and presumably supplied it to the plant. A less-beneficial species didn't get more carbon when it had access to more phosphorus, perhaps because it didn't give much of the phosphorus to the plant. Similarly, the cooperative strain apparently responded to differences in carbon supply from the plant, allocating more phosphorus to where it was getting more carbon. So sanctions appear to go both ways.

LITERATURE CITED

Bever J. D., S. C. Richardson, B. M. Lawrence, J. Holmes, and M. Watson. 2009. Preferential allocation to beneficial symbiont with spatial structure maintains mycorrhizal mutualism. Ecology Letters 12:13-21.

Kiers E. T., M. Duhamel, Y. Yugandgar, J. A. Mensah, O. Franken, E. Verbruggen, C. R. Felbaum, G. A. Kowalchuk, M. M. Hart, A. Bago, T. M. Palmer, S. A. West, P. Vandenkoornhuyse, J. Jansa, and H. Bücking. 2011. Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333:880-882.

Kiers E. T., R. A. Rousseau, S. A. West, and R. F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81.

Oono R., C. G. Anderson, and R. F. Denison. 2011. Failure to fix nitrogen by non-reproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates. Proceedings of the Royal Society B 278:2698-2703.

August 12, 2011

This week's picks

Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis Toby Kiers, who previously demonstrated host sanctions against cheating rhizobia, now shows that plants give less carbon to less-beneficial mycorrhizal fungi. I hope I can find time to discuss this paper in more detail soon.

Natural variation in Pristionchus pacificus dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones "strains may have evolved to induce dauer formation precociously in other strains in order to reduce the fitness of these strains"

Nest Inheritance Is the Missing Source of Direct Fitness in a Primitively Eusocial Insect

Polyandrous females benefit by producing sons that achieve high reproductive success in a competitive environment

Kin selection in den sharing develops under limited availability of tree hollows for a forest marsupial

Aging of the cerebral cortex differs between humans and chimpanzees "significant aging effects in humans were... individuals that were older than the maximum longevity of chimpanzees. Thus... brain structure shrinkage in human aging is evolutionarily novel and the result of an extended lifespan"

Bacterial persistence by RNA endonucleases

Host-parasite local adaptation after experimental coevolution of Caenorhabditis elegans and its microparasite Bacillus thuringiensis

Sperm chemotaxis, fluid shear, and the evolution of sexual reproduction

August 7, 2011

Nitrogen-fixing cereals?

This week's paper was published in Science (Beatty and Good 2011). It discusses the prospects for developing cereals, like wheat or rice, that can use ("fix") atmospheric nitrogen. This paper was brought to my attention both by my wife, Cindy, by Andy McGuire. As my first graduate student, at UC Davis, Andy tested the use of legume "green manures", which form symbioses with nitrogen-fixing rhizobia bacteria, to supply nitrogen to a subsequent wheat crop. (McGuire et al. 1998)

This week's paper suggests three approaches. Maybe we could engineer cereals to host rhizobia in root nodules, similar to those found on legumes. Maybe we could encourage looser associations between cereals and bacteria to fix nitrogen in or on the plant, even without nodules. Or, maybe we could engineer the plants themselves to fix nitrogen.

The authors note that the proposed cereal-root nodules would need to provide a low-oxygen environment, to protect the key enzyme, nitrogenase. Just keeping oxygen low isn't that difficult. Legume nodules have a physical barrier to gas diffusion that limits oxygen influx to the nodule interior, and it might not be that hard to do something similar in cereals. But rhizobial nitrogen fixation is powered by respiration, which requires lots of oxygen. So rhizobia need a high oxygen flux, in addition to a low oxygen concentration. Diffusion is slow at the low concentrations beyond the diffusion barrier, so diffusion of free oxygen within rhizobia-infected cells can't meet demand. Much of the oxygen is carried by diffusion of a plant hemoglobin, whose high concentration makes the inside of legume root nodules red.

And that's not the end of the challenges we would need to overcome to put functional root nodules on cereals. Suppose the diffusion barrier were just thick enough that respiratory uptake drops oxygen concentration from atmospheric (21 kPa) to the targeted near-zero concentration (1 kPa, say) across the diffusion barrier. What if the respiration rate drops to 90% of it's current value? (A slight decrease in soil temperature could have this effect, as could a shortage of photosynthate.) The concentration drop across the barrier is proportional to the flux (Fick's Law of Diffusion, similar to Ohms law for electricity), so the concentration drop would now be 18 kPa instead of 20 kPa. So the nodule-interior oxygen would now be 3 kPa instead of 1 kPa. 3 kPa is probably high enough to destroy nitrogenase.

Evolution has solved this problem, too, at least in legumes. As conditions change, legumes adjust the gas permeability of their nodules to keep oxygen low enough to protect nitrogenase, but high enough for respiration to meet their nitrogen-fixation needs. When sheep graze clover plants, the resulting photosynthate shortage decreases nodule respiration, so you might expect nodule-interior oxygen levels to rise, perhaps endangering nitrogenase. But clover plants decrease their nodule gas permeability decreases so much that nodule-interior oxygen actually decreases, rather than increasing (Hartwig et al. 1987, Denison and Okano 2003). Cereal root nodules would need something similar.

If we could engineer cereal crops to allow infection by rhizobia and support their reproduction inside root nodules that actively regulate oxygen supply, maybe the rhizobia would fix nitrogen there... at first.

But, like all living things, rhizobia evolve. Any mutation that reduced rhizobial investment in nitrogen fixation would free resources for additional rhizobial reproduction. If there were only one rhizobial genotype per plant, this "cheating" would be self-defeating, because a nitrogen-starved plant would have less photosynthate to support rhizobia. But, with multiple genotypes per plant, we have a "tragedy of the commons", favoring cheaters.(Denison 2000, West et al. 2002)

Legume evolution has found at least a partial solution to this problem, too, although there's probably room for improvement. Although moderate levels of cheating may be tolerated (Kiers et al. 2006), major diversion of resources from nitrogen fixation to rhizobial reproduction triggers host "sanctions", which reduce the fitness of rhizobial cheaters (Kiers et al. 2003, Oono et al. 2011). If we don't want nitrogen-fixing cereals to waste photosynthate supporting nonfixing rhizobia, they would need to impose sanctions, too. Or maybe growing them in rotation with sanction-imposing legumes hosting the same rhizobia would be enough to keep rhizobial cheaters rare.

What about the second option, cereals without nodules, but associating with nitrogen fixers? To meet a significant fraction of a cereal's nitrogen needs, we would need to regulate oxygen supply, as in nodules. And we would soon face the same problem of cheaters (Kiers and Denison 2008), so we'd also need some form of sanctions. If we're have to duplicate the functions of nodules anyway, why not copy nodules, rather than starting from scratch?

Engineering the cereals themselves to fix nitrogen, without rhizobia, would solve the problem of cheaters. The article suggests that it might be possible to add nitrogen fixation to plant mitochondria, the current site of respiration, or to chloroplasts, responsible for photosynthesis. Photosynthesis generates oxygen, which would tend to destroy nitrogenase. But the authors say that "some cyanobacteria perform photosynthesis and nitrogen fixation in the same space but at separate times" - maybe chloroplasts could somehow shield nitrogenase from oxygen during the day, when they're photosynthesizing, and activate nitrogenase only at night. This seems possible, at least in theory. But could it be done soon enough to help avert looming food shortages?

The article closes with the hope that "if nitrogen supply and carbon metabolism can be closely coupled, excess nitrogen would not be lost to the environment." That is already true of legumes, which shut down nodules when they have as much nitrogen as they need (Denison and Harter 1995). But this feedback control evolved - legumes that wasted photosynthate on "extra" nitrogen fixation were out-competed by more-frugal mutants - it would not be an "automatic" outcome of any of the approaches proposed.

So, again, any attempt to develop nitrogen-fixing cereals would benefit from copying what legume nodules already do. It's too bad that we don't yet know the mechanisms that regulate oxygen supply in legume nodules, impose sanctions on rhizobial cheaters, or adjust nitrogen-fixation rate to match nitrogen needs. Regulation of nodule gas permeability appears to be involved in all three, but we don't know how gas permeability is regulated. It's too bad that nobody wants to fund that kind of research any more.

LITERATURE CITED

Beatty P. H., A. G. Good. 2011. Future Prospects for Cereals That Fix Nitrogen. Science 333:416-417.

Denison R. F. 2000. Legume sanctions and the evolution of symbiotic cooperation by rhizobia. American Naturalist 156:567-576.

Denison R. F., Y. Okano. 2003. Leghaemoglobin oxygenation gradients in alfalfa and yellow sweetclover nodules. Journal of Experimental Botany 54:1085-1091.

Denison R. F., B. L. Harter. 1995. Nitrate effects on nodule oxygen permeability and leghemoglobin. Nodule oximetry and computer modeling. Plant Physiology 107:1355-1364.

Hartwig U., B. Boller, and J. Nösberger. 1987. Oxygen supply limits nitrogenase activity of clover nodules after defoliation. Annals of Botany 59:285-291.

Kiers E. T., R. F. Denison. 2008. Sanctions, cooperation, and the stability of plant-rhizosphere mutualisms. Annual Review of Ecology, Evolution, and Systematics 39:215-236.

Kiers E. T., R. A. Rousseau, and R. F. Denison. 2006. Measured sanctions: legume hosts detect quantitative variation in rhizobium cooperation and punish accordingly. Evolutionary Ecology Research 8:1077-1086.

Kiers E. T., R. A. Rousseau, S. A. West, and R. F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81.

McGuire A. M., D. C. Bryant, and R. F. Denison. 1998. Wheat yields, nitrogen uptake, and soil water content following green manure vs. fallow. Agronomy Journal 90:404-410.

Oono R., C. G. Anderson, and R. F. Denison. 2011. Failure to fix nitrogen by non-reproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates. Proceedings of the Royal Society B 278:2698-2703.

West S. A., E. T. Kiers, E. L. Simms, and R. F. Denison. 2002. Sanctions and mutualism stability: why do rhizobia fix nitrogen? Proceedings of the Royal Society B 269:685-694.


July 23, 2011

Beneficial infections?

Endophytes are microbes (often fungi) that infect plants without causing obvious disease. Some endophytes appear to benefit their plant hosts. How do they do this, and why? I will introduce these questions before discussing this week's paper,(Redman et al. 2011) which shows dramatic benefits to rice from particular endophytes.

How might endophytes benefit plants? Mycorrhizal fungi extend out into the soil, where they can get phosphorus and other resources to give their plant hosts. In contrast, endophytes are typically found completely inside the plant, so any resources they "give" the plant must be modified versions of resources they got from the plant in the first place. Nitrogen is a possible exception -- rhizobia bacteria convert atmospheric nitrogen to forms plants can use, but the oxygen-sensitivity of the key enzyme apparently restricts this process to controlled-oxygen environments, such as legume root nodules.

Although endophytes don't have access to external resources, they can make chemicals the plant can't, such as toxins that protect the plant from being eaten. Or, they might make chemicals that the plant could make itself, but in larger amounts than the plant would otherwise make, at least at a particular time and place. For example, endophytes can make plant hormones, which could stimulate growth.

But what do we mean by "stimulate?" If all of the phosphorus, nitrogen, and carbon in the endophyte comes from the plant, any stimulation must result from the plant using its own resources differently than it would without the endophyte. In other words, the endophyte is manipulating the plant. For whose benefit? That leads to my second question.

Why do endophytes benefit plants? That is, why have endophyte strains that benefit their hosts more sometimes out-competed strains that benefit their hosts less, over the course of endophyte evolution? Mutant endophyte strains that don't make plant-defense toxins or (beneficial?) plant-manipulating hormones must arise. Making these chemicals uses resources the endophyte could otherwise use to reproduce more inside the plant. For strains that make beneficial chemicals to persist over evolution, they must have some advantage that outweighs this cost. I can imagine several ways in which beneficial endophytes might have an advantage.

The first is "group selection", with the group being all the endophytes inside an individual plant. Plants with more-beneficial endophytes grow more than plants with less-beneficial endophytes, and larger plants support more endophytes. If each plant contains only a single genotype of endophyte, this mechanism should work well. But defense of cacao leaves from pathogens was provided by a diverse community of endophytes.(Arnold et al. 2003) If a healthier shared host was the only benefit each endophyte received, wouldn't "free-rider" mutants that invest less in host defense tend to spread?(Denison et al., 2003b; Kiers and Denison 2008)

Maybe the endophytes make antifungal toxins mainly to kill each other, and defense against fungal pathogens is just a valuable side-effect. Such "byproduct mutualism" is an example of the second reason that more-beneficial endophytes may persist.

The third hypothesis is a minor variation on by-product mutualism. Endophyte infection is so common that plants may have evolved to depend on products produced by endophytes, even if the plants (or their ancestors) could produce those products themselves. For example, why might a plant be genetically programmed to make too little of some hormone that would maximize its reproduction? Perhaps because most of its ancestors were infected by endophytes producing that same hormone, so for the plant to make even more of it would have reduced fitness.

Third, maybe individual plants containing multiple strains of endophyte somehow favor the most-beneficial strains, reversing the benefit "free-riders" would otherwise have. Host sanctions against less-beneficial rhizobia(Kiers et al. 2003, Simms et al. 2006, Oono et al. 2011) and mycorrhizal fungi(Bever et al. 2009) have been reported, but is anything similar possible with endophytes?

Fourth, some apparent benefits to plants from endophytes may be misleading. Increased root growth may look like a benefit, but remember that the carbon and nitrogen in that root come from the plant, not the endophyte. So, at least in the short term, increased root growth usually comes at the expense of decreased shoot growth or more rapid depletion of reserves. For example, root-associated microbes that increase root growth of wheat can decrease final yield.(Kapulnik et al. 1987) Even if an endophyte-induced change in resource allocation increases seed production of plants growing individually in pots in a greenhouse, the same change might decrease seed production under competitive conditions in the field.

Now to this week's paper.(Redman et al. 2011) PLoS One is open access, so you can read the whole paper on-line. Regina Redman and colleagues inoculated rice with three different fungal endophytes, which had been isolated from plants growing under salt- or temperature-stress conditions. The fungi produced the plant hormone, IAA (auxin), at least in culture. This is consistent with manipulation of the host as a mechanism, although they didn't detect IAA in the plants themselves.

Although their focus was on stress tolerance, results under nonstress conditions were particularly interesting. Right after germination, infected and noninfected seedlings look similar (their Fig. 2). But after three days, the dry weight of three-day old seedlings not infected with endophytes averaged 60 milligrams (dry weight), while endophyte-infected seedlings averaged 105 mgDW (their Fig. 1). Both weights must include contributions from early photosynthesis, since rice seeds typically weigh only 20-30 mg. Somehow, the endophyte must have increased photosynthesis.

But how could the endophyte increase photosynthesis, if all the resources in the endophyte came from the plant? Actually, right after inoculation, the endophyte would still have some nitrogen and phosphorus acquired during culture. But would they have enough to share to significantly enhance early seedling growth?

Alternatively, the endophyte might have manipulated the plant into using its own resources differently than it would have without the endophyte. (We could call this manipulation "signaling" if the endophyte is providing the plant with useful information for mutual benefit,(Ratcliff and Denison 2011) but what information would an endophyte entirely inside a plant have that the plant itself wouldn't?)

For example, plants can photosynthesize faster if they open the stomatal pores in their leaves more, but that also uses up the soil water around their roots faster, increasing the risk of running out. Could an endophyte-induced increase in stomatal opening over-ride the plant's own water-use strategies? Sure, but what are the chances that the endophyte's strategy is better for the plant? That would seem unlikely, at least under the conditions where the plant evolved. But we wouldn't necessarily expect plant strategies that evolved in the field to be ideal in the greenhouse. A small change in either direction would have a 50% chance of being an improvement. Maybe the endophyte got lucky.

I've suggested increased stomatal opening as one way the endophyte could have increased seedling photosynthesis. Later in growth, however, endophyte-infected plants used less water than those without endophytes and took longer to wilt after watering (their Fig. 3). It's not clear, however, how much of the water use went through stomata, as opposed to evaporating from the soil surface. The endophyte-infected plants were much bigger than the noninfected plants by then, so they would have shaded the soil surface more.

As an alternative to greater stomatal opening, that about allocation to roots? Photos suggest that the noninfected seedlings initially invested more resources in shoots than in roots, whereas the endophyte-infected ones invested more in roots. If the endophytes infect mainly via the root, it's easy to understand why they might manipulate the plant to make more root. But why would plants have evolved to make too little root, when not infected by endophytes? Again, I see two likely possibilities. Maybe the plant's greater allocation to shoot is optimal for the conditions where it evolved(Denison et al. 2003, Denison in press) (germinating underwater in rice fields) but this gives too little root growth under the experimental conditions used in this study. This seems the most likely explanation. Alternatively, rice may be adapted to the presence of endophytes that produce similar hormones to those used in this study, so they have evolved to make hormone amounts that are suboptimal when not infected by endophytes.

Late in growth there were differences between treatments in reactive oxygen species, and the endophyte-infected plants had higher seed yields. The paper also shows beneficial effects on rice growth under low-temperature stress. But I would like to understand the benefits of the endophyte to three-day-old unstressed seedlings before getting into such details.

For practical applications, a more-complete understanding of how endophytes benefit plants would be useful, either to help us identify even better endophytes or to breed crops that get the same benefits with whatever endophytes they usually have now. Understanding endophyte evolution could be equally important. If it is some form of group selection that gives more-beneficial endophytes an edge over free-riders, can we maintain that process in agriculture? If some plant are imposing sanctions on less-beneficial endophytes, we certainly want to preserve that plant trait in our crop-breeding programs, or look for it in wild species and traditional crop cultivars.(Denison et al., 2003a, Denison in press) On the other hand, if endophytes are manipulating their plant hosts in ways that always benefit the endophyte, but which benefit the plant only under certain conditions, then we need to test endophytes under conditions more similar to how the crops will be grown in the field. In any case, this is a very interesting paper which (with related papers from the same group) could lead to exciting new approaches to improving crop production.


LITERATURE CITED

Arnold A. E., L. C. Mejia, D. Kyllo, E. I. Rojas, Z. Maynard, N. Robbins, and E. A. Herre. 2003. Fungal endophytes limit pathogen damage in a tropical tree. Proceedings of the National Academy of Sciences USA 100:15649-15654.

Bever J. D., S. C. Richardson, B. M. Lawrence, J. Holmes, and M. Watson. 2009. Preferential allocation to beneficial symbiont with spatial structure maintains mycorrhizal mutualism. Ecology Letters 12:13-21.

Denison R. F. in press. Darwinian agriculture: how understanding evolution can improve agriculture. Princeton University Press, Princeton.

Denison R. F., E. T. Kiers, and S. A. West. 2003a. Darwinian agriculture: when can humans find solutions beyond the reach of natural selection? Quarterly Review of Biology 78:145-168.

Denison R. F., C. Bledsoe, M. L. Kahn, F. O'Gara, E. L. Simms, and L. S. Thomashow. 2003b. Cooperation in the rhizosphere and the "free rider" problem. Ecology 84:838-845.

Kapulnik Y., Y. Okon, and Y. Henis. 1987. Yield response of spring wheat cultivars (Triticum aestivum and T. turgidum) to inoculation with Azospirillum brasilense under field conditions. Biology and Fertility of Soils 4:27-35.

Kiers E. T., R. F. Denison. 2008. Sanctions, cooperation, and the stability of plant-rhizosphere mutualisms. Annual Review of Ecology, Evolution, and Systematics 39:215-236.

Kiers E. T., R. A. Rousseau, S. A. West, and R. F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81.

Oono R., C. G. Anderson, and R. F. Denison. 2011. Failure to fix nitrogen by non-reproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates. Proceedings of the Royal Society B :doi: 10.1098/rspb.2010.2193.

Ratcliff W. C., R. F. Denison. 2011. Alternative actions for antibiotics. Science 332:547-548.

Redman R. S., Y. O. Kim, C. J. D. A. Woodward, C. Greer, L. Espino, S. L. Doty, and R. J. Rodriguez. 2011. Increased Fitness of Rice Plants to Abiotic Stress Via Habitat Adapted Symbiosis: A Strategy for Mitigating Impacts of Climate Change. PLoS ONE :e14823.

Simms E. L., D. L. Taylor, J. Povich, R. P. Shefferson, J. L. Sachs, M. Urbina, and Y. Tausczik. 2006. An empirical test of partner choice mechanisms in a wild legume-rhizobium interaction. Proceedings of the Royal Society B 273:77-81.


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"

January 26, 2011

Plants punish cheaters' relatives

This week's paper is the fourth from Ryoko Oono's PhD thesis. "Failure to fix nitrogen by non-reproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates" was just published on-line in Proceedings of the Royal Society.
AlfalfaSanctions.jpg
Rhizobia are bacteria that can live either in soil or in root nodules, like those shown above. Legume plants (alfalfa, soybean, the lupines loved by Monty Python and many wild species) let rhizobia in because the rhizobia (usually) convert atmospheric nitrogen into forms the plant can use.

But what if the rhizobia don't deliver? What if, once established inside a nodule, they use plant resources only for their own reproduction? In my most-cited paper, Toby Kiers showed that soybean plants impose fitness-reducing "sanctions" on rhizobia that fail to fix nitrogen. Ellen Simms' lab found similar results with wild lupines. But Ryoko had three good reasons to question whether certain legumes, including alfalfa and pea, impose sanctions similar to soybean's.

Continue reading "Plants punish cheaters' relatives" »

January 12, 2011

Making symbiotic rhizobia more efficient

This week I'll discuss a recent paper by Ryoko Oono, one of five from her PhD work. (If you want to hire her as a postdoc, better hurry!) Comparing Symbiotic Efficiency between Swollen versus Nonswollen Rhizobial Bacteroids, published in Plant Physiology, is available for anyone to read on-line.

Here's a little background. Rhizobia are soil bacteria, best known for infecting the roots of legume plants (clover, lupine, bean, pea, alfalfa, and many others) and multiplying inside root nodules, where they "fix" nitrogen gas from the atmosphere, converting it into forms their plant hosts can use, instead of relying on fertilizer.

Thumbnail image for AlfalfaNodules2.jpg


Left: Alfalfa nodules; copyright Inga Spence, used by permission. Below left: nonswollen bacteroids. Below right: swollen bacteroids.
Thumbnail image for Bacteroids.jpg

Apparently, rhizobia in the soil never fix nitrogen. Inside root nodules, however, some of them develop into bacteroids, which use some of the plant-supplied carbon they consume to power nitrogen fixation. They may also hoard some carbon for their own future survival and reproduction, a possible source of conflict with their host.

In nodules of some legume hosts, including pea and alfalfa, bacteroids are swollen (above right) and have lost the ability to reproduce. In other hosts, bacteroids don't look that different from the free-living rhizobia, and retain the ability to reproduce. Why this difference?

Continue reading "Making symbiotic rhizobia more efficient" »

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.
Seed-iriartea.jpeg
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!

Continue reading "Mutualisms in a changing world: an evolutionary perspective" »

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.
SolarTrackingAlfalfa.jpg
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?

Continue reading "Why do leaves really track the sun?" »

September 22, 2010

Garbage in, garbage out, in modeling symbiosis

Every year or two, someone publishes a computer model showing how easy it would be for cooperation between species to evolve, if only the world were fundamentally different than it actually is. In particular, many models incorrectly assume that there is only one symbiont genotype per host individual.

The latest paper to make this incorrect assumption was published in Proceedings of the National Academy of Science, and titled "Economic contract theory tests models of mutualism." The paper admits that:

"the fact that legumes are often infected by multiple strains of rhizobia [symbiotic bacteria that provide plants with nitrogen] remains a problem, because our model assumes only one type of agent."
Similarly, each individual plant typically interacts with several different mycorrhizal fungi and many different pollinators. How much difference does this make? Enough difference to completely reverse their conclusions that "positive feedback between host fitness and symbiont fitness is sufficient to prevent cheating."
West2002.jpg
We showed in 2002 that symbionts that benefit their hosts more would out-compete those that benefit their hosts less (even in the absence of "host sanctions", discussed below), if there were only one symbiont genotype per host (above right). That is the situation incorrectly assumed by Weyl et al. (2010). In the real world, however, with multiple symbionts per host, strains that divert more host resources to their own reproduction would win (above left). For rhizobia, if nitrogen is readily available in the soil (s=0.5), then as few as two strains per host is enough to undermine cooperation, unless hosts impose sanctions on cheaters. Source: West et al. (2002) "Sanctions and mutualism stability: why do rhizobia fix nitrogen?" Proc. Roy. Soc. B 269:685-694.

Weyl et al. (2010) is one of the 100+ papers to cite our 2002 paper, but the critical importance of multiple symbionts per host doesn't seem to have sunk in. If you're looking for a model that represents an actual advance on our 2002 paper, rather than an embarassing retreat, I recommend Maren Friesen's "Mixed infections may promote diversification of mutualistic symbionts: why are there ineffective rhizobia?", J. Evol. Biol. 23:323.

West et al. (2002) also showed that then-hypothetical "host sanctions" imposed by legume plants against symbiotic rhizobia that fail to provide them with nitrogen can prevent the evolutionary breakdown in rhizobial cooperation shown above. Toby Kiers subsequently showed that soybean plants, at least, do actually impose such sanctions on individual root nodules that fail to provide the host with nitrogen ("Host sanctions and the legume-rhizobium mutualism", Nature 425:78). But, Friesen and Mathias asked, what if some nodules contain more than one genotype of rhizobia? Depending on the frequency of mixed nodules, they showed that rhizobial "cheaters" can coexist with more-beneficial strains.

August 19, 2010

Evolution-proof pest-resistant crops?

This week's paper is "Alarm pheromone habituation in Myzus persicae has fitness consequences and causes extensive gene expression changes", published in PNAS by Martin de Vos and others.

Aphids suck. This wouldn't be too big a problem for their host plants, except that they sometimes transmit viruses. Some plants repel these pests by giving off gases very similar to the chemical alarm signals aphids release when attacked by predators. Could crops be genetically engineered to do this? Probably, but would it work, or would the aphids evolve to ignore these signals and keep on sucking?

To answer this question, the authors studied aphids on plants genetically engineered to make aphid alarm signal.

Continue reading "Evolution-proof pest-resistant crops?" »

July 31, 2010

Evolutionary history of yucca moths

I've written a few posts about ancestral-state reconstruction, where we use molecular or other information from living species to infer the traits of their shared ancestors. But I really like this post in which PhD student Jeremy Yoder describes his own work.

There's a nice diagram showing the general approach, then he looks at yucca moths and their relatives to figure out what their ancestors did. Yucca moths, like fig wasps, lay their eggs in flowers. Their larvae eat seeds, but the moths pollinate the flowers, so it's not too bad a deal overall. Their ancestors, he concludes, fed inside developing flowers, but without pollinating them. Maybe the world is getting a little more cooperative, after all.

May 19, 2010

15 minutes of fame

Science writer Carl Zimmer has posted his "Meet the Scientist" podcast interview with me on the Microbe World web page.

A story about our PLoS One paper was 2010's most-viewed research report on the University of Minnesota web page.

Separately, my PhD student, Will Ratcliff, was one of four students featured on the University of Minnesota web page. In the video (upper right, labeled "Multimedia"), he alternates with three social scientists.

May 15, 2010

Evolution of DNA methylation in animals, plants, and fungi

This week, I will try to explain what DNA methylation is and some of the reasons why it's important, before discussing this week's paper on how DNA methylation has evolved.

The paper is "Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation", published in Science by Assaf Zemach and others from the lab of Daniel Zilberman.

DNA methylation usually refers to the attachment of a methyl (CH3) group to a cytosine, one of four DNA bases (C, in DNA's A,T,C,G alphabet). Here's a link showing one way cytidine can get methylated. And this Wikipedia article shows cytosine in place in double-stranded RNA. (DNA would be similar, but with T instead of U.)

The functions of DNA methylation mostly come from the reduced transcription of RNA from methylated stretches of DNA. Surprisingly, when a new DNA copy is made (e.g., when one of our cells divide), methylation patterns are generally copied, too. Together, these two facts explain many of DNA methylation's functions.

First, DNA methylation is key to imprinting, whereby genes inherited from one parent are often shut down, perhaps for life, by methylation. Imprinting often reflects an unconscious battle between male and female parents over whether to maximize growth of this particular offspring, whatever the consequences for the mother's future survival and reproduction, or take or more long-term view. Earlier, I discussed the possible role of imprinting in mental illness.

Continue reading "Evolution of DNA methylation in animals, plants, and fungi" »

May 7, 2010

E-word in NYT -- a bigger surprise than Roundup-ready weeds?

There have been isolated reports, for years, of various weeds evolving resistance to glyphosate (sold commercially as Roundup etc.), but now glyphosate-resistance is showing up in pigweed, a major problem for farmers in the US and elsewhere. Among alternative ways to kill weeds, other herbicides are mostly more toxic and break down more slowly, whereas mechanical cultivation tends to increase erosion.

On the positive side, maybe more people will buy my book on Darwinian Agriculture, although I'll have to revise it before publication to turn what was a prediction into a fact. Maybe I can get some Neanderthal crackpot with a radio show to accuse me of deliberately spreading Roundup-resistant weeds to increase sales. You can't buy publicity like that! But I'd rather have clean rivers than a best-selling book.

I was impressed that many of the experts discussing the problem in the New York Times referred to "evolution" or "natural selection", although one referred to weeds as "opponents that can adjust" (as if individual plants were trying different ways to survive herbicides) and said that some weeds can "mutate to survive", as if mutation were somehow directed. Plants have evolved so that individuals can adjust to certain changes in their environment (drying soil, for example). But it's populations, not individuals, that evolve. And, in this case, they evolved mainly because herbicide-susceptible individuals did not survive. I assume the author knows this, but some readers could be misled.

Maybe now people will start paying more attention to management practices that slow the evolution of herbicide resistance. Resistance-management programs for insect pests, to slow the evolution of resistance to the Bt toxin, seem to be working reasonably well, but there's nothing similar in place for weeds yet.

One important difference is that the insects plaguing an individual farmer may well come from a distant neighbor, so there's little individual incentive to implement expensive resistance-management programs. An individual farmer's weed problems, on the other hand, are much more dependent on how they were managed on that same farm in the past. So farmers may be more motivated to invent and implement resistance-management strategies for weeds.

One of my favorite weed management strategies is alternating, every few years, between using a field for grazed pasture, where weeds of row crops tend to die out, in rotation with row crops, where pasture weeds tend to die out. That requires farmers with the expertise and willingness to work with both crops and livestock, however. And milk or meat from animals eating mostly grass and clover may be more expensive than the same products produced in a feedlot.

May 6, 2010

Do legume hosts benefit from suppressing rhizobial reproduction?

This week's paper is by my PhD student Ryoko Oono, with major contributions from Imke Schmitt (University of Minnesota faculty) and Janet Sprent, who was an expert on legume-rhizobium evolution long before I started working on the problem.

"Multiple evolutionary origins of legume traits leading to extreme rhizobial differentiation" has been published on-line in New Phytologist.

Rhizobia are soil bacteria, but a lucky few accept invitations from legume plants to infect their roots, multiply a million-fold or more inside a nodule, and then convert ("fix") atmospheric nitrogen into a form that the plant can use. When the plant dies (or sometimes sooner), an unknown fraction of the rhizobia in each nodule escape back into the soil.

Below left is what rhizobia look like in the soil and in the nodules of some legume hosts, including soybean. In other hosts, including pea, they swell up and/or change their shape (below right, same scale) as they differentiate into the nitrogen-fixing bacteroid form. The swollen form is apparently nonreproductive (like worker bees), but copies of their genes can still end up back in the soil. This is because some of their clonemates in the same nodule haven't become bacteroids yet and so retain the ability to reproduce, like queen bees.
Bacteroids.jpg
The extreme differentiation shown above right is imposed by the legume host. But why? Are swollen bacteroids somehow more beneficial to the plant? Or are bacteroid swelling and their losing the ability to reproduce side-effects of some other process that may or may not benefit the plant?

Ryoko reasoned that, if a plant trait has evolved repeatedly over the course of evolution, then it is probably beneficial to the plant. On the other hand, a trait that has been abandoned repeatedly is probably harmful. But has either of these happened?

Continue reading "Do legume hosts benefit from suppressing rhizobial reproduction?" »

April 16, 2010

Sanctions and cheating in pollination and protection mutualisms

The most-cited paper from my lab is one by Toby Kiers, showing that soybean plants impose fitness-reducing sanctions on "cheating" rhizobia, which multiply inside root nodules but then fail to provide their hosts with nitrogen. This week I will briefly discuss two recent papers on the role of sanctions in two different kinds of mutually beneficial interactions between species.

Toby is also one of the coauthors on the first paper by Ryutaro Goto and others. The author/year citation (Goto 2010 ) reminds me of programming computers in Fortran, but the full title is "Selective flower abortion maintains moth cooperation in a newly discovered pollination mutualism." The second paper, by David Edwards and others, discusses ants that protect trees from browsing animals. This paper asks, "Can the failure to punish promote cheating in mutualism?"

Clochidion trees in Japan are pollinated by moths. Like the moths that pollinate yuccas and the wasps that pollinate figs, these moths lay eggs as they pollinate, and their larvae then consume some seeds. What keeps the moths from laying too many eggs in a given flower?

Continue reading "Sanctions and cheating in pollination and protection mutualisms" »

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" »

January 17, 2010

Altruistic punishment by fig trees?

As I was getting ready to write about some of the talks at the Applied Evolution Summit, I received a very interesting paper: Host sanctions and pollinator cheating in the fig tree - fig wasp mutualism, which was recently published in Proceedings of the Royal Society by Charlotte Jander and Allen Herre.

Fig-tree fruits are lined with many little flowers. Female wasps crawl inside to lay their eggs, often carrying pollen from the fig where they, themselves, hatched from an egg. Different fig species host different wasp species. Some wasp species are like many other pollinators, carrying pollen only by accident; fig trees pollinated by these species have to make lots of pollen. Other figs are pollinated by wasps that actively collect pollen and actively pollinate flowers inside fig fruits; these fig species can make less pollen, which frees resources to make more seeds.

But there is presumably some cost to the wasps of transporting pollen. Why not save this cost, travel light, and lay eggs in a fig fruit without pollinating its flowers? This is essentially the same question people in my lab have asked about rhizobia, the bacteria that provide legume plants with nitrogen: once rhizobia have reproduced inside a root nodule, why stick around and invest resources in pulling nitrogen out of the atmosphere and converting it to a form the plant can use?

The questions are similar and so are the answers....
wasp.JPG
Wasp inside a fig; photo by Charlotte Jander.

Continue reading "Altruistic punishment by fig trees?" »

December 18, 2009

Tradeoff-free longevity?

I'm working on my talk for the Applied Evolution Summit, so don't have time to write a detailed post, but here are some papers that looked interesting, with brief comments on some of them:

Amino-acid imbalance explains extension of lifespan by dietary restriction in Drosophila
(published in Nature by Richard Grandison, Matthew Piper & Linda Partridge)
Dietary restriction reduces reproduction and increases longevity in many species. This study, using fruit-flies, showed that adding the amino acid, methionine, to a restricted diet restored total lifetime reproduction to that of fully-fed flies, but with the greater longevity of restricted-diet flies. Extrapolating to humans, the paper suggests that

the benefits of dietary restriction for health and lifespan may be obtained without impaired fecundity

But, if there would be no reproductive cost to doing so, why haven't flies evolved the ability to discard the "extra" food they get when fully-fed -- except for the methionine -- and live longer? I suspect that the restricted-plus-methionine diet affects the timing of reproduction, but data on timing weren't reported. (Instead, they give an "index of lifetime fecundity.") If overall population size is increasing (as fully-fed flies might expect), individuals that reproduce earlier make a disproportionate contribution to the gene pool. So the evolutionary trade-off may be between longevity and earliness of reproduction, not total reproduction. If population is decreasing, however, individuals who delay reproduction make a larger contribution to the gene pool, as laid out in our "shrinking pool" hypothesis. My guess is that flies respond to the restricted-plus-methionine diet as a cue predicting population decline and reproduce later, thereby gaining the observed increase in longevity. Extrapolating to humans again, we might be able to develop diets or other treatments that increase life-span and health, but which cost us teenage pregnancy. Hmmm... might be worth it.

Click "aging" at right for other posts relevant to this topic.

Regulating Alternative Lifestyles in Entomopathogenic Bacteria

Mozambican Grass Seed Consumption During the Middle Stone Age
If our ancestors were eating grass seeds 100,000 years ago, as this paper seems to show, what kind of selection, inadvertent or perhaps deliberate, were they imposing on those grasses?

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

On the Origin of Species by Natural and Sexual Selection


Coots use hatch order to learn to recognize and reject conspecific brood parasitic chicks
"When experimentally provided with the wrong reference chicks, coots can be induced to discriminate against their own offspring"

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Have giant lobelias evolved several times independently? Life form shifts and historical biogeography of the cosmopolitan and highly diverse subfamily Lobelioideae (Campanulaceae)
DNA analysis suggests that giant Lobelias evolved once and then spread, even to remote places like Hawaii, rather than evolving separately in different locations.

July 31, 2009

Grants!

Just as I was starting to dip into retirement savings to keep my lab going, we got word that both of the grant proposals we sent to the NSF in the latest round were funded, one of them with money from Obama's stimulus funding. We won't be paying ourselves any billion-dollar bonuses, but I may be able to get two months salary this year after all. Both proposals are resubmissions, significantly improved based on suggestions and criticisms from past reviewers. Both projects will use rhizobia, bacteria best known for providing legume plants with nitrogen, but the second project may have eventual applications in medicine (e.g., curing persistent infections) rather than agriculture. The summaries below are intended for a nonscientific audience, such as members of Congress.

"Suppression of rhizobial reproduction by legumes:
implications for mutualism"

(with Prof. Michael Sadowsky, largely based on ideas and preliminary results from grad student Ryoko Oono -- see this recent review article we wrote with Toby Kiers)

Rhizobia are bacteria that can live in soil, but also symbiotically, inside root nodules on plants like soybean or alfalfa. Although many rhizobia provide their host plants with nitrogen, saving farmers billions in fertilizer costs, less beneficial strains cause problems in some areas. Some hosts, including alfalfa and pea, make rhizobia swell up as they start to provide nitrogen. Unlike the nonswollen rhizobia from soybean or cowpea nodules, swollen rhizobia apparently lose the ability to reproduce, but does rhizobial swelling somehow benefit the plant?

To find out, the investigators will map this trait on the family tree for crops and wild plants that host rhizobia, to see if causing swelling evolved more than once, suggesting a positive benefit to the plants. Three dual-host rhizobia (plus mutants that differ in their ability to hoard resources) will be used to measure effects of rhizobial swelling on costs and benefits to the plants. Plant defenses against rhizobia that provide little or no nitrogen, already demonstrated in soybean, will be tested in species that impose bacterial swelling.

This research will increase understanding of a symbiosis that supplies nitrogen to agricultural and natural ecosystems, with implications for other important symbioses. Results could guide the development of crops that selectively enrich soils with the best rhizobia, decreasing future fertilizer requirements. Educational opportunities will be provided for undergraduates, at least one graduate student, and a postdoctoral researcher. Two female high school students have already won trips to the International Science Fair for research done in the principal investigator's laboratory, where such mentoring will continue to be a priority.

Evolution of persistence in the model bacterium, Sinorhizobium
(with Prof. Michael Travisano, largely based on ideas, preliminary data, and writing by grad student Will Ratcliff, with some ideas from Andy Gardner and colleagues -- see the second paper discussed in this post -- and possible relevance to our work on evolution of aging.)

Some bacteria can enter a nongrowing "persister" state that allows them to survive antibiotics and other treatments that normally kill them. By suspending growth, they may also free resources for their genetically identical clonemates.

Most species form only a few persisters. This makes persisters hard to study, despite their importance in long-term infections. However, certain harmless bacteria from plant roots can form up to 40% persisters. These will be used to determine whether persisters benefit mainly from enhanced stress resistance or by increasing the growth of their clonemates.

Successful completion of this research will provide two main benefits: First, this research will determine the conditions that favor the spread of persister-forming bacterial strains over nonpersister strains, and the genetic basis of persistence. This can provide direct medical benefits by aiding the development of novel management strategies, drug targets, and eventually treatments for patients infected with persister-forming bacteria. Second, some conclusions may apply to other species that are difficult to eradicate because they, too, form dormant, stress-resistant stages. These include many agricultural weeds and some species of mosquito. One key advantage of the proposed approach is speed: experiments that would take decades with weeds or mosquitoes can be conducted in months with bacteria. This research will provide training opportunities and jobs for undergraduates, high school students, and a post doctoral researcher.

I am planning to accept another grad student for autumn 2010.

July 24, 2009

Microbes evolve; flies evolve and learn

"Can plants predict the future?" asked one of my Crop Ecology lectures at UC Davis. Yes, they can. Plants use decreasing daylength to predict oncoming winter, and flower early enough to finish seed development before it gets too cold. Some plants detect early signs of drying soil and reduce their own water use, saving water in the soil for later.(Davies & Zhang. 1991, Bano, et al. 1993) Others detect "distress signals" from neighbors under insect attack, turning on chemical defenses in anticipation (Karban, et al. 2004).

But these anticipatory responses do not require learning: a beneficial change in individual behavior in response to individual experience. An alfalfa plant will never learn that the farmer always irrigates before it actually runs out of water. At least, I assume it won't. An evolving alfalfa population is a different story. Over a few generations under irrigation, genotypes that reduce their water use as the soil starts to dry (thereby reducing their growth) will be out-competed by genotypes that keep using water and growing.

Like plants, microbes can predict the future. As in plants, this trait can evolve. As they pass through the gut, bacteria typically see lactose before they see maltose. So they have evolved to "anticipate" maltose availability, turning genes for maltose use on as soon as they are exposed to lactose. After 500 generations of evolution on lactose without maltose, however, the bacteria have lost lose this anticipatory response, so that they turn maltose genes on only when they actually see maltose.(Mitchell, et al. 2009) The title of the news story in Nature about this work asked whether microbes can "learn from history", but this is clearly not an example of individual cells modifying their responses to lactose based on their individual experience.

Individual insects can learn. But is learning always a good thing? Aimee Dunlap, a grad student in my department working with David Stephens, just published a paper in Proceedings of the Royal Society exploring the conditions under which natural selection will favor learning (Dunlap & Stephens. 2009).
Fly Learning Graphics.jpg

Continue reading "Microbes evolve; flies evolve and learn" »

May 30, 2009

Whom do cheating bacteria cheat: host plants or other bacteria?

Bacteria known as pseudomonads produce and release chemicals (defensive toxins) that protect plants from fungi that would otherwise attack their roots. In return, the roots release various organic compounds that serve as food for the bacteria.

The "in return" part has always bothered me. Each root system is associated with millions of bacteria. In a 2003 paper (Cooperation in the rhizosphere and the "free rider" problem. Ecology 84, 838-845), we pointed out that this system is a potential tragedy of the commons. Mutant bacteria that don't make root-protecting chemicals free up resources for their own reproduction, so we might expect them to out-compete more-beneficial strains. If these "cheaters" become common enough, the host plant might be killed by fungi, but that would hurt the beneficial strains around that root system just as much as it hurt the cheaters. We suggested that the bacteria make these toxic chemicals to protect themselves, with protection of roots as a side effect. Research by others, including some of the authors of this week's paper, has provided data consistent with this hypothesis. For example, toxins made by pseudomonads protect them from predators.

More recently (in Annual Review of Ecology, Evolution, and Systematics), Toby Kiers and I suggested that cooperation between microbes and plants is better understood as cooperation among microbes. For example, by providing their host plant with the nitrogen it needs to grow, rhizobia (root-nodule bacteria) help all the other rhizobia infecting the same plant.

This week's paper shows that defensive toxin production by pseudomonads is similar. Toxin production by pseudomonads may benefit the plant and may benefit individual cells, but it also benefits other pseudomonads nearby. "Predators promote defence of rhizosphere bacterial populations by selective feeding on non-toxic cheaters" was published in The ISME Journal by Alexandre Jousset and colleagues in Germany and Switzerland. These pseudomonads produce various toxins, especially when there are many of them in close proximity. This dependence of toxin production on bacterial density is an example of quorum sensing. Mutants "defective" in quorum sensing have been shown to grow (i.e., reproduce by dividing) faster, because they save the cost of toxin production. Can these "cheaters" free-load on defensive toxin producers nearby, essentially hiding behind their chemical defenses?

Continue reading "Whom do cheating bacteria cheat: host plants or other bacteria?" »

May 8, 2009

"If evolution is true, why are there still chimps?"

I once heard PZ reply to this popular creationist question by pointing out that, although many Minnesotans are descended from Norwegians, there are still Norwegians. This isn't really a good analogy, however, because Minnesotans and Norwegians aren't separate species. We know this because they can interbreed, producing healthy children. At the end of this post I suggest a better answer, indirectly inspired by this week's paper.

Two of evolutionary biology's central questions are: how do species change over generations? and how does one species split into two? We have many detailed examples of small evolutionary changes occurring over days (in bacteria) or years (in animals and plants), so one would have to be very close-minded to deny major evolutionary change over millions of years. But major evolutionary change is not enough, by itself, to split one species into two. One subpopulation within a species must change, while the rest of the species either stays the same or changes in different ways. This divergence cannot happen if the two subpopulations continue to interbreed at high rates. In other words, speciation requires some reproductive isolation.

Often, reproductive isolation is a byproduct of geography. After a few individuals (or a pregnant female) cross a mountain range or are blown from the mainland to an island, they no longer interbreed with their ancestral population. Over many generations, random genetic drift or nonrandom natural selection can change the isolated population enough that they can no longer produce healthy offspring with the original population, even if they come back into contact.

Sometimes speciation can occur without a major geographic barrier, but reproductive isolation is still required. This week's paper shows that this has happened and is still happening in Europe.

"A continuum of genetic divergence from sympatric host races to species in the pea aphid complex", by Jean Peccoud and others, was just published online in the Proceedings of the National Academy of Science.
aphid.jpg
Photo by Jean Peccoud

Continue reading ""If evolution is true, why are there still chimps?"" »

May 1, 2009

Sibling rivalry in plants

This week I will discuss two papers, both dealing with plants and competition, in the context of genetic relatedness that might be expected to moderate competition:
"Growing with siblings: a common ground for cooperation or for fiercer competition among plants?" by Ruben Milla and colleagues (Proceedings of the Royal Society), and
"Do plant parts compete for resources? An evolutionary viewpoint" by Victor Sadras and me (New Phytologist).

Earlier I discussed a paper by Susan Dudley and Amanda File showing that some plants grow less root when interacting with related than with unrelated neighbors. Spending less resources on roots could have freed resources for more seed production, but they didn't measure that. Now Milla and colleagues have.
lupinus.JPG

Continue reading "Sibling rivalry in plants" »

April 24, 2009

Optimal bet-hedging?

Suppose, in an average year, that weather is best for survival of young seedlings in early June. If a plant could make only one seed, it should make one targeted to germinate at the beginning of June. (Plants have some control over when their seeds will germinate, based on plant-hormone concentrations, seed-coat thickness, etc.)

Given variability among years, however, a plant that produces many seeds may have more descendants if those seeds germinate at various times, rather than risking everything on one date. On the other hand, too much variation in germination time may be as risky as too little. For example, seeds germinating really late may be killed by frost. How does actual variation in germination timing among seeds of individual wild plants compare with the optimum amount of variation? This week's paper is apparently the first to answer this question.

"Fluctuating natural selection accounts for the evolution of diversification bet-hedging" was published in Proceedings of the Royal Society by Andrew Simons, of Carleton University in Canada.

Continue reading "Optimal bet-hedging?" »

April 17, 2009

Mindless manipulation

This week I'll discuss a recent paper from our lab. But first, here are links to three other papers that look interesting:

Evidence from the domestication of apple for the maintenance of autumn colours by coevolution Some insect pests avoid trees whose leaves turn red in autumn and do poorly on those trees, but can trees "lie" or is there an unbreakable link between red color and poor quality as a host, perhaps because "aphids grow better on trees that drop their leaves later [because they have enough nitrogen they can risk losing high-N leaves in frost?], which are known to have fewer autumn colours [because, by the time they lose chlorophyll, UV levels are too low to require the protection provided by red anthocyanins?]."?

Functional morphology of the ankle and the likelihood of climbing in early hominins Modern chimps use their ankles, when climbing trees, in ways some early hominins (1-4 million years ago) probably couldn't, based on fossils.

Cooperation and virulence of clinical Pseudomonas aeruginosa populations
Patients with pneumonia are sicker when bacterial cells cooperate by producing individually costly virulence factors, but bacterial populations evolved "cheaters" that don't make these factors within 9 days.

---------------------------------------------------------------
In our paper, "Rhizobitoxine producers gain more poly-3-hydroxybutyrate in symbiosis than do competing rhizobia, but reduce plant growth", published online in The ISME Journal, my PhD student Will Ratcliff describes experiments showing how symbiotic nitrogen-fixing bacteria can manipulate their plant hosts.

Continue reading "Mindless manipulation" »

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?" »

February 7, 2009

Happy Darwin Day!

Several of us are meeting for dinner tonight in honor of Darwin's 200th birthday, February 12. Our hostess suggested bringing a favorite Darwin quote. It's hard to choose! Here are some I'm considering:


I have invariably found that our knowledge, imperfect though it be, of variation under domestication, afforded the best and safest clue. I may venture to express my conviction of the high value of such studies, although they have been very commonly neglected by naturalists.

...variations, however slight and from what ever cause proceeding, if they be in any degree profitable to the individuals of a species, in their infinitely complex relations to other organic beings and to their physical conditions of life, will tend to the preservation of such individuals, and will generally be inherited by the offspring. I called this principle, but which each slight variation, if useful, is preserved, by the term Natural Selection, in order to mark its relation to Man's power of selection.

We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man's feeble efforts, as the works of Nature are to those of Art.

If it profit a plant to have its seeds more and more widely disseminated by the wind, I can see no greater difficulty in this being effected through natural selection, than in the cotton-planter increasing and improving by selection the down in the pods on his cotton-trees.

As more individuals are produced than can possibly survive, there must in every case be a struggle for existence, either one individual with another of the same species, or with the individuals of distinct species, or with the physical conditions of life. It is the doctrine of Malthus applied with manifold force to the whole animal and vegetable kingdoms; for this case there can be no artificial increase of food, and no prudential restraint from marriage.

That climate acts in main part indirectly by favoring other species, we clearly see in the prodigious number of plants which in our gardens can perfectly well endure our climate, but which never become naturalized, for they cannot compete with our native plants nor resist destruction by our native animals.

Look at a plant in the midst of its range, why does it not double or quadruple its numbers? We know it can perfectly well withstand a little more heat or cold, dampness or dryness, for elsewhere it ranges into slightly hotter or colder, damper or drier districts. In this case we can clearly see that if we wish in imagination to give the plant the power of increasing in number, we should have to give it some advantage over its competitors, or over the animals which prey on it.

What natural selection cannot do, is to modify the structure of one species, without giving it any advantage, for the good of another species; and though statements to this effect may be found in works of natural history, I cannot find one case which will bear investigation.

There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.

December 21, 2008

Spatial structure and the evolution of cooperation between microbes and plants

Evolutionary theory suggests that cooperation should often be unstable, even when it benefits all concerned. Toby Kiers and I discussed this problem and some possible solutions in a recent review article in Annual Review of Ecology and Evolution. Meanwhile, Jim Bever and colleagues have published some important experimental data in Ecology Letters, helping to explain cooperation between plants and fungi, a little too late to include in our review. Their paper is titled: "Preferential allocation to beneficial symbiont with spatial structure maintains mycorrhizal mutualism."

Many bacteria and fungi associated with plant roots benefit more from healthy plants than from dead or dying ones. If each individual plant were colonized by only one strain of bacteria or fungus, then strains that helped their host plants (by providing them with nitrogen or phosphorus, for example) would indirectly help themselves, gaining an evolutionary edge over their competitors of the same species. These beneficial strains would become more common in each generation. In other words, cooperation would evolve.

The problem is that each plant is typically associated with several strains of each species of bacteria or fungus. Strains that invest less in helping the plant have more resources to spend on their own reproduction. If less-generous strains benefit equally from the contributions of more-generous strains on the same plant, then less-generous strains will become more common over generations. In other words, “cheating? will evolve.

Continue reading "Spatial structure and the evolution of cooperation between microbes and plants" »

August 30, 2008

How does gene duplication allow evolutionary innovation?

Genes with new functions do not magically appear from nowhere, or so most scientists assume. (If I thought that evolution, perhaps especially human evolution, was being guided by some supernatural individual or group, I would be looking for such “genes from nowhere? rather than whining that theories with no evidence should get equal time. Not that they want schools to teach all theories that lack evidence, of course, just ones favored by their particular religion or short-term economic interests.)

Random duplication of existing genes is often a key step, but there are at least two different ways in which gene duplication could facilitate evolutionary innovation. Once there are two copies of a gene, one could evolve a new function without interfering with the old gene’s function. Or, a single gene could evolve two different functions, doing neither of them particularly well. Then, gene duplication would allow the two copies to evolve separately, each being optimized for a different function. This week’s paper shows that evolution has followed this second pathway at least once, and perhaps often. The paper also provides yet another example of how molecular methods are providing new details on how evolution works.

Escape from adaptive conflict after duplication in an anthocyanin pathway gene? was published in Nature by David L. des Marais – apparently not the the David J. des Marais who has published on evolution of photosynthesis – and Mark Rausher, at Duke University in North Carolina. They looked at genes whose enzyme products make pigments for flower colors.

Continue reading "How does gene duplication allow evolutionary innovation?" »

July 26, 2008

Would the host want anyone to starve?

This week’s paper (Ratcliff, et al., in press) is from my lab.

The relationship between a legume plant and the rhizobium bacteria living in its root nodules is usually beneficial to both. Rhizobia convert nitrogen from the atmosphere into a form their plant host can use to make proteins. Rhizobia benefit from infecting plants because they reproduce more inside nodules than they would in the soil. They can also acquire certain resources in nodules. In particular, they can accumulate large amounts of energy-rich PHB – up to 50% of their own weight!

But there can also be conflicts of interest between rhizobia and their host plants. Resources used to make PHB could have been used, instead, to acquire more nitrogen for the plant. Therefore, mutant rhizobia that don’t make PHB provide their hosts with more nitrogen (Cevallos, et al., 1996). So why do most rhizobia make PHB? Our hypothesis has been that the rhizobia themselves benefit from having more PHB. This contrasts with an earlier hypothesis that rhizobia store PHB so that they can use the energy for the benefit of the plant. Consistent with our hypothesis, mutants defective in PHB metabolism reproduce less (Cai, et al., 2000). However, mutations can have complex interacting effects, making it hard to be sure that differences in PHB were the only cause of differences in reproduction. So Will Ratcliff decided to compare rhizobia that were genetically identical but had different amounts of PHB per cell.
centrifuge.jpg

Continue reading "Would the host want anyone to starve?" »

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" »

May 10, 2008

Regulation of sex ratios in plants

“Under drought conditions,? says Bänziger, CIMMYT’s director for corn research, “the maize plant puts more resources into pollen formation and less into seeds.? From the plant’s point of view this makes sense. Pollen is much cheaper energy-wise for the plant to make, and, if the pollen manages to fertilize another plant’s seed, the drought-afflicted parent will still contribute 50% of its genes to the offspring. But this is of little help to farmers, who sell kernels, not pollen." -- Nature 452:273

Maize plants are hermaphrodites, having both male (pollen-producing) and female (seed-producing) flowers. Other plant and animal species have two sexes, such as males and females. From the title, “Density-dependent regulation of sex ratio in an annual plant?, I assumed that this week’s paper (by Marcel Dorken and John Pannell, published in American Naturalist) would be about how parent plants adjust the male:female ratio in their offspring, a topic I have discussed previously.

But no. Mercurialis annua is stranger than that. Its two “sexes? are male and hermaphrodite.

Continue reading "Regulation of sex ratios in plants" »

April 12, 2008

Fear of flying -- in plants

“Every one is familiar with the difference between the ray and central florets of, for instance, the daisy… But with respect to the [two types of] seeds, it seems impossible that their differences in shape…can be in any way beneficial?—Charles Darwin

The theory of evolution is famously linked to the Galapagos Islands, but this week’s paper “Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta,? published in Proceedings of the National Academy of Science, studied much smaller “islands.? In an urban environment dominated by concrete, patches of soil around sidewalk trees (below left) are among the few places where plants can grow.
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Photo credits: Gilles Przetak and Eric Imbert.

Members of the daisy or sunflower family (Asteraceae) often produce two types of seeds (above right) on the same disk-shaped composite flower head. Seeds from the center of the disk are light in weight and plumed, so they are easily dispersed by wind. Those from the outer edge of the disk are heavier and not plumed, so they tend to fall near the mother plant. Although Darwin apparently failed to see the benefit of having two types of seeds, this kind of diversity acts as a form of bet-hedging. Wind dispersal of seeds over a wide area decreases the chances that all of a plant’s offspring will be killed.

Then why not disperse all of the seeds? Because, given that the mother plant managed to reproduce -- many plants don't -- conditions near the mother plant may be better than where most wind-blown seeds might land. This was particularly true in the study discussed here. Earlier, Jonathan Silvertown pointed out, in an essay titled “When plants play the field," that the ratio of the two seed types changes in beneficial ways with changes in flower head diameter. The area of a disk increases four-fold as the circumference doubles, giving proportionally more of the wind-dispersed central seeds. So the plant will always drop some seeds in the same place that it managed to reproduce. But if favorable conditions lead to larger flower heads, more seeds will be dispersed by wind over a larger area, where they can compete with other plant's seedlings rather than with each other.

So, without any genetic change, this disk-size dependence adjusts the ratio of dispersing to nondispersing seeds to match current conditions. But what if conditions consistently favor more or less seed dispersal? Can this ratio also evolve, with a genetic change over generations?

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April 9, 2008

Welcome, fellow Dr. Tatiana fans!

Olivia Judson's latest column includes a good summary of work in my lab on cooperation between soybean plants and the rhizobium bacteria that (typically) provide them with nitrogen. As she points out, "cheating" is less likely to evolve in symbiont populations if they are transmitted in eggs or seeds, relative to symbionts that are acquired from the environment. In the former, if the host dies before reproducing, the symbiont dies, too. Symbionts without brains (bacteria, say) can't anticipate the effects of their actions; it's just that those whose genetically programmed behavior increases host survival become more common over generations.

Similarly, low symbiont diversity within an individual host may favor symbiont investment in costly activities that benefit the host. If each host has many different symbionts, on the other hand, then helping the host indirectly benefits competing symbionts sharing that host.

Rhizobium bacteria reach new host plants through soil, not via seeds, and they can do so even if the host dies without reproducing. Furthermore, each individual plant has multiple strains of rhizobia, which should undermine cooperation. Why then, do most rhizobia use their limited energy supply to fix nitrogen, giving most of it to the host plant? Why not use that energy for their own reproduction, instead?
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Although there are several rhizobium strains per plant, they are typically segregated into individual root nodules. So, Toby Kiers and I reasoned, if plants monitor individual nodules and do something nasty to those that provide less nitrogen, that would act as a form of natural selection against cheating rhizobia. A computer model by Stuart West came to similar conclusions. To test this hypothesis, we forced some nodules to cheat, by surrounding them with an argon-oxygen atmosphere lacking nitrogen gas. Control nodules on the same plant got normal air, which is 80% nitrogen. Would rhizobia freed from the burden of fixing nitrogen redirect resources into their own reproduction? Would the plant impose sanctions on nonfixing nodules? If the answers to these questions are yes and yes, what would be the overall effect of cheating on rhizobium reproductive success?

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March 9, 2008

Tricky parasites winning the evolutionary arms race

Two papers this week describe recently discovered sophisticated adapatations of two different parasites: Gall insects can avoid and alter indirect plant defenses, published in New Phytologist by John Tooker and colleagues, and Parasite-induced fruit mimicry in a tropical canopy ant, published in American Naturalist by Steve Yanoviak and colleagues (if you're in a hurry, skip to the end for amazing photos).

Various plants recruit "bodyguards" when attacked by insects. For example, when caterpillars start munching on corn (maize) plants, the plants (including uninjured leaves) release gaseous chemicals called terpenoids. These terpenoids attract parasitic wasps, which lay their eggs into the caterpillars. This eventually kills the caterpillars, which presumably benefits the plant. But what if the caterpillars could prevent the plant from signaling to the wasps? As far as I know, caterpillars haven’t evolved this trick (yet), but there are apparently some insects – the Hessian fly, Mayetiola destructor (say) – that do not trigger signaling when they feed on wheat plants. There are at least two possible explanations…

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February 18, 2008

Natural enemies complicate reproductive tradeoffs

Semelparous plants and animals are those that reproduce only once, whether after a few months of growth (annual plants, like wheat) or after years (“century plant? or most salmon). Iteroparous species iterate. That is, they reproduce repeatedly. For example, perennial grasses may produce seeds every year for a decade or more.

One reason this difference matters is that perennial crops may have some environmental benefits, relative to annual crops. Plowing, traditionally more common with annual than perennial crops, can greatly increase soil erosion, especially on steep slopes. So there is increasing interest in developing perennial grain crops as an alternative to wheat.

However, perennial plants have lower seed yield than their annual relatives, so we would need to devote more land to agriculture to get the same amount of grain. One reason for the yield difference is that an annual plant can transfer most of the carbon (energy) and nitrogen (needed for protein) from its leaves, stem, and roots into its seeds. It’s going to die anyway, so the next generation gets its accumulated wealth. A perennial plant needs to hold back some carbon and nitrogen for winter survival and spring regrowth. The more resources it puts into this year’s seed production, the less it can carry forward to support reproduction next year.

This week’s paper shows that iteroparous plants face additional costs when they reproduce, namely, ecological costs. “Herbivore-mediated ecological costs of reproduction shape the life history of an iteroparous plant? was written by Tom Miller and colleagues at the University of Nebraska (where I’ll be speaking on Darwinian Agriculture in April) and published in American Naturalist.

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January 10, 2008

Ants en't ents

Science advances by disproving previously-tenable hypotheses. For example, "The earth is <10,000 years old" was disproved by annual sediment layers long before we were able to estimate the actual age. Actually, Tom Kinraide and I argued in "Strong inference -- the way of science" that a hypothesis needs to be explanatory as well as falsifiable. So for a young earth to ever have qualified as a hypothesis, it would first have needed to explain at least some real world observations. Right off hand, I can't think of any actual data that an unbiased person would look at and say, "Well, these data would make sense, but only if we assume the earth is <10,000 years old."

Similarly, if someone wanted to convert "intelligent design" from religious whining into a scientific discipline, we'd need some falsifiable hypotheses. Suppose, for example, we hypothesized that current features of plants and animals (not just their single-celled, distant ancestors) were supernaturally-imposed designs to maximize their success. That hypothesis is consistent with the many examples of sophisticated adaptations (err, "design"), but what can we conclude from the many examples of maladaptation ("bad design")? Maladaptation is predicted by evolutionary theory (when current conditions don't match those under which past selection occurred, for example) but if some design team is continuously intervening in evolution, do maladaptations imply that they had a busy week? If so, should we expect the problem to instantly disappear, once they get around to it?

This week's paper is another example of the pattern we see repeatedly in biology: many sophisticated adaptations, but also serious "design flaws." In particular, Acacia trees can be fooled into feeding and housing ants that are harming them.

Breakdown of an Ant-Plant Mutualism Follows the Loss of Large Herbivores from an African Savanna was published this week in Science by Todd Palmer and five coauthors, three of whom I know from my years at UC Davis.

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June 27, 2007

Individual and kin selection in legume-rhizobium mutualism

OK, I've been critiquing other people's work for a while. Your mission, should you choose to accept it, is to critique something I've written. It's the summary for a grant proposal I'm about to submit. It will be reviewed by ecologists and/or evolutionary biologists, but they're not likely to be specialists in legume-rhizobium symbiosis. So if something isn't clear to an intelligent but nonspecialist audience, you'll let me know, right? If you're not all too busy reading the many interesting evolution articles in today's New York Times, that is. By the way, the great Myxococcus xanthus photo in Carl Zimmer's article is from Supriya Kadam, who did her PhD with Greg Velicer and just finished a year as a postdoc in my lab.

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June 18, 2007

Can plants recognize kin?

This week's paper is "Kin recognition in an annual plant", by Susan Dudley and Amanda File of McMaster University, just published online in Biology Letters.

Researchers in several countries have recently shown that roots respond differently to another root from the same plant than they do to a root from a different plant. Typically, they grow more aggressively towards a neighbor's root than towards one of their own. But what if the neighbor is a close relative?

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June 3, 2007

Scientific controversy: dinosaur-tail soup ?

This week I want to talk about scientific controversies. In politics or religion, any difference of opinion may qualify as a controversy, which some may try to "settle" by killing those with opposing views. Most scientists would agree that unsupported opinion isn't enough to make a scientific controversy. A scientific question is controversial only if people are actually publishing data that seem to lead to different conclusions.

Two papers in press in Proceedings of the Royal Society illustrate current scientific controversies. The first is "A new Chinese specimen indicates that 'protofeathers' in the Early Cretaceous theropod dinosaur Sinosauropteryx are degraded collagen fibers" by Theagarten Lingham-Soliar (linghamst@ukzn.ac.za) and colleagues at the Universities of KwaZulu-Natal and North Carolina and the Chinese Academy of Sciences.

The title pretty much says it all. (Collagen is what gives shark-fin soup its distinctive texture, hence the title of this entry.) If the conclusions in this paper become generally accepted, how would that change our overall understanding of evolution?

The two elements of evolutionary theory that upset creationists most wouldn't be affected at all, of course. Our confidence that the universe is a million times older than Bible-based estimates, and that humans and chimps share a recent common ancestor, is based on multiple lines of evidence for each, none of it dependent on which dinosaurs had feathers, if any.

But what about the claim that birds are descended from dinosaurs? Let's see what a leading textbook, "Evolutionary Analysis", says. Page 44: Sinosauropteryx had what "some paleontologists believe are primitive feathers." Page 45: they cite several papers, one questioning this conclusion. "More convincing are [true feathers on] the dromesaur fossils." Page 553: "Luis Chiappe (1995) used skeletal characters to infer the phylogeny [family tree] of early bird lineages." The tree shown has protofeathers near the base, followed by true feathers. If the P. Roy. Soc. paper is correct, that would only require revising the earliest branches of his tree.

So this is a real controversy, but it's only a controversy about where feathers appeared in the family tree of dinosaurs and birds. As the paper says, "the wider question of whether or not birds originate from dinosaurs does not concern the present study." The main fossil evidence that they did comes from analysis of skeletons, not feathers. We don't have DNA from dinosaurs, but genetic comparisons among living species suggest that birds are more closely related to crocodiles than to mammals (Science 283:998). So birds-from-dinosaurs still seems likely.

The second paper is "Context dependence in the coevolution of plant and rhizobial mutualists" by Katy Heath (heat0059@umn.edu) and Peter TIffin, whose lab is next to mine. Among other things, this paper shows that plants infected by two different strains of rhizobium bacteria often grew less than those infected only with the worst of the two strains. This result may become controversial soon, when Toby Kiers and I publish data apparently showing that plants infected by two different strains can grow more than those infected with only the best strain. Our experiments were done with soybean, whereas theirs used a wild relative of alfalfa, which houses rhizobia in a different type of root nodule (see photos). Also, our two strains were much more different than theirs. So maybe this doesn't really qualify as a controversy, at least not yet.

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Nodule photos taken in our lab (c) Inga Spence... licensing from www.alamy.com.

When there is a controversy, should it be taught? We certainly shouldn't teach a conclusion as certain when it is still (genuinely) controversial. And students should learn about some past scientific controversies, to understand how they were resolved. The triumph of evolution would be a good example. Exposure to some current controversies would be good, too, assuming teachers have time to keep up with the literature, well enough to know what has been settled (at least until convincing new data to the contrary are published) and what is still controversial. I remember Professor Spanswick, at Cornell. telling us "I found the evidence for the chemiosmotic hypothesis convincing, but always presented it as a controversy... until Mitchell won the Nobel Prize for it."

May 29, 2007

Coevolution and gene flow

Two species coevolve when changes in either lead to changes in the other. This includes “arms races? between species that compete with each other, but also interactions that benefit both species. “Gene flow? is the movement of genes from one population into another, of the same or related species. For example, some genes in modern cows seem to have come from mating with wild aurochs, before they went extinct. Gene flow often provides new genes; some may be useful to the recipient population. For example, pollen from transgenic sugar beets could transfer herbicide resistance (along with other crop genes) to related weed beets. More often, genes that were useful in the source environment may be harmful to the recipient population. Natural selection will tend to eliminate these, unless gene flow rates are too high. For example, if plants growing on toxic soil around an old mine are outnumbered by neighbors on nontoxic soil nearby, gene flow may swamp natural selection, preventing evolution of tolerance to toxic soil.

This week I’ll discuss a review article on coevolution and then an experimental paper showing how gene flow can affect coevolution. The review is “Variable evolution? by Elizabeth Pennisi, published in the May 4 issue of Science. It discusses coevolution of wild parsnip with the webworms that eat them and coevolution of pine trees with birds and squirrels, among other topics.

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April 6, 2007

Darwinian agriculture I

Next week, I'm speaking at a one-day symposium on "Darwinian Agriculture: the evolutionary ecology of agricultural symbiosis", in Wageningen, The Netherlands. So, instead of reviewing a recent paper, this week I'm going to discuss some of the not-quite-so-recent papers on which my talk will be based. The following week, I plan to summarize some of the talks I hear at the meeting.

I may do the same thing in August, when my grad students and I speak at the much larger Ecological Society of America meetings in San Jose, California. Feel free to comment if you feel cheated of your weekly paper review, and I might reconsider. The Evolution meetings are in Christchurch, New Zealand, this year, but my grant won't stretch that far.

"Darwinian Agriculture: when can humans find solutions beyond the reach of natural selection?" was the title of a paper that Toby Kiers, Stuart West, and I published in 2003. Our answers to the title question suggested how increased understanding of past and ongoing evolution could improve: 1) breeding of crops and livestock, and 2) design of agricultural ecosystems.

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