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September 11, 2014

Applying evolutionary biology to address global challenges

That's the title of a review article just published online by Science.
The US National Science Foundation, which is funding some of the authors and previously funded my research on evolution of symbiotic cooperation, is highlighting the article on their website.

Past and ongoing evolution have important implications for health, agriculture, and conservation of biodiversity, but communication among scientists applying evolutionary biology to different practical problems has been limited. That started to change in 2010, when a bunch of us (including most authors of today's paper) met on Heron Island, Australia, at the Applied Evolution Summit. Scott Carroll (UC Davis and Institute for Contemporary Evolution) had a lead role in both the meeting and the review article.

Evolutionary changes occur over generations, so crop pests and disease-causing pathogens with short generation times can evolve quickly, undermining our control measures. Species with longer generation times, including humans and some endangered species, evolve too slowly to keep pace with changes in their environments. For example, food preferences that evolved when meat and sugar were scarce may lead to unhealthy diet choices today.

Our paper discusses various ways to slow harmful evolution. Refuges not exposed to selection (e.g., by insecticides or fishing with nets) may slow evolution of insecticide-resistant pests or evolution of smaller fish. This approach partly depends on insect pests or fish from the refuges mating with individuals from outside. Refuges might be less effective for populations that reproduce asexually, such as bacteria or cancer cells.

To protect valued species that are evolving too slowly, we may be able to modify the environment to better match their inherited traits. Taxing unhealthy food might help, assuming we're sure which foods are unhealthy. For wild species, moving them to environments to which they're better adapted may work. Obsession with native species may blind us to the fact that their native range is now warmer than it was when they evolved. Unless we can reverse climate change, saving those species may require moving them (or allowing them to migrate) further from the equator or to a higher elevation.

Despite the authors' shared interests in evolution and in practical problems, applying insights from one field to another can be difficult. But I hope that this review will be helpful, both to practitioners and to students of evolution that have not yet narrowed their career options.

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 18, 2013

Modular mice, experimental evolution, Bayesian enzymes, environmental extinction

Here are some papers that look interesting this week:

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

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

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

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

December 27, 2012

Antibiotic resistance, camouflage, exinction...

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

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

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

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

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

September 14, 2012

This week: fossils, epidemics, cooperation, and aging

Arthropods in amber from the Triassic Period "arthropods some 100 Ma older than the earliest prior records in amber"

Unifying the spatial epidemiology and molecular evolution of emerging epidemics "spatial parameters of an emerging epidemic [can] be directly estimated from sampled pathogen genome sequences"

Evolution of cooperation and skew under imperfect information "full cooperation may not be achievable due to private information over individuals' outside options"

No third-party punishment in chimpanzees "Dominants retaliated when their own food was stolen, but they did not punish when the food of third-parties was stolen, even when the victim was related to them. "

Ageing: Mixed results for dieting monkeys
Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study "Our study suggests a separation between health effects, morbidity and mortality"

September 7, 2012

This week's picks

Stone tool production and utilization by bonobo-chimpanzees (Pan paniscus)
Just last week, we gave a kid a copy of "Monkey with a tool belt." No, this paper doesn't show that humans are descended from bonobos. DNA evidence shows that the bonobo-chimp split occurred after humans split from the common ancestor of all three.

Reproductive queue without overt conflict in the primitively eusocial wasp Ropalidia marginata "The dominance rank of an individual is not a significant predictor of its position in the succession hierarchy. "

Predatory Fish Select for Coordinated Collective Motion in Virtual Prey
"collective motion could evolve as a response to predation, without prey being able to detect and respond to predators"

Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis
"disease severity is predicted by the evolutionary dynamics of hepatitis C virus"

August 9, 2012

Darwinian agriculture and Darwinian medicine: beyond resistance management

DarwinianMedicine.jpg Thumbnail image for BookCover.gif


Evolution happens. Careless use of antibiotics selects for antibiotic-resistant pathogens, careless use of insecticides (including crops that make their own insecticides) selects for pesticide-resistant insect pests, and careless use of herbicides selects for herbicide-resistant weeds.

Many people seem to assume that this well-known problem, evolution of resistance, is all there is to "Darwinian medicine" or "Darwinian agriculture." But check the tables of contents of the books above. You'll only find one chapter on the "arms race" between pathogens and their hosts and one chapter (titled "Stop Evolution Now!") that focuses on slowing the evolution of resistance to pesticides and other pest-control measures.

Both books (Nesse and Williams, 1994, Denison, 2012) and the earlier review articles on which they were based (Williams and Nesse, 1991, Denison, et al., 2003) devote much more space to the implications of past evolution.

"If evolution by natural selection can shape sophisticated mechanisms such as the eye, heart, and brain, why hasn't it shaped ways to prevent nearsightedness, heart attacks, and Alzheimer's disease?"

Similarly, biotechnology allows us to increase the expression of crop genes that enhance drought tolerance, but

"mutations that increase gene expression happen all the time, and natural selection maintains those that are beneficial to the plant. So why does corn normally have lower expression of this gene than was obtained by genetic engineering?"

We don't have definite answers to these questions. Both books present hypotheses with various amounts of supporting data, but additional research is needed. With aging populations and rising food prices, maybe there will even be some money available to fund that research.

Should evolutionary biologists working on fundamental problems and/or wild species consider adding applied work to their research portfolios? If so, you or your students might get some useful ideas from Nesse and Williams or from my book, just published by Princeton University Press.

Literature Cited

Denison RF. 2012. Darwinian agriculture: How understanding evolution can improve agriculture. Princeton: Princeton University Press.

Denison RF, Kiers ET, West SA. 2003. Darwinian agriculture: when can humans find solutions beyond the reach of natural selection? Quarterly Review of Biology 78: 145-168.

Nesse RM, and Williams GW. 1994. Why we get sick: The new science of Darwinian medicine. New York: Vintage Books.

Williams GW, Nesse RM. 1991. The dawn of Darwinian medicine. Quarterly Review of Biology 66: 1-22.

August 3, 2012

Defense against malaria, cuckoos, mobile elements, and creationists

Fighting malaria with engineered symbiotic bacteria from vector mosquitoes
"symbiotic bacteria to deliver antimalaria effector molecules to the midgut lumen"

PLoS Biology: The Evolutionary Consequences of Blood-Stage Vaccination on the Rodent Malaria Plasmodium chabaudi
"recombinant blood stage malaria vaccines can drive the evolution of more virulent malaria parasites"

Cuckoos Combat Socially Transmitted Defenses of Reed Warbler Hosts with a Plumage Polymorphism
"social learning is specific to the cuckoo morph that neighbors mob"

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs
evolving defenses against active mobile elements

A complete insect from the Late Devonian period
400 million years ago? Like 400 million years (to three significant digits) before the Earth was created?

January 20, 2012

Also this week...

Variation in cognitive functioning as a refined approach to comparing aging across countries "The degree to which demographic aging translates into societal challenges depends to a considerable extent on the age at which mental functioning becomes significantly impaired.... In several countries with older populations, we find better cognitive performance on the part of populations aged 50+ than in countries with chronologically younger populations."

Large-scale, spatially-explicit test of the refuge strategy for delaying [sprayed] insecticide resistance
"refuges delayed resistance and treated cotton fields accelerated resistance"

The evolutionary basis of human social learning "We tested nine hypotheses derived from theoretical models, running a series of experiments..."

Collaborative learning in networks "In contrast to prior work, however, we found that efficient networks outperformed inefficient [slower] networks, even in a problem space with qualitative properties thought to favor inefficient networks."

Historical contingency affects signaling strategies and competitive abilities in evolving populations of simulated robots "populations with the more complex [but less efficient] strategy outperformed the populations with the less complex strategy"

The spread of a transposon insertion in Rec8 is associated with obligate asexuality in Daphnia "this element may be in the process of spreading through the species"

December 29, 2011

Shrimp on treadmills

Politicians who didn't hesitate to spend a trillion dollars invading and occupying Iraq apparently think they can win a few votes from ignoramuses by ridiculing spending on scientific research. Their latest target is "shrimp on treadmills." Here's a NSFW (National Science Foundation Website) link to the project in question.

Looks worthwhile to me. They're studying how bacterial infection affects respiration and swimming ability in shrimps and crabs. One could argue that the main beneficiaries are the shrimp and crab industries, so they should have paid part of the cost. But work with one species often helps us understand other species. Much of what we know about genetics of humans and crops goes back to research done with fruit flies. I'm glad Thomas Hunt Morgan didn't have to depend on the banana industry to fund his research.

I agree that we should be scrutinizing public spending to make sure we're getting value for money, but NSF is a model of efficiency and transparency. How about starting with the most-expensive programs and working down? And it seems only fair to give those criticized a chance to respond.

February 24, 2011

This week's picks

Responses to the Assurance game in monkeys, apes, and humans using equivalent procedures "...only a subset of humans achieved these efficient outcomes, and pairs of both other species did so as well"

The origin and dynamic evolution of chemical information transfer
"chemicals are emitted, which can unintentionally provide information (cues) and... act as direct precursors for the evolution of intentional communication (signals)."
"In most cases, the excrements are cues, but the behavioural modulations... constitute signals helping to draw receivers' attention to the cues "
"males prefer flower bouquets to the sexual pheromone of local females, presumably because [the orchid] exploits pre-existing sensory biases of their pollinators"

Classic Selective Sweeps Were Rare in Recent Human Evolution
"amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations"

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
"the Thaumarchaea (including Nitrosopumilis maritimus in our analysis) forms an independent group distinct from the Crenarchaea or Euryarchaea"

Footprints pull origin and diversification of dinosaur stem lineage deep into Early Triassic "...a few million years after the Permian/Triassic mass extinction (252.3 Ma)"

Optimal antiviral treatment strategies and the effects of resistance
"contrary to previous results, it is always optimal to treat at the maximum rate provided that this treatment occurs at the right time. "

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions
"transparent Daphnia hosts and fluorescently-labelled spores of the bacterium"

February 18, 2011

Free downloads of applied evolution papers...

...from the Applied Evolution Summit (Heron Island, 2010) are available, temporarily, from Evolutionary Applications.

I've already discussed part of my paper, "Past evolutionary tradeoffs represent opportunities for crop genetic improvement and increased human lifespan".

I also made minor contributions to two overview papers:
Evolutionary principles and their practical application
and Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems.

Check out these and other exciting papers and download the ones you want, before they go behind a pay-wall. Some of these would be great for participatory seminars.
turtle.JPG

February 16, 2011

Sleep as a survival strategy

This week's paper, Bacterial persistence and bet hedging in Sinorhizobium meliloti, was just published in Communicative and Integrative Biology. It's a brief but important follow-up to a paper in Current Biology, which I've already discussed.

Bacterial persisters are a serious medical problem. An infection that appears to have been cured by antibiotics sometimes "springs back to life." Evolutionary biologists have focused on cases where the renewed infection is caused by an antibiotic-resistant mutant, a classic example of evolution by human-imposed selection. Sometimes, however, the resurgent bacteria are still susceptible to the original antibiotic, yet bounce back after one or more treatments. What gives?

Many antibiotics only kill bacteria that are actively growing. So, if a few cells go dormant, these persisters may survive until the antibiotic breaks down, even if they aren't otherwise resistant.

Will Ratcliff recently reported that Sinorhizobium meliloti bacteria, best known as the nitrogen-fixing, root-nodule symbiont of alfalfa, can also make dormant cells. When S. meliloti cells divide, under starvation conditions, the elder daughter inherits most of the accumulated wealth (energy-rich polyhydroxybutyrate or PHB) and the younger daughter goes off to seek her fortune. You can see this unequal allocation of PHB in the Nile-red-stained image of a dividing cell, below right.PHB.jpg
This apparent bet-hedging strategy is much more organized and more common than the random, one-in-a-thousand process that seems typical of human pathogens. A rhizobial population that starts with the usual normal distribution of PHB (above left) divides, initially, into one with roughly equal numbers of persisters and growers (above center).

Our original paper showed that about 70% of the high-PHB S. meliloti persisters are still alive after 528 days without food. So the well-known ability of rhizobia to survive in soil for months or years between legume hosts may not depend on their ability to out-compete other soil bacteria for limited food supplies.

But how relevant is this work with rhizobia, which benefit their legume hosts by providing them with nitrogen, to the antibiotic-resistant bacterial persisters that cause disease? In this new paper, Will Ratcliff showed that...

Continue reading "Sleep as a survival strategy" »

February 10, 2011

Evolution of cooperation, disease, relatives, birds...

Some recent papers that look interesting:

The evolution of host protection by vertically transmitted parasites

Cooperation among non-relatives evolves by state-dependent generalized reciprocity

Before senescence: the evolutionary demography of ontogenesis

Costs of memory: lessons from 'mini' brains

Land inheritance establishes sibling competition for marriage and reproduction in rural Ethiopia

Major global radiation of corvoid birds originated in the proto-Papuan archipelago

Within and transgenerational immune priming in an insect to a DNA virus

Multiple strategies in structured populations

Long-term isolation of a highly mobile seabird on the Galapagos

December 28, 2010

How "mostly harmless" bacteria manipulate the immune system

"It may be better to keep alive the goose that lays the golden eggs than to kill it. But this argument depends on the assumption that, if you do not kill the golden goose, no one else will either: that is, it assumes that the host is infected by a single clone of symbionts." -- Maynard Smith 1989 Nature 341:284-285.

This week, I'll discuss a paper recently published in Science: Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System?, by Yun Kyung Lee and Sarkis K. Mazmanian. They argue that gut bacteria produce "signals that are recognized by host receptors to mediate beneficial outcomes for both microbes and humans."

Well, how nice! What sort of outcomes would be beneficial for a gut microbe? Reproducing a lot in the gut and spreading to lots of new hosts would be good. How to do this? Diarrhea seems promising. That might sicken or even kill the human, but does that matter to the microbes? Paul Ewald has pointed out that pathogens whose spread depends on host mobility may evolve lower virulence, so people with the flu feel well enough to go to work and spread it. Pathogens that spread via sewage to drinking water, though, may spread more readily if they cause more severe diarrhea. But we also need to consider conflicts of interest among gut bacteria, not just conflicts of interest with the host. For example, species X might trigger diarrhea before species Y has had time to reproduce much. If so, then species Y might benefit from suppressing, or at least delaying diarrhea.

More generally, the diversity of bacteria in the gut creates a "tragedy of the commons", where bacterial strains that pursue their own interests would rapidly out-compete hypothetical strains that sacrificed their own interests for the "greater good", either of the host or of the entire gut bacterial community.

Or so I would predict. But what about those mutually beneficial "signals?"

Continue reading "How "mostly harmless" bacteria manipulate the immune system" »

June 4, 2010

Cancer's deep evolutionary roots

This week's paper, "Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa" was published in BMC Biology by Tomislav Domazet-Lošo and Diethard Tautz. Each of our cells is descended from an unbroken lineage going back to the first living cell. Most cells in an adult, however, are at the end of the line and will have no descendants. Exceptions include sex cells, stem cells, and cancer cells.

We consider cancer an aberration, but think back to the first multicellular life, which may have resembled Trichoplax. A Trichoplax has an upper and a lower layer of cells, and not much in between. They can reproduce by dividing in half, producing two offspring with hundreds of cells each (video). Or they can bud off propagules containing a small number of cells. They also seem to be able to reproduce sexually, from a fertilized single-cell egg, although complete development from an egg hasn't been documented. A Trichoplax can reform from separated cells, sometimes combining cells from two individuals. In such a chimeric organism, cells with different genotypes could compete for resources and reproductive opportunities, undermining collective success. Similar problems can occur when social amoebae get together to form a stalk for their spores. Even in a genetically uniform organism, a mutant cell could start reproducing (perhaps generating many propagules) at the expense of the whole. Today, we call cells that reproduce at the expense of the whole cancers, but something similar would presumably have been a problem for the earliest multicellular organisms.

Presumably? The authors of this week's paper used "phylostratigraphic tracking" to see when the ancestors of our cancer-suppressing genes evolved. Sure enough, there was an evolutionary burst of such genes right around the time when multicellular animals first evolved.

March 10, 2010

Why hasn't natural selection eliminated Alzheimer's?

Tradeoffs.

The Alzheimer's Disease-Associated Amyloid beta-Protein Is an Antimicrobial Peptide
[See comment below for an earlier paper making this suggestion.]

Life-long protection against brain infections, in exchange for increased risk of dementia at an age few of our ancestors reached? Sounds like a reasonable tradeoff to me. Except that now we may have better options:

"it raises the possibility of preventing amyloidosis from initiating by pre-emptive targeting of pathogens/insults that stimulate the brain's innate immune system."

All we need is a good noninvasive way to detect brain infections early, so we can treat them with nonAlzheimer's-inducing antibiotics before amyloid beta-protein gets into the act.

January 22, 2010

Evolution threatens Darwin

Dengue ("breakbone") fever was much in the news last month in Australia last month, when I was there for the Applied Evolution Summit. The mosquitoes that spread this deadly disease are currently found in Queensland, where we were, but not further west, in the city of Darwin. They were found in Darwin in the early 1900s, however. Could some combination of climate change, human activity, and evolution put Darwin at risk once again? That was one of the questions discussed by Ary Hoffmann at the summit, largely based on a paper titled "Integrating biophysical models and evolutionary theory to predict climatic impacts on species' ranges: the dengue mosquito Aedes aegypti in Australia", published in Functional Ecology last year.

Continue reading "Evolution threatens Darwin" »

November 16, 2009

Return of the viruses

I just read a disturbing post on the amusingly-titled serious-science blog "Mystery Rays from Outer Space", discussing two examples of human pathogens that apparently escaped from laboratories. The key evidence, in each case, is evolution... or rather, lack of evolution....

Continue reading "Return of the viruses" »

August 7, 2009

Ants versus fungi

Ants that grow fungi for food have to control other fungi that attack their gardens, but what about fungi that attack the ants themselves? Two papers published recently reveal surprising sophistication in both ants and fungi.

Sandra Anderson and colleagues discuss "The life of a dead ant: the expression of an adaptive extended phenotype" in American Naturalist. Richard Dawkins coined the term "extended phenotype" to refer to a consistent effect of a gene inside an individual on something outside that individual. For example, it might be possible to link differences in the shape of webs made by different spiders to genetic differences among those spiders. This week's paper shows that ants infected by certain fungi show complex behavior that benefits the fungi. Ants infected by fungi with different genes would probably not show this behavior, but the genes involved have not yet been identified.

Before the fungus-infected ants die, they attach themselves (by biting) to the underside of leaves that are ideally located for fungal reproduction: on the cooler and moister north side of trees, near (but not on) the ground. The researchers showed that these locations were favorable for fungal reproduction by moving infected ants higher in the canopy or down to the ground. Ants on the ground mostly disappeared, but fungi grew abnormally in those that remained. Fungi were unable to compete their life-cycle on ants moved higher in the canopy.

I can imagine a fungus producing an ant hormone (or perhaps destroying a particular neuron) to make its ant host bite a leaf, but getting ants to bite leaves in a particular humidity and temperature range and then hold on until dying seems pretty sophisticated. It would be easier if the ants spent most of their time in that zone anyway, but the one ant colony they found was much higher, about 15 meters.

The second paper shows greater sophistication on the part of the ants. "Adaptive social immunity in leaf-cutting ants" was published by Tom Walker and William Hughes in Biology Letters. The paper is freely available on-line.

These social ants protect each other from fungal infection by grooming each other, much like meerkats or baboons. Ants exposed to the fungus got groomed about twice as long as ants exposed to a control solution without the fungus, or about three times as long if their nest had been exposed to the same fungus two days before. (Another example of learning in insects.) Ants placed in nests that were previously exposed to the fungus were twice as likely to survive for two weeks after they were inoculated.

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 9, 2009

Has natural selection been asleep at the switch?

"This new forage has great insect resistance", effused a former colleague, "we just need to eliminate the toxins that keep sheep from eating it."

Genetically engineered drought-tolerant crops are introduced with great fanfare, only to disappear when they turn out to have low yield under nondrought conditions.

When natural selection falls short of perfection, it may be because "you can't get there (some desirable adaptation) from here (current genotypes)" without passing through a series of intermediate generations that would have lower fitness. Natural selection favors genotypes best-adapted to current conditions, which are not necessarily steps towards any long-term improvement.

But natural selection often seems to miss even "simple" improvements, that might be achieved by changing as little as one DNA base. Such small changes are often enough to increase or decrease expression of key genes, for example. This sort of evolutionary progress may be blocked by tradeoffs, e.g., between seed production under different conditions (e.g., wet vs. dry), or between the competitiveness of individual plants and their collective seed production.

So what are we to make of two recent papers (in Science and Nature, respectively, discussed in Science News) on extending lifespan, one using calorie restriction and the other using the antibiotic, rapamycin?

Calorie restriction has been shown to increase longevity in model species like nematode worms and mice, but this latest study shows clear benefits in monkeys. The obvious question -- at least, it was obvious to me -- is why has past natural selection given monkeys (and fruitflies, and nematodes, and mice...) appetites that make them eat more than is good for them?

At least, that seemed to be the question, until it was shown that food odors can reverse the beneficial effects of calorie restriction, at least in fruitflies and nematodes. In humans, soft drinks with artificial sweeteners turn out to be just as likely to cause "metabolic syndrome" (related to diabetes) as those with sugar. So apparently our lives can be shortened by a perception of abundance, not just by actually eating too much. What is going on here?

In this case, the evolutionary tradeoff seems to be between current and future reproduction. As discussed in last week's post, delaying reproduction usually decreases fitness (representation in the next generation, relative to others) when population is increasing, but delaying reproduction can increase fitness when population is decreasing. Calorie restriction predicts population decline, triggering physiological responses that delay reproduction and thereby increase longevity. So do bitter-tasting foods, traditionally eaten only during famines. Food odors or sweet tastes have the opposite effect, because they predict population increase.

But what about life extension by rapamycin? One known tradeoff is suppression of the immune system, so we might get longer lives only in a hypothetical germ-free environment. But could the protein target of rapamycin (TOR) also be important to reproduction? Is this yet another example of a longevity-vs.-reproduction tradeoff?

April 8, 2009

Evolution-Proof?

Which animals kill the most humans? Lions and tigers and bears? Oh no, malaria-transmitting mosquitoes! The risks of using insecticides to kill mosquitoes may be outweighed by the benefits, but those benefits only last until mosquito populations evolve resistance. Careful use (insecticide-treated bed-nets, for example, rather than spraying wetlands) can slow the evolution of resistance, but we haven't yet achieved a goal I recently saw on a bumper sticker, namely, to "Stop Evolution Now!"

Can we do better? A paper published today suggests a new approach. "How to make evolution-proof insecticides for malaria control" was written by Andrew Read and colleagues. It's in the open-access journal, PLoS Biology, so you can read the whole article for details, but here's my summary:

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March 3, 2009

Mixed infections, for better or worse

If being infected is bad, is being infected by two different pathogens at once even worse? Not necessarily, as this week's paper shows. "Quorum sensing and the social evolution of bacterial virulence" was published in Current Biology by Kendra Rumbaugh and colleagues. Their results contradict an earlier prediction, although not the fundamental evolutionary principle behind that prediction.

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January 23, 2009

Staying ahead in the evolutionary arms race with viruses

This week's paper uses molecular methods to reveal new details of the evolutionary arms race between primates, including humans, and viruses. "Protein kinase R reveals an evolutionary model for defeating viral mimicry" was published in Nature by Nels Elde and colleagues in Seattle.

Protein kinase R (PKR) is an important defense against viruses in many species, from humans to yeast. When it detects a virus inside a cell, it activates eIF2-alpha, which shuts down protein production in that cell. With protein production blocked, the virus can't replicate and spread to other cells. Viruses, however, have evolved counter-measures. These include molecules that resemble eIF2-alpha. These molecular mimics interact with PKR and prevent its normal defensive activity.

Viral epidemics can be a major cause of death, so we expect populations to evolve PKR resistant to the eIF2-alpha-mimics produced by viruses. Can we find evidence of such evolution in primates?

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January 19, 2009

Safe-crackers have vaults in their cells

This is the most amazing thing I've seen in awhile. Vaults are abundant in our cells and bigger than ribosomes and apparently I'm not the only biologist who had never heard of them. They seem to be important in defense against bacteria, but nobody understands them in detail yet, apparently.

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.

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May 25, 2008

Pest control for ants

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(Top) A small leafcutter worker atop a leaf guards her sister against attacks by parasitic flies. Ants carrying leaves cannot use their mandibles for defense, so they carry hitchhikers to ward off the parasites. (Bottom) The fungus garden in a nest of Atta leaf-cutter ants. Notice the diversity of ant sizes within a colony, from the large red soldier ants to the minute orange ants tending to the garden. Atta ants have some of the most sophisticated caste systems among the social insects. -- photos and captions from Alex Wild (mymercos.net)

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This week’s paper, “Black yeast symbionts compromise the efficiency of antibiotic defenses in fungus-growing ants" by Ainslie Little and Cameron Currie, was just published in Ecology. Elsa Youngsteadt interviewed me, among others, for a story in Science about this research.

I’ve never done research on the fungal “farms" of ants and termites, but I’ve been interested in them every since a camera company bought a close-up photo (not Photoshopped like this one) of an ant carrying a leaf along a barbed wire “bridge" on its way back to its nest, from my mycologist father, William Denison. Dad was best known for pioneering research in the tops of tall trees, but never had to fight a shaman, as far as I know.

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May 3, 2008

Sharing diseases with relatives and neighbors

Not enough people voted on the Reader’s Choice, so this week’s paper is “Phylogeny and geography predict pathogen community similarity in wild primates and humans? by Jonathan Davies and Amy Pedersen, published in Proceedings of the Royal Society.

Many humans diseases, from flu to AIDS, come from other species. Similarly, diseases from dogs are an increasing threat to lions, while cat diseases kill sea otters. Are there general rules that predict how likely two species are to share diseases?

To find out, the authors analyzed several large data sets on diseases of humans and 117 other species of primate (apes, monkeys, etc.). They hypothesized that species are more likely to share diseases if they live near each other and/or if they are more closely related, that is if they share a more recent common ancestor. This is similar to how we define relatedness in humans: brothers and sisters have more recent common ancestors (parents) than cousins do (grandparents). Fortunately, the family tree for primates is relatively uncontroversial, at least among scientists.

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December 7, 2007

The ghost of infections past, present, and future

Summary: A 39-year record of host-parasite interaction, recovered from sediment layers in a pond, is consistent with rapid coevolution.
Link: Host-parasite /`Red Queen/' dynamics archived in pond sediment

As I've discussed previously, archival samples often prove useful for answering questions that weren't being asked when the samples were collected. But what if nobody collected and preserved the samples you need for your research? Maybe you can find a "natural archive" that has what you need.

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August 3, 2007

Left behind: social amoebae

This week's paper, published in Science (317:679) is "Immune-like phagocyte activity in the social amoeba" by Guokai Chen, Olga Zhuchenko, and Adam Kuspa of the Baylor College of Medicine.

Cells of the social amoeba, Dictyostyleium discoideum forage individually, but eventually group together into a "slug", which crawls through the soil for days before eventually forming a spore-tipped stalk. Previous work with this species has looked at conflicts of interest over which cells have to sacrifice future reproduction (as spores) and become part of the stalk. This week's paper uncovers another example of apparent altruism in Dictyostelium, which may shed light on the evolution of a key part of our immune system.

As a Dictyostelium slug crawls through the soil, some cells are left behind. Are these just random sluggards? Or do they function like human phagocytes, the immune system cells that gobble up bacteria?

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July 9, 2007

Selection beats design, again

This week's paper is "HIV-1 proviral DNA excision using an evolved recombinase" by Indrani Sarkar and others, published in Science (vol.316, p.1912). This paper is yet another example showing that selection (natural or artificial) can outperform design.

To illustrate the point, let me start with a well-known example from plant breeding. Suppose you wanted to make broccoli, starting with its ancestor, wild kale? You could cross them, identify which genetic differences are most responsible for the large edible inflorescence, and transfer those genes to the wild kale. But what if broccoli didn't exist?

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March 31, 2007

Can a selfish gene stop malaria?

A bird that risks her life to lead a fox away from her chicks may be influenced by a "selfish gene" (Dawkins, 1976). Genes can't think, of course. However, a gene causing behavior that risks the loss of one copy of itself (in the mother) will become more common over time, if this same behavior often saves more than one copy of itself (in the chicks). The gene can be considered "selfish", in the sense that the welfare of the mother, her species, or the whole ecosystem only indirectly affect the gene's spread. It's as if each gene were at war with rivals (other versions of the gene, or alleles) for its place on the chromosome.

The selfish gene concept is now being used to design new methods to control the spread of disease. Mosquitoes that resist infection by the malaria parasite can be made by genetic engineering. Unfortunately, the small benefit (to a mosquito) of resistance to this parasite is probably not enough for resistant mosquitoes to take over in the wild, because most of the animals they bite aren't infected. (It would be nice if the laws of nature always favored human welfare, but they don't.)

How can we make such beneficial genes spread through mosquito populations? This week's paper, "A Synthetic Maternal-Effect Selfish Genetic Element Drives Population Replacement in Drosophila" by Chun-Hong Chen and colleagues at Cal Tech and UCLA, published on-line in Science, demonstrates one interesting approach.

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March 12, 2007

Less-vicious viruses evolve in viscous cannibal populations

This week’s paper is “Local interactions select for lower pathogen infectivity? by Michael Boots and Michael Mealor, University of Sheffield, published in Science (vol. 315, pgs. 1284-1286) and suggested by my wife.

The evolution of greater or lesser infectiousness in pathogens has important implications for health of plants and animals, including humans. Evolution is a process that follows its own rules and humans can’t control it completely, but we can sometimes influence it, just as we may be able to constrain the course of a river or limit the spread of a forest fire.

One factor over which we have some control is the ease with which a pathogen spreads from one host individual to another. For example, a bacterium on the skin of one patient in a hospital can’t jump to another patient in a different room, but it may be able to hitch a ride with a doctor or nurse who forgets to change gloves between patients. Intestinal bacteria reach new hosts easily if untreated sewage is dumped into the same river used for drinking water, even if the bacterium is so virulent that the host is too sick to walk around and infect others.

Paul Ewald has suggested that easy transfer between hosts favors the evolution of greater virulence (Oxford Surveys in Evolutionary Biology 5:215-245). For example, cholera spreading through South America in 1991 evolved greater virulence in countries with poor water supplies, but lesser virulence in countries with better water supplies. So not only were more people infected in countries with polluted water supplies, but the infected people were sicker.

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