February 5, 2010

Tradeoff-free drought resistance?

I'm working on the last chapter of my book, Darwinian Agriculture: where does Nature's wisdom lie?, and will be sending it to Princeton University Press soon for their review process. So I'm alert for any information that might make me change my main conclusions.

One theme of the book, and also of my recent talk at the Applied Evolution Summit, is that past natural selection is unlikely to have missed simple, tradeoff-free improvements. So I'm always skeptical when someone speculates that we could double crop yield just by increasing the expression of some newly discovered "drought-resistance gene." My rationale is that mutants with greater expression of any given gene are simple enough to have arisen repeatedly over the course of evolution. (This contrasts with more-complex adaptations, like the ability to form a symbiotic relationship with nitrogen-fixing bacteria, which natural selection may have had fewer opportunities to test.) If past natural selection has repeatedly rejected these "drought-resistant" mutations, then they must have been some negative effects on fitness, at least in past environments.

But could some mutations repeatedly rejected by past natural selection still be beneficial in agriculture? Maybe. Tradeoffs that constrained past natural selection need not always constrain us, as discussed below. But, I suggested at the meeting, we can't just ignore them.

However, someone called my attention to Drysdale wheat, developed in Australia, and reported to have higher yield under drought than older varieties, without any apparent yield penalty under wetter conditions. Is this an example of a tradeoff-free improvement missed by past natural selection?

The answer can be found in a very interesting paper, Breeding for high water use efficiency, published in Journal of Experimental Botany in 2004 by A.G. Condon, R.A. Richards, G.J. Rebetzke and G.D. Farquhar. If you are at all interested in this topic, the entire paper is well worth reading. But here are some key points....

Continue reading "Tradeoff-free drought resistance?" »

February 4, 2010

Carnival of evolution

A roundup of recent blog posts on evolution at Skeptic Wonder.

January 29, 2010

Rafting

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Apart from sea turtles, the only wild animals I saw on Heron Island were birds. Lots and lots of birds. They made so much noise, I needed earplugs to sleep at night.
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But I can't really complain; they were there first. In addition to birds and bats, many islands were colonized by plants and nonflying animals, often long before humans evolved.

How did they get there? When enough water was tied up in glaciers, sea levels were lower, so some of today's islands were connected to the mainland. Darwin showed that plant seeds can be carried in mud on the feet of birds. Coconuts can migrate by floating in ocean currents, although there are other hypotheses to explain their presence on particular islands. But what about animals that can't fly ? Even if they can swim short distances, what about sharks, like those below (seen from the beach at Heron Island)?
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Small animals may have floated to even distant islands on driftwood "rafts." That only works if currents flow from the mainland to the island, however. CurrentlyAt present, currents flow from Madagascar to the African mainland. In Mammalian biodiversity on Madagascar controlled by ocean currents, published in Nature, Jason Ali and Matthew Huber argue that Madagascar was previously reachable by currents from Africa. Since then, continental drift moved Madagascar into its current position, cutting off the supply of rafting animals from Africa.

Rafts can be made of ice, rather than trees. An earlier paper, Frequent Long-Distance Plant Colonization in the Changing Arctic used DNA analysis to show that plants reached Svalbard from multiple mainland sources. Surviving there seemed to be a bigger problem than getting there. (Thanks to Odd Arne Rognli for calling my attention to this paper.)

But I'm still impressed by aborigines reaching Australia 40,000 or more years ago and by monkeys reaching the New World perhaps 40 million years ago.

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" »

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....
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Wasp inside a fig; photo by Charlotte Jander.

Continue reading "Altruistic punishment by fig trees?" »

January 2, 2010

Travel tips: free WiFi etc. in Brisbane

This entry was written in Brisbane, en-route to the Applied Evolution Summit. My train north, The Spirit of the Outback, was stranded in the outback, due to flooding. Fortunately, since I needed to catch the boat to Heron Island tomorrow morning, Rail Australia added a special high-speed train -- made me feel like Professor Moriarty!. Meanwhile, I had most of the day free in beautiful Brisbane. So here are some travel tips for anyone thinking about visiting the area.
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1) For free WiFi, try the State Library (above right). They leave it on even when the library itself is closed, and there's a nice interior courtyard out of the sun and rain -- we've had a good mix of both this week -- with stone benches full of students and visitors using their laptops to access email, etc. The library is near the up-stream end of South Bank park, just across the river from the central business district (CBD). The park itself is wonderful, with several museums, a swimming area near but not in the river, ice cream (we liked New Zealand Natural) and more substantial food, lots of places to sit and relax.

2) Brisbane is very pedestrian-friendly. South Bank park is connected to the CBD by two pedestrian and bike bridges (both with sheltered places to sit, one with drinking-water fountains), plus one shared with cars. We paid $23 each for 1-week transit passes which are valid on ferrys across the river, City Cats boats up and down the river, buses (including the one we took to the great botanic garden, planetarium, and look-out on Mt. Coot-tha), and even on the section of the airport train between South Bank and the Roma Street station where I'll catch my train tonight. The Roma Street Parkland, right by the station, is great, too. Lots of interesting plants (bottle-trees, Banksia), birds (including Australian wood ducks and very colorful and talkative lorikeets), and iguana-like water dragons.

3) Consider staying on Kangaroo Point. In addition to buses and ferrys to the CBD, there were steps down to the river a few blocks from the Paramount Motel, where we stayed (more like a short-term apartment rental, with full kitchen) and then a nice walk to South Bank Air Train station and other South Bank attractions. There was a well-stocked 24-hour store nearby and a full grocery store within about 1 km.

4) Take a trip with Bushwacker Ecotours. Our trip to Springbrook National Park was great. Our guide, Megan, was very knowledgeable and entertaining. She spotted the trap-door spiders and glow-worms in earth banks along the trail, told us how male bush turkeys (which we saw) make compost piles to keep their eggs warm, pointed out tree-scars made by sugar gliders, etc. A high point for me was seeing Casuarina, a nitrogen-fixing tree that looks like a conifer, is more closely related to beeches than to the nitrogen-fixing legumes I study and hosts different nitrogen-fixing symbionts in its root nodules, and has separate male and female plants. For those less-interested in natural history (not readers of this blog, surely, but perhaps your partner?) the walks have lots of beautiful waterfalls and a chance to hand-feed wild (well, unconfined) parrots. Be advised that the climb up out of the valley is equivalent to climbing several flights of stairs with a bit of walking between flights.
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I should probably mention that restaurant meals here cost 1.5-2x what they would in the US. But the botanic gardens and parks are all free, so it hasn't been too expensive, apart from airfare.

I'll write something about the Applied Evolution Summit soon.

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.

December 11, 2009

Delaying reproduction: the "disposable germline" hypothesis

This week's paper sheds new light on trade-offs between longevity and reproduction in Caenorhabditis elegans. This nematode worm is popular with medical researchers because it has a simple nervous system, insulin-like hormones, etc., yet it can be grown in Petri dishes, where it can mature and start reproducing two days after hatching from a tiny egg.

At various stages during this maturation process, C. elegans can essentially put life on hold. Environmental cues, particularly food shortage, switch them off their normal developmental pathway onto a side-track, where they can survive for months without food, but without maturing. Once food returns, they resume development.

This week's paper reports a new kind of developmental delay in individuals on the verge of reproductive maturity. "Starvation Protects Germline Stem Cells and Extends Reproductive Longevity in C. elegans" was published in Science, by Giana Angelo and Marc R. van Glist, working at the Fred Hutchison Cancer Resarch Center, in Seattle.

When worms with developing eggs are starved just before reproducing, some of them "die in childbirth", as the eggs hatch inside their bodies and emerge. Others, however, delay reproduction. Most of the developing germ cells apparently end up getting digested "for fuel", rather than becoming eggs. The adults can then survive for a month or more. Once fed, they resume reproduction, although they then lay fewer eggs than if they hadn't been starved. So an individual who would have started to lay eggs on day 2 can start on day 30 instead, a 15-fold delay in reproductive maturity.

Why do they do this? The authors have identified some genes that help control this process. But evolutionary biologists ask a different kind of "why" question: why have genes for delaying reproduction under starvation displaced genes for reproducing at the usual age?

A common answer is that they are waiting for "better conditions." But better how? Maybe they can produce more eggs if they wait until there's more food. But the relative success of different genes depends on the timing of reproduction, not just the number of offspring. An individual that produces a few eggs early might have lots of great-grandchildren by the time an individual who delayed reproduction started to lay eggs. A key point is that evolutionary changes in the genetic composition of populations depend on the relative performance of individuals with different genes. Maybe there will be more food later, but there will be more food later for everyone: for individuals who delayed reproduction and for the descendants of those who didn't.

It turns out that the one "better condition" that really makes it worthwhile to delay reproduction is a decrease in overall population size. -- not the increased resources per individual that you might get with lower population, but lower population itself. This is because each offspring added to a smaller gene pool will have a disproportionately large effect on the composition of future generations. As we put it in a recent paper, "When Stress Predicts a Shrinking Gene Pool, Trading Early Reproduction for Longevity Can Increase Fitness, Even with Lower Fecundity."

Under our "smaller pond" hypothesis, starvation provides worms with information, specifically, information predicting a decreasing population. That makes delaying reproduction a promising strategy. Even if the worm ends up laying fewer eggs (which isn't necessarily the case, depending on the direct effects of food supply on egg production), they will join a smaller gene pool. Individuals delaying reproduction will therefore be over-represented in future generations.

Food supply isn't the only factor predicting whether population will increase or decrease. If it's crowded, even a large food supply may not last long. Nematodes have previously been shown to detect the degree of crowding, essentially by smelling each other. Crowding can contribute to delays in maturation earlier in life. This week's paper shows that this is also true for adults that delay reproduction. If starved individuals are removed from the crowd, they resume reproduction, even without food. If there are few other worms around -- they probably can't tell the difference between "few" and "none" -- this is their big chance to found a dynasty.

The authors propose a "disposable germline" hypothesis. This is an allusion to Kirkwood's discredited "disposable soma" hypothesis, which attempted to explain trade-offs between reproduction and longevity as the result of limited resources: not enough calories to reproduce and also maintain healthy bodies. Although the "disposable soma" hypothesis has been cited hundreds of times, it hasn't been quite the same since people discovered that starvation increases longevity. To explain this result under the "disposable soma" hypothesis, you would have to assume that starving individuals save so many calories by not reproducing that they actually have more calories available for maintenance than if they had all the food they could eat.

December 1, 2009

Wildlife and plants near Brisbane?

My wife and I will spend a few days in Brisbane between Christmas and New Years, before I go to the Applied Evolution Summit. Any suggestions for places to visit nearby? We like seeing new species of plants and animals.

Better ant fungus farming through chemistry

Leaf-cutter ants feed the leaves to fungi and eat the fungi. Another fungus can parasitize their crop. A few years ago, it was reported that bacteria living on the ants' bodies make antifungal compounds that kill the parasite.

I wondered about this: wouldn't a bacterium that invests resources in antifungal production grow more slowly than a mutant that avoids this costly investment? In the long run, this might hurt ants and bacteria alike, but natural selection has no foresight. So why haven't bacterial "cheaters" that don't make antifungals displaced "altruists" that do? When yeasts (single-cell fungi) were found on the same ants, I suggested that antifungal production might benefit individual bacteria in their war with the yeasts, with activity against the parasitic fungus as a side effect. (Similarly, bacteria that make antibiotics that protect plant roots from fungi have their own selfish reasons.)

Consistent with this hypothesis, it turns out that the antifungal chemicals made by the bacteria aren't active only against the parasitic fungi, and may even harm the fungal crop. But the bacteria presumably benefit the ants more than they harm them, because the ants have specialized structures and secretions whose main function seems to be to support the bacteria. At least, this is true of some fungus-growing ant species. Other species have apparently abandoned use of these bacteria. Instead, they control harmful fungi with antibiotics they make themselves, in special glands. This is an example of a species abandoning one symbiosis (ant/bacteria) when it's no longer beneficial, while retaining a beneficial symbiosis (ant/fungus).
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Black lines shows fungus-growing ant lineages that rely on antibiotics they make themselves, rather than those made by symbiotic bacteria, to control parasitic fungi that attack their fungal crop.
Source: Hermógenes Fernández-Marín, Jess K. Zimmerman, David R. Nash, Jacobus J. Boomsma and William T. Wcislo (2009) Reduced biological control and enhanced chemical pest management in the evolution of fungus farming in ants. Proceedings of the Royal Society B 276:2263-2269.

November 25, 2009

Not so fast!

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

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

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

Celebrating "The Origin of Species" everywhere

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Poster advertising Darwin symposium in Beckley, West Virginia, where I was a USDA researcher for several years.

Yesterday, I'm told, was the 150th anniversary of the publication of The Origin of Species. In honor of this occasion, and of the 200th anniversary of Darwin's birth, 12 February 1809, there were major symposia at the Universities of Cambridge and Chicago, and minor ones all over; I wasn't the only one to make a commemorative cake, although I thought mine was more scientific than most, but probably not as tasty as if it had evolved, with selection imposed by human preferences.

November 23, 2009

Off-topic: Jam Hound helps musicians improve their skills

When I was a grad student, I used to enjoy weekly play-along "jam sessions", where a group of people would get together and play old-time, bluegrass, or Celtic music. The better musicians were mostly pretty patient with us beginners, but I sometimes wished I could practice a bit beforehand, learning songs at my own speed. I could usually do fairly well on penny whistle, but could never keep up on banjo or hammer dulcimer. What I needed was Jam Hound, a free website set up by my brother, Glenn, a mandolin and guitar player and computer genius.

So far, the site includes:
* Rhythm Track Generator
* Ear Training
* Fingerboard Tutors
...mainly intended for musicians, including beginners, playing folk songs and fiddle tunes.

If you're interested, have a look and leave a comment if you have any suggestions for improvements.

Are ants' fungus gardens a source or sink for nitrogen?

This week's paper, Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants, has already been discussed by Ed Yong, whose blog is among my favorites, and by the always-interesting Susan Milius of Science News. When she interviewed me, I endorsed the main conclusions of the article but expressed skepticism on one point.

The paper clearly shows that the fungus "gardens" cultivated by leaf-cutter ants contain bacteria that extract nitrogen from the air. The part I wondered about was their statement that:

Continue reading "Are ants' fungus gardens a source or sink for nitrogen?" »

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" »


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