Category Archives: science

Science online, Neo-Fisherian whale snot edition

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Chad Orzel, over at Uncertain Principles, is giving up blogs (reading, not writing, anyway) for Lent. He has a good point w/r/t the echoic effects of political blogs and political-ish posting on science blogs* – it’s tempting to follow suit, if only for the blood-pressure benefits. Fortunately, there’s also plenty of online writing about new knowledge, and that’s what I aggregate on Fridays:


Gesundheit. Photo by erikogan.
  • Collecting whale snot: It is, improbably, even more complicated than it sounds. (The Thoughtful Animal)
  • We have seen the population bomb, and it is us: The solution to unsustainable birthrates in developing countries is to develop them, right? Maybe not: while birthrates decline as development improves, highly developed countries often see their birthrates increase. (Tomorrow’s Table)
  • Yes, there’s a blog dedicated to spirochetes now: The bacterium that causes Lyme disease takes days to move from the gut of a newly-infected tick to the salivary glands, apparently because it stops moving when it hits the gut. (Spirochetes Unwound)
  • So far, no saber-toothed dentures found: Analysis of a large sample of broken fossil teeth of Smilodon fatalis suggest that saber-toothed cats frequently resorted to chewing on bones. (Laelaps)
  • Who doesn’t already do this? Seriously: Scientists should report p-values, rather than just calling results “significant.” (i’m a chordata! urochordata!)
  • Well, that’s unexpected: Bacteria growing in the fungus gardens cultivated by leafcutter ants are capable of nitrogen fixation. (Laura’s Animals/Wildlife Blog)
  • Your (great-to-the-nth-grand) mother was a crab: A new reconstruction of the arthropod evolutionary tree, employing 62 nuclear genes, suggests that the common ancestor of insects was a crustacean. (Palaeoblog)
  • Malaria and degenerative bone disease: Extensive analysis of Tutankhamen’s mummy (and others) suggests that it was not, in fact, all that good to be the Pharaoh. (NPR, NY Times)
  • Here be dragons: Teeny-tiny, adorable dragons. (SciencePunk)
  • OK, this is a little bit political: The Obama stimulus package was pretty good for NSF-funded researchers. (dechronization

*Why, yes, I’m currently re-reading David Foster Wallace’s Consider the Lobster. Why do you ask?

Caught between birds and squirrels, limber pines go both ways

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ResearchBlogging.orgResponding to natural selection often means compromising between different selective forces. A brief paper published online early at Evolution documents one such case – limber pine trees’ compromise between protecting their seeds from squirrels, and making them accessible to the birds that disperse them. Pulled between these conflicting selective sources, some limber pine populations grow cones in a wider variety of shapes [$a].



Cones of the limber pine must balance protection against squirrels with accessibility for seed-dispersing Clark’s nutcrackers. Photos by Fool-On-The-Hill and almiyi.

Seeds of the limber pine are cache-dispersed by Clark’s nutcrackers. That is, the birds collect pine seeds to cache as a winter food source, but they collect many more than they need, and forget lots of them, and forgotten seeds are often able to sprout. However, squirrels also like pine seeds, and they harvest them before the birds start caching seeds. These two seed-harvesters generate conflicting selection on limber pine cones [$a]. Nutcrackers go for cones with lots of seeds protected by thinner scales; but so do squirrels.

However, pine-nut-eating squirrels are not present everywhere limber pines grow. The new study’s authors, Siepielski and Benkman, take advantage of this quirk of distributions to perform a natural experiment, comparing pines that only need to satisfy their seed dispersers with pines that also need to defend against seed predators. Surveying cone shapes in populations of each class, they found that limber pine populations facing conflicting selection were bimodal, with trees mainly growing either squirrel-defended short, thick-scaled cones, or nutcracker-friendly longer, thin-scaled cones. Populations growing in regions without squirrels produced only nutcracker-friendly cones.

This apparently simple pattern conceals more complicated dynamics – in fact, as the authors disclose in the Discussion section, many other limber pine populations are solely composed of trees producing squirrel-defended cones. This is because, when pines establish in areas with large squirrel populations, nutcrackers may never colonize the area, or may visit less frequently and disperse fewer seeds. Without nutcracker dispersal, seeds are mainly dispersed after the cones fall, by rodent species that (unlike squirrels) forage on the ground. This makes squirrel defense the only selective priority. Populations displaying both cone types probably only arise in unique conditions, the authors say, where squirrels are present but not at high density.

References

Siepielski, A., & Benkman, C. (2007). Convergent patterns in the selection mosaic for two North American bird-dispersed pines. Ecological Monographs, 77 (2), 203-20 DOI: 10.1890/06-0929

Siepielski, A., & Benkman, C. (2009). Conflicting selection from an antagonist and a mutualist enhances phenotypic variation in a plant. Evolution DOI: 10.1111/j.1558-5646.2009.00867.x

Science online, Darwin 201 edition

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Today is, of course, the 201st anniversary of the birth of Charles Darwin. This not being a big, round number, there are somewhat fewer festivities planned than last year. Over at Ecographica, Johnny’s taken the effort to assemble some new celebratory links. Meanwhile, online science writers continue to explore the “endless forms most beautiful” of the natural world:


Photo by SARhounds.
  • Big-beaked hornbills have short little tongues, so they feed by scooping up food in their beaks, and then tossing it back with a shake of their heads in a “ballistic” feeding maneuver. (NeroDojo)
  • Species at low levels of the food chain seem to be shifting their seasonal habits to compensate for climate change more rapidly than species at higher levels. (Conservation Magazine)
  • A new survey estimates that, in one upstate New York county, 45,000 mammals are road-killed every year. (Conservation Magazine, again)
  • Conservation plans focused on carbon-sequestering regions would probably also preserve a lot of biodiversity – but they’d also miss some critical diversity hotspots. (Conservation Maven)
  • Two variants of a gene involved in muscle development are correlated with the performance of thoroughbred racehorses. (Living the Scientific Life)
  • Two genes have been identified that seem to be associated with stuttering. Curiously, they both code for proteins involved in a cellular process that doesn’t have any obvious connection to speech. (Imagining Geek)

ResearchBlogging Awards nominees

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Research Blogging Awards 2010The blogs nominated for the first annual Research Blogging Awards have been posted. Thanks to whoever nominated D&T! Nominations will remain open until the 11th, after which a panel of judges will select five to ten finalists in each category, and the ResearchBlogging.org community will vote for winners.

Science online, fragmented pandas edition

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The new month sees Dave Munger launching his new project, The Daily Monthly, which will feature daily posts on a new topic each month. The effect is like a long-form magazine article released in serial form. The inaugural topic, AIDS in America, is already really interesting. Meanwhile, ocean blogger Miriam Goldstein has closed shop at the Oyster’s Garter to join Deep Sea News. In actual science news:


Photo by auntie rain.
  • No surprise here: fragmented forest makes poor panda habitat. (The Voltage Gate)
  • Close observation of decaying fish (ugh!) shows that the traits most useful for reconstructing evolutionary relationships might be the ones least likely to fossilize. (dechonrization)
  • Protecting ecosystems may not always mean not manipulating them. (The EEB & flow)
  • Alligators pump air through their lungs in a one-way flow – just like birds. (The Reptipage)
  • How do you figure out how ants navigate? Put them on teeny-tiny stilts. (The Thoughtful Animal)
  • British medical journal The Lancet finally gets around to retracting a flawed, twelve-year-old study that suggested a link between vaccination and autism. (The retraction statement is free online, with registration. News coverage is ubiquitous, but Michael Specter is in the running for most coldly furious about the whole debacle.)
  • Freshwater eels appear to have evolved from ancestors that lived in the deep sea. (Deep Sea News)

Dethroning the Red Queen?

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ResearchBlogging.orgRegular readers of Denim and Tweed know that I’m fascinated by the evolution of species interactions: interactions between plants and nitrogen-fixing bacteria, Joshua trees and yucca moths, parasitoid wasps and butterflies, and between ants and the trees they guard. I tend to think that coevolutionary interactions not only determine the health of natural populations, but shape their evolutionary history. But would I feel that way if I were a paleontologist?

Running just to stay in place

The idea that interactions between species matter goes all the way back to the origins of evolutionary biology in the writing of Charles Darwin:

What a struggle between the several kinds of trees must here have gone on during long centuries, each annually scattering its seeds by the thousand; what war between insect and insect – between insects, snails, and other animals with birds and beasts of prey – all striving to increase, and all feeding on each other or on the trees or their seeds and seedlings, or on the other plants which first clothed the ground and thus checked the growth of the trees! (On the Origin of Species, 1859: 74-5)

This image of constant struggle among living things was more formally encapsulated in a 1973 paper by Leigh Van Valen (which paper is not, alas, available online), who proposed that constant coevolution with other species should mean that natural populations of living things are constantly adapting – in response to competitors, mutualists, predators, parasites – without gaining ground in the struggle, because the other species are also adapting. Van Valen lifted an image from Lewis Carroll’s Through the Looking-Glass, in which the Red Queen tells Alice that, in the strange world of Looking-Glass Land, “… it takes all the running you can do, to keep in the same place.”

They were running hand in hand, and the Queen went so fast that it was all she could do to keep up with her … The most curious part of the thing was, that the trees and the other things around them never seemed to changed their places at all.


“… it takes all the running you can do, to keep in the same place.” Image from Through the Looking-Glass, via VictorianWeb.

Thus, this idea that fuels much of my research, and a great deal of scientific study over the last three decades, is often identified with the Red Queen. What is interesting about this result is that Van Valen wasn’t interested in species interactions as such; he was trying to explain a pattern in the fossil record – that, for a wide variety of living things, the probability that a species would go extinct was independent of its age. That is, species that have been around for ten million years are no better adapted to their environments than species that have just formed; the probability of extinction is constant.

Van Valen’s explanation for this result was that something must constantly act to prevent living things from becoming better adapted, and better able to resist extinction, over time – specifically, the Red Queen’s race against other living things. Whenever a species “loses” the race, it goes extinct, regardless of how long the race has been up to that point. A similar pattern applies to the creation of new species – if coevolutionary interactions often help create reproductive isolation, then new species should also form at a roughly constant rate [$a]. Since this is what we observe, many biologists conclude that coevolution is responsible for the diversity of life on Earth.

What if the race doesn’t matter?

Fortunately for the advance of knowledge, however, not all evolutionary biologists have the same perspective. Paleontologists, for instance, tend to think that the year-to-year dynamics of the Red Queen race don’t make much difference in the longer run, over millions of years. They’d argue that most of the evolutionary change induced by coevolution between species is too variable and fleeting to have much effect on the rates at which species are formed and go extinct. Under this view, random geological events – continents splitting, mountain ranges rising, volcanoes erupting – are more likely to create new species and force them to extinction.


What matters more in the history of life, the biological environment, or the physical environment? Photos by Martin Heigan and Cedric Favero.

This competing model should also lead to a roughly constant rate of species formation and extinction, but it predicts a different pattern of variation around that constant rate than the coevolutionary Red Queen does. If most speciation and extinction events are caused by coevolution, then the time periods between speciation events should follow a normal distribution – forming a “bell curve” with most periods close to the average length, and symmetrical tails of longer and shorter periods of time. On the other hand, if many different, individually rare geological events are the most common cause of speciation and extinction, the periods between speciation events should follow an exponential distribution, with most periods being shorter than the average, but a long tail of longer periods as well.

This contrast is the crux of a study recently published in Nature. The paper’s authors, Venditti et al., examined 101 evolutionary trees estimated from genetic data, including groups like the dog family, roses, and bees. For each group’s evolutionary tree, they determined the distribution of the lengths of time periods between speciation events. A majority of the trees – 78% – supported the exponential model. That is, 78% of the groups of organisms examined had evolved and diversified in a fashion best explained by geology, not coevolution. None of the groups fit the normal distribution, and only 8% fit the related lognormal distribution.

The Red Queen is dead, long live the Red Queen!

This result suggests that within many groups of organisms, the physical environment is a more common cause of reproductive isolation or extinction than the biological environment. However, this isn’t to say that species interactions don’t matter. As Van Valen originally noted, extinction rates may be roughly constant within large groups of organisms, like those examined by Venditti et al., but those constant rates vary from group to group. These differences in rate may still depend on species interactions, because species interactions can shape how prone a population is to reproductive isolation.

For instance, a group of plants that has lousy seed dispersers may form new species in response to much smaller, and more common, geological barriers than a group of plants whose seeds can travel for hundreds of miles. Additionally, species interactions that promote diversity within the interacting species may mean that when geology creates isolation, the resultant daughter species are more different from each other than they would otherwise be, and less likely to re-merge if they come into contact again. Under that scenario, speciation caused by the physical environment would act to preserve variation [$a] created by the biological environment.

So, perhaps the Red Queen doesn’t operate the way we thought she did, with constant coevolutionary races spinning off new species and killing off others. But that hardly means that Red Queen processes don’t matter in the long run.

References

Benton, M. (2010). Evolutionary biology: New take on the Red Queen. Nature, 463 (7279), 306-7 DOI: 10.1038/463306a

Futuyma, D. (1987). On the role of species in anagenesis. The American Naturalist, 130 (3), 465-73 DOI: 10.1086/284724

Stenseth, N., & Maynard Smith, J. (1984). Coevolution in ecosystems: Red Queen evolution or stasis? Evolution, 38 (4), 870-80 DOI: 10.2307/2408397

Van Valen, L. (1973). A new evolutionary law. Evolutionary Theory, 1 (1), 1-30

Venditti, C., Meade, A., & Pagel, M. (2009). Phylogenies reveal new interpretation of speciation and the Red Queen. Nature, 463 (7279), 349-52 DOI: 10.1038/nature08630

Science online, independently-evolved sonar edition

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Photos by Thomas Hawk and Tolka Rover.

Whether you’re doing it underwater or in the air, echolocation apparently requires the same kind of adaptation. New Scientist reports that parallel evolutionary changes to the same gene allow both dolphins and bats to hear the high-frequency sounds they use for sonar. In other online science news:

“Chemical camouflage” lets leafhoppers hide from their own bodyguards

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ResearchBlogging.orgMany insects in the order Hemiptera – the “true” bugs – have evolved a way to hire their own protection by excreting sugary “honeydew.” Honeydew attracts ants, who tend honeydew-producing bugs like livestock, protecting them from predators and even disease. Honeydew is cheap to make because honeydew producers typically make a living sucking the sap of their host plants; they’re trading sugar and water, which they have in abundance, for safety.


Camponotus crassus ants protect Guayaquila xiphias leafhoppers, apparently mistaking them for part of their host plant. Detail of Silveira et al., figure 1.

But there’s a catch. Ants make good bodyguards because they are carnivorous – and they’re perfectly willing to start eating their flock. A natural history note in the latest issue of The American Naturalist suggests that one group of ant-protected bugs deals with this problem by cloaking themselves in chemicals that make the ants think they’re part of the host plant [$a].

The study’s authors determined that organic compounds on the cuticle of the honeydew-producing leafhopper Guayaquila xiphias, which is often tended by the ant Camponotus crassus, were similar to compounds on the surface of the leafhoppers’ preferred host plant. They presented ants with freeze-dried leafhoppers whose cuticles were washed clean with solvent, and found that the ants were much more likely to attack washed leafhoppers than unwashed ones; the ants were also more likely to attack leafhoppers they found on plants other than the preferred host. Finally, the authors replicated the earlier experiments using moth larvae coated with leafhopper cuticle compounds, and found that the “chemical camouflage” conferred the same protection on a different insect species.

This neat result shows how hazardous honeydew-producers’ relationship with their ant bodyguards can be – they have to hide from the ants even as they offer them an inducement to stick around!

Reference

Silveira, H., Oliveira, P., & Trigo, J. (2010). Attracting predators without falling prey: Chemical camouflage protects honeydew‐producing treehoppers from ant predation The American Naturalist, 175 (2), 261-8 DOI: 10.1086/649580

Science online, share and share alike edition

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Wednesday saw Greta and Dave Munger turn off the virtual lights at Cognitive Daily after five years of high-quality, and often participatory, science writing. No other science blog that I know regularly asked its readers to join studies, however informal, of the very concepts it covered – not just writing about science, but practicing it. It’s sad to see it end, but I’m looking forward to the new project Dave teases at the end of the announcement. Elsewhere in the science blogosphere:


Photo by Gary Simmons.
  • Europe’s fisheries aren’t likely to recover by 2015, as planned under a 2002 treaty. (Conservation Bytes)
  • The American Naturalist will begin requiring authors to deposit all data, not just genetic sequences or phylogenetic trees, in publicly-accessible online repositories. (skeetersays)
  • Shorebirds may migrate in part because there are fewer nest predators at higher latitudes. (Living the Scientific Life)
  • Natural selection imposed on native species by invasive species might make prairie grass communities better able to resist new invasions. (Conservation Maven)
  • Lemurs might have colonized Madagascar by rafting on driftwood – a new model of ocean currents shows that it might have been easier than previously thought. (Laelaps)

Evolving from pathogen to symbiont

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This post was chosen as an Editor's Selection for ResearchBlogging.orgRecently the open-access PLoS Biology published a really cool study in experimental evolution, in which a disease-causing bacterium was converted to something very like an important plant symbiont. The details of the process are particularly interesting, because the authors actually used natural selection to identify the evolutionary change that makes a pathogen into a mutualist.

Life as we know it needs nitrogen – it’s a key element in amino acids, which mean proteins, which mean structural and metabolic molecules in every living cell. Conveniently for life as we know it, Earth’s atmosphere is 78% nitrogen by weight. Inconveniently, that nitrogen is mostly in a biologically inactive form. Converting that inactive form to biologically useful ammonia is therefore extremely important. This process is nitrogen fixation, and it is best known as the reason for one of the most widespread mutualistic interactions, between bacteria capable of fixing nitrogen and select plant species that can host them.


Clover roots, with nodules visible (click through to the original for a nice, close view. Photo by oceandesetoile.

In this interaction, nitrogen-fixing bacteria infect the roots of a host plant. In response to the infection, the host roots form specialized structures called nodules, which provide the bacteria with sugars produced by the plant. The bacteria produce excess ammonia, which the plant takes up and puts to its own uses. The biggest group of host plants are probably the legumes, which include the clover pictured to the right, as well as beans – this nitrogen fixation relationship is the reason that beans are the best source of vegetarian protein, and why crop rotation schemes include beans or alfalfa to replenish nitrogen in the soil.

For the nitrogen-fixation mutualism to work, free-living bacteria must successfully infect newly forming roots in a host plant, and then induce them to form nodules. The chemical interactions between bacteria and host plant necessary for establishing the mutualism are pretty well understood, and in fact genes for many of the bacterial traits, including nitrogen-fixation and nodule-formation proteins thought to be necessary to make it work are conveniently packaged on a plasmid, a self-contained ring of DNA separate from the rest of the bacterial genome, which is easily transferred to other bacteria.

This is exactly what the new study’s authors did. They transplanted the symbiosis plasmid from the nitrogen-fixing bacteria Cupriavidus taiwanensis into Ralstonia solanacearum, a similar, but disease-causing, bacterium. With the plasmid, Ralstonia fixed nitrogen and produced the protein necessary to induce nodule formation – but host plant roots infected with the engineered Ralstonia didn’t form nodules. Clearly there was more to setting up the mutualism than the genes encoded on the plasmid.


Wild-type colonies of Ralstonia (tagged with fluorescent green) are unable to enter root hairs (A), but colonies with inactivated hrcV genes are able to enter and form “infection threads,” like symbiotic bacteria (B). Detail of Marchetti et al. (2010), figure 2.

This is where the authors turned to natural selection to do the work for them. They generated a genetically variable line of plasmid-carrying Ralstonia, and used this population to infect host plant roots. If any of the bacteria in the variable population bore a mutation (or mutations) necessary for establishing mutualism, they would be able to form nodules in the host roots where others couldn’t. And that is what happened: three strains out of the variable population successfully formed nodules. The authors then sequenced the entire genomes of these strains to find regions of DNA that differed from the ancestral, non-nodule-forming strain.

This procedure identified one particular region of the genome associated with virulence – the disease-causing ability to infect and damage a host – that was inactivated in the nodule-forming mutant strains. As seen in the figure I’ve excerpted above, plasmid-bearing Ralstonia with this mutation were able to form infection threads, an intermediate step to nodule-formation, where plasmid-bearing Ralstonia without the mutation could not. Clever use of experimental evolution helped to identify a critical step in the evolution from pathogenic bacterium to nitrogen-fixing mutualist.

References

Amadou, C., Pascal, G., Mangenot, S., Glew, M., Bontemps, C., Capela, D., Carrere, S., Cruveiller, S., Dossat, C., Lajus, A., Marchetti, M., Poinsot, V., Rouy, Z., Servin, B., Saad, M., Schenowitz, C., Barbe, V., Batut, J., Medigue, C., & Masson-Boivin, C. (2008). Genome sequence of the  beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Research, 18 (9), 1472-83 DOI: 10.1101/gr.076448.108

Gitig, D. (2010). Evolving towards mutualism. PLoS Biology, 8 (1) DOI: 10.1371/journal.pbio.1000279

Marchetti, M., Capela, D., Glew, M., Cruveiller, S., Chane-Woon-Ming, B., Gris, C., Timmers, T., Poinsot, V., Gilbert, L., Heeb, P., Médigue, C., Batut, J., & Masson-Boivin, C. (2010). Experimental evolution of a plant pathogen into a legume symbiont. PLoS Biology, 8 (1) DOI: 10.1371/journal.pbio.1000280