By Rob Mitchum

In 1972, a physicist named Robert May tried his hand at a different scientific discipline, publishing a simple formula that inflamed the field of ecology. Scientists studying the structure of natural ecosystems had long assumed that diversity was an inherently good thing — those ecosystems stocked with thousands of species were likely more resistant to extinctions, changes in climate, or other challenges. May, with a physicist’s eye for simplicity, crafted a model that predicted the stability of an ecosystem using just the number of species and how strongly they interact with each other. But when it was used, May’s formula provided a surprising and counter-intuitive result: species-rich ecosystems, such as rain forests and coral reefs, should be too unstable to exist.

That paper, published in Nature under the title “Will a Large Complex System be Stable?” (May’s answer: No), was both a major step for computational ecology and the ignition of what came to be called the diversity-stability debate. The disagreement between May’s model and what ecologists saw in reality provoked the question of how nature rescues what should be an unstable ecosystem, allowing it to survive. Ecologists began looking for what May called “devious strategies” — the workarounds that a natural system uses to increase its species capacity without sacrificing its stability. Soon, May’s elegant formula became swollen with additions meant to reconcile the mathematical predictions with field observations.

Stefano Allesina, assistant professor of Ecology & Evolution at the University of Chicago, decided to take a different approach. Rather than building even more complex additions on to May’s model, Allesina and graduate student Si Tang, sharpened their pencils and went back to the original source, tweaking the model by thinking about the general types of ways species interact in nature. Their new model, published 40 years after the original in the same journal, adjusted May’s formula to incorporate predator-prey or consumer-resource relationships, where one species profits at the expense of another. The small changed allowed the model to describe an ecosystem where stability is possible even with an infinite number of species.

“Predator-prey relationships are stabilizing. We can fit much larger ecosystems if there’s a backbone of predator-prey interactions, and see a lot of species happily co-existing ever after,”Allesina said. “We kind of solved this one puzzle of how can we see very many species in an ecosystem. But then we open different puzzles.”

May’s original model, designed to be as general as possible, assumed random interactions between species. But in nature, two species can interact with each other in one of three general ways: as predator and prey, as competitors, or as part of a mutalistic relationship. In the predator-prey or consumer-resource relationship, one species benefits from another species’ loss, be it a lion eating a gazelle or a caterpillar eating a leaf. Competition theoretically has a negative effect on the two species fighting over the same food source, while mutualism (rarely seen in nature) can benefit both participants. By building each of these three relationships separately into May’s model, Allesina and Tang discovered that these interactions each produce very different ecosystems.

In the predator-prey condition, the stability of the ecosystem is increased such that a large number of species can be supported. In the competition and mutualism systems, the ecosystem is highly unstable and vulnerable to perturbation.

“What we are showing is that of all the types of interactions you can have, only predator-prey can support an infinite number of species,” Allesina said. “If you look in nature, there are very obvious consumer-resource relationships everywhere, and maybe this system assembles so easily because these relationships provide a lot of stability.”

read more

By Matt Wood

Sometimes scientific discoveries happen by accident. Henri Becquerel discovered radioactivity when a uranium rock he left wrapped up in a drawer with some X-ray equipment imprinted itself on a photographic plate. Alexander Fleming discovered penicillin when he noticed that mold growing in a staphylococcus culture was killing all the bacteria around it. In 2007, Catherine Pfister and her colleague Timothy Wootton made their own accidental discovery. They were studying how species interact in the coastal waters around Tatoosh Island off the northwestern tip of Washington state when they found something alarming about the chemistry of the seawater—a discovery that points to the adverse effects of increasing amounts of fossil fuel carbon in the atmosphere.

As a routine part of their work, Pfister and Wootton were measuring pH levels in the waters around Tatoosh Island. Such readings are usually the boring part of field research, providing context for the rest of the experiments. “If you were studying tree growth you’d always have to be measuring the weather,” said Pfister, an associate professor of ecology and evolution at the University of Chicago, “And this is the weather for us, what the ocean is like.”

Instead of the slight declines predicted by models, however, Pfister and Wootton, a professor of ecology and evolution, found that pH levels in the water were dropping at an order of magnitude faster than expected.

The pH levels in seawater are part of the basic chemistry of the ocean. Plants and animals develop and interact in a certain pH and evolve as it changes naturally over time. What concerned Pfister and Wootton was how the rapid drop in pH they recorded would affect the ecosystem. “We all know that there’s a strong pH dependence of biological reactions, and we don’t know how those reactions will change if pH changes rapidly,” Pfister said.

Rapid decline in seawater pH is a symptom of what’s called “ocean acidification,” or decreasing alkalinity as ocean water absorbs increasing amounts of carbon dioxide from the atmosphere generated by burning fossil fuels. Scientists estimate that the ocean absorbs at least a third of that carbon dioxide.

In 2008, they published their findings about the declining pH levels in PNAS. What they didn’t know at the time was whether those readings were part of a sustained trend or just an unexpected natural variation. “We have a lot of concern about that,” Pfister said. “We haven’t been measuring [pH levels] for that long in the ocean. There’s a very short instrumental record in the ocean, and the instrumental record only goes back to the 1990s.” Most of the pH data on record was also from tropical waters and the open ocean, in areas with less species diversity than the rich coastal waters around Tatoosh Island.

To find out if their measurements represented a new trend, they turned to a tried and true method of measuring historical ocean environments: sea shells, specifically the shells of the California mussel (cross section pictured above). Mussel shells are made of calcium carbonate and grow annual layers or bands just like trees. Scientists often use hard structures like this to infer things about the environment in which an organism lived, so the chemical composition and growth patterns of these mussel shells can be used to study the chemical composition of the ocean.

The results of this study are published in a new paper in PLoS ONE. Pfister, Wootton, graduate student Sophie McCoy and colleagues from the University of Chicago Department of Geophysical Sciences analyzed carbon and oxygen isotopes in shells that had been growing near their instruments for the past decade, as well as shells collected by researchers 30 to 40 years ago and ones provided by the local Makah tribe from over 1,000 years ago. Carbon isotope levels drop in conjunction with pH. When they compared the shells from the three different time periods, they found that the ones from the last decade showed a precipitous drop in carbon isotope values similar to the pH decline recorded by their instruments in the earlier research. The findings both confirmed the earlier measurements and demonstrated that shells might be used to measure historical pH levels in water when no instrumental record exists.

Unfortunately, Pfister says that they’re left with another mystery. read more

The evidence for recent, accelerating global climate change is very strong, as it is for the role we humans have played in influencing our Earth’s weather. But for the most part, there have been few direct tests of how climate change could affect the organisms that inhabit our planet. Much of the evidence on this point is either anecdotal, correlational, or based upon predictive models, such as reports that 1 billion people will be forced to relocate due to climate changes or predictions of increased extinction risk due to changes in temperature, ocean chemistry, sea level, and other factors. None of these studies get at a crucial question that will determine the true impact of these environmental shifts: in a footrace between climate change and evolution, what will win?

Two studies published today in Science suggest an answer for one particular species, the small flowering plant Arabidopsis thaliana. Just as the fruit fly Drosophila melanogaster has become an important tool for scientists studying animal genetics, Arabidopsis is the model organism of choice for studying plant genes. Researchers around the world - including the laboratory of Joy Bergelson, professor and chair of evolution & ecology at the University of Chicago - have characterized the genome of Arabidopsis and looked at the variation within the species.

“Arabidopsis is pretty much ubiquitous; it’s been collected in most parts of the world. You find it throughout Eurasia, Russia, up through Scandinavia and down through the Iberian peninsula,” Bergelson said. “So, as a community, we now we have thousands and thousands of lines from all over, many of which are housed in this lab.”

Those resources allowed Bergelson’s laboratory and another group from Brown University to study the relationship between climate change and evolution in this plant species via two separate experiments. In the first, a team led by University of Chicago postdoctoral researcher Angela Hancock applied the popular methodology of genome-wide association studies (GWAS) to the plant, with a twist. Instead of looking for gene variants associated with a particular characteristic of the plant itself, the team looked for variants associated with different climate variables, such as temperature, precipitation, and humidity. (If it sounds familiar, ScienceLife wrote about a similar study Hancock performed with human genetics in 2010.)

Their analysis produced a list of climate-associated genes that reflect familiar biological processes, controlling aspects of photosynthesis, growth, energy metabolism, and other activities important to plant health. To test whether these genes were truly related to a plant’s fitness in a given climate, the researchers tested their ability to predict how well a plant would grow when grown in one particular climate, that of Lille France, based on the number of favorable variants that they carried. Happily, the gene variants were truly predictive, suggesting that the variants produced by their GWAS indeed played a role in a plant’s ability to grow and reproduce in a given climate.

“You can actually predict pretty decently changes in the relative fitness of plants just based on the results from our worldwide scan,” Bergelson said. “It didn’t have to work - it was a longshot really - but we were happy to see that it did work.”

But for the future of climate change, the more critical question was how these variants initially appeared in the Arabidopsis genome. For many of the climate-associated variants, the University of Chicago team found evidence of “selective sweeps,” an evolutionary process where a new, favorable mutation appears and spreads rapidly through a species. In the case of Arabidopsis, this finding suggests that the plant adapted to shifts in climate thanks to the random appearance and subsequent spread of these helpful mutations, rather than drawing from pre-existing genetic variation. But in times of rapid climate change, there may not be sufficient time to wait for those genetic changes to occur.

“The key there is that the variant is novel, and so the extent to which a plant or an organism depends on sweeps to adapt to climate means that there is an intrinsic delay,” Bergelson said. “As the climate continues to change, they may not have the standing variation that they would need to adapt. That’s going to slow things down.”

read more