Enrichment and diversity loss: a mechanism tested

To paraphrase Thomas Henry Huxley: How stupid of us not to have thought of that!

In what has to be one of the most elegant and simple experiments I've seen in a long time, Yann Hautier, Pascal Niklaus and Andy Hector tested a basic mechanism of why nutrient enrichment results in species loss. This is a critically important issue as it has been repeatedly shown that while adding nitrogen to plant communities causes increases in productivity, species go locally extinct. We may bare witness to local diversity declines because human activity has greatly increased nutrient deposition. This pattern has been observed for a couple of decades, but the exact mechanism has never been adequately tested, with some camps believing that enrichment increases below-ground competition for other resources that become limiting, or above ground for light.

As reveled in the most recent issue of Science, Hautier et al. performed an exceedingly simple experiment; they added light to the understory of plant communities with or without nitrogen additions. They made two compelling observations. First, when communities were enriched without elevated light, they lost about 3 of the 6 initial species compared to the control, while light addition in the enriched communities maintained the 6 member community (as did a light only treatment). The second result was that the light plus nitrogen treatment obtained much higher biomass than either the nitrogen or light only treatments, and in fact the light only treatment did not significantly increase productivity, meaning that the communities are not normally light-limited. Further, they failed to detect any elevated belowground competition for other resources.

These results reveal that nutrient enrichment causes diversity loss because increased plant size increases light competition and plants that grow taller with elevated nitrogen are better light competitors. An old problem solved with the right experiment.

Hautier, Y., Niklaus, P., & Hector, A. (2009). Competition for Light Causes Plant Biodiversity Loss After Eutrophication Science, 324 (5927), 636-638 DOI: 10.1126/science.1169640

People value rare species; at least from their computers

Do people value rare species more than common ones? This is an important question for conservation because not only does valuation justify public funds being spent conserving rare species, but valuation can have negative implications as well. In what is called the ‘anthropogenic Allee effect’, increased valuation can increase species desirability –thus enhancing monetary value for exotic pets, building ecotourism lodges in sensitive habitats, or exotic tasty dishes (ah, The Freshman). In what is probably the most unique approach to assessing whether behavior is affected by the notion of species rarity, Angula and Courchamp, at the Université Paris Sud, used a web-based slideshow measure the amount of time people would wait to see a slideshow of rare versus common species.

Cleverly, they created a French website where visitors could select to view either a slideshow of common or rare species (and the links randomly changed positions on the site). The trick was that a download status bar appears and freezes near the end, and so Angula and Courchamp were able to measure how many visitors selected the rare species show and how long they waited until they gave up. Visitors were much more likely to select the rare species and to wait longer to see them.

I think that this study is extremely neat for two reasons. First it offers a novel way to quantify valuation, and second, it shows how the internet can be used to assess conservation issues in an efficient low-cost way.

Now will they please just show us the pictures of the cute, endangered species!

Angulo, E., & Courchamp, F. (2009). Rare Species Are Valued Big Time PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005215

A mechanism on why communities of exotic species are less diverse than communities of native species

Plant communities dominated by exotics tend to be less diverse than plant communities dominated by natives. Apparently, few people have been curious enough to plan an experiment to try to further understand why this is the case. A recent paper in ecology letters Brian Wilsey and collaborators showed the results of an experiment designed to explore this. What they did is to create monocultures of a series of exotics and natives species, and mix cultures of exotics (a mix of 9 exotics, zero natives ) and mix cultures of natives (9 natives, zero exotics). They found that large exotics (plants with high aboveground biomass) tended to be even bigger when growing in mix cultures than in the monocultures, so big plants got bigger, which tend to reduce plant richness since it may displace other plants. On the other hand, for natives, small plants tended to get bigger, which is a mechanism for promoting biodiversity (communities may be more even). This research highlights the importance of understanding the mechanisms of plant coexistence and the fact that exotic species may behave very differently than native species.

Wilsey, B., Teaschner, T., Daneshgar, P., Isbell, F., & Polley, H. (2009). Biodiversity maintenance mechanisms differ between native and novel exotic-dominated communities Ecology Letters, 12 (5), 432-442 DOI: 10.1111/j.1461-0248.2009.01298.x

Climate change increases West Nile Virus outbreaks in the U.S.

According to a study recently published in Environmental Health Perspectives, climate change has increased the prevalence of West Nile Virus infections in the United States. In one of the largest surveys of West Nile Virus cases to date, the authors find a correlation between increasing temperature and rainfall and outbreaks of the mosquito-borne disease between 2001 and 2005. Because warming weather patterns and increasing rainfall are both projected to accelerate with global warming, the authors predict that climate change will exacerbate West Nile Virus outbreaks in the future.

In the study, Dr. Jonathan Soverow and his collaborators matched more than 16,000 confirmed West Nile cases in 17 states to local meteorological data.

Warmer temperatures had the greatest effect on outbreaks. By extending the length of the mosquito breeding season and decreasing the amount of time it takes mosquitoes to reach their adult, biting stage, warmer weather means more biting mosquitoes longer. Moreover, increasing temperature speeds multiplication of the virus within insects, so mosquitoes in warmer climates have a greater viral load, making them more likely to infect humans.

Increased precipitation was also correlated with higher rates of West Nile Virus infection. A single, heavy rainstorm resulting in two or more inches of rain increased infection rates by 33%, while smaller storms had less of an effect on infection rates. Heavier rainfall events can increase disease prevalence by creating pools of water in which mosquitoes can breed and by increasing humidity, which stimulates mosquitoes to bite and breed. Total weekly rainfall had a smaller but significant effect on West Nile Virus infections, with an increase of 0.75 inch of rain/week increasing the number of infections by about 5%.

Warmer, wetter weather patterns might expand the niches of the mosquito species that carry West Nile Virus. In California, for instance, several mosquito species carrying the West Nile Virus have extended their ranges into higher elevations and coastal areas as temperatures have warmed. Changing weather patterns might also affect certain species of birds that are reservoirs for West Nile Virus. For example, droughts can push bird populations into urban areas, making West Nile Virus outbreaks in human populations more likely.

Soverow, J.E., G.A. Wellenius, D.N. Fisman, and M.A. Mittleman. 2009. Infectious disease in a warming world: How weather influenced West Nile Virus in the United States (2001-2005). Environmental Health Perspectives. Online 16 March 2009 DOI: 10.1289/ehp.0800487

Letting out your little Monet

I realized, sometime not too long ago, that I really enjoy adding aesthetically pleasing details to my figures in scientific publications. All scientists look at hundreds of boring, monochromatic scatterplots, bar charts and ordination plots every month, so why not make them a little more appealing? If done right, the benefits are that people are more likely to remember your key figures and perhaps results, you can convey more information by incorporating imagery, and you may actually get a little joy out of preparing those figures. The downfalls are, if done poorly, they are distracting and publishing color figures is always costly for print editions.

Here are some examples of artistically augmented publication figures -but if you have other good examples, let me know and I'll add them:
This is from a recent Ecology Letters from Crutsinger, Cadotte (me) and Sanders (2009), 12: 285-292, trying to explain how we partitioned arthropod diversity into spatial components.


This one is from Ellwood et al. (2009) in Ecology Letters 12: 277-284, which shows co-occurrence null histograms for patterns of arthropods at various hight locations on trees.

This one is from Crutsinger et al (2006) Science 313: 966-968 that displays patterns at differing trophic levels by juxtaposing photos of specific tropic members.















Finally, the use of drawings and images to illustrate phylogenetic trends in phenotypic evolution is particularly useful. Above are two examples, on the left is from Carlson et al. 2009 Evolution 63: 767-778, showing patterns of darter evolution; and on the right is from Oakley and Cunningham 2002 PNAS 99: 1426-1430, showing evolutionary pathways of compound eyes.


And here's one from Dolph Schluter (2000) American Naturalist 156: S4-S16, using drawings to illustrate how fish morphology corresponds to an abstracted index on the bottom axis.

Here are two from Joe Baily while working in Tom Whitham's Cottonwood Ecology Group that are effective ways to remind the reader what the treatments or dependent variables were (elk herbivory, leaf shape/genotype) and what the response variables were (bird predation, wood consumption by beavers). The left hand figure is from Baily & Whitham (2003) Oikos 101: 127-134 and the one on the right is from Baily et al. (2004) Ecology 85: 603-608.

Here is a great one posted by Ethan on Jabberwocky Ecology on Hurlbert's Unicorn!

The evolutionary meaning of autumn colors

As a kid growing up in Ontario, Canada, I have vivid memories of vast expanses of forests set ablaze by their autumn colors. Whole landscapes look like the canvas of a painter whose love of red, orange, gold and yellow are readily apparent. But, like most biologists, I had been taught that these colors are simply the by-product of leaf senescence, nothing more than a biochemical accident. I was amazed to read Marco Archetti's recent work showing that there may actually be adaptive benefits to changing leaf color in autumn and for particular colors. Generally the adaptive benefits involve either protection against abiotic factors or as a response to plant-animal interactions. One of his interesting results is that autumn coloration has evolved repeatedly and cannot be explained by being related to an ancestor who changed colors, rather that there must be some other evolutionary or adaptive explanation. While he suggests a large number of candidate hypotheses, some more plausible than others, I'll list five for example:

1) Sunscreen: Pigments provide photoprotection against photooxidation during the recovery of nutrients.

2) Leaf warming: Colors absorb light and warm the leaves during cooling temperatures.

3) Coevolution: Tells overwintering insects that the tree is not suitable (poisonous or low nutrition) for hibernation.

4) Camouflage: Many insects lack red photoreceptor, making leaves difficult to see -thus protecting trees from overwintering pests.

5) Unpalatability: Pigments (e.g., red -anthocyanins) are unpalatable.

So, we may quibble about particular hypotheses, but the point for me is that there may be deeper explanations as to why certain species produce the vivid colors they do. At a minimum, Archetti provides ammunition to experimental botanists and evolutionary biologists for testing new hypotheses. I'll never look at an autumn forest the same again.

Archetti, M. (2009). Classification of hypotheses on the evolution of autumn colours Oikos, 118 (3), 328-333 DOI: 10.1111/j.1600-0706.2008.17164.x

Archetti, M. (2008). Phylogenetic analysis reveals a scattered distribution of autumn colours Annals of Botany, 103 (5), 703-713 DOI: 10.1093/aob/mcn259

Archetti, M., Döring, T., Hagen, S., Hughes, N., Leather, S., Lee, D., Lev-Yadun, S., Manetas, Y., Ougham, H., & Schaberg, P. (2009). Unravelling the evolution of autumn colours: an interdisciplinary approach Trends in Ecology & Evolution, 24 (3), 166-173 DOI: 10.1016/j.tree.2008.10.006

Conserve now or wait for the data?

E. O. Wilson, referring to the ethical imperative we should apply to the conservation of life, said “The ethical imperative should be, first of all, prudence. We should judge every scrap of biodiversity as priceless while we learn to use it and to come to understand what it means to humanity” (pg. 351, The Diversity of Life). Although, I would argue we should aim to learn biodiversity’s value, both intrinsic and extrinsic, as opposed to what it solely means to humanity, his point is protect now, study later. The reason being that there is still so much to learn in order to adequately assess the Earth’s biological riches, by the time we inventory and map a fraction of biodiversity, we would have lost numerous unique regions and species. Of course the opposing point of view is that we need detailed information in order to best use limited resources to best protect biodiversity. This is a major philosophical divide. In a recent, important paper by Hedley Grantham and colleagues published in Ecology Letters, the question of how long should we wait to take conservation actions was empirically tested.

The authors used simulations based on 20 years of habitat loss data from the biologically-rich Fynbos region of South Africa and knowledge about spatial distribution of Protea diversity. Protea surveys (The Protea Atlas) have been carried out over 20 years, inventorying 40,000 plots and recording 381 species within the Proteaceae. They began their simulations with no information about Protea diversity patterns and included annually increasing knowledge, set against annual habitat destruction. They showed that waiting to make conservation decisions after only 2 years resulted in species loss, because habitat loss far outweighed any advantage to gaining more information. Further, more detailed information did not appear to increase the effectiveness of conservation decisions over cruder habitat-level maps.

The philosophical divide between protect now-learn later versus the need for detailed information to maximize resources appears bridgeable. It seems that by just accumulating some rough data may go a long way towards making those important conservation decisions. Of course, the irony is that this study needed 20 years of data to adequately assess this.

Grantham, H., Wilson, K., Moilanen, A., Rebelo, T., & Possingham, H. (2009). Delaying conservation actions for improved knowledge: how long should we wait? Ecology Letters, 12 (4), 293-301 DOI: 10.1111/j.1461-0248.2009.01287.x

Being a clover isn’t always so lucky

Happy St. Patrick’s Day! I thought that covering an article about Trifolium (clover) seemed very appropriate. In a recent paper, Matthias Schleuning and colleagues examine the population dynamics of Trifolium montanum, a species in decline in central Germany. They examined the relative threats of habitat fragmentation and degradation on T. montanum’s population dynamics. They found that both degradation and fragmentation were having serious negative impacts. Degraded habitats in this system mean the shift away from nutrient-poor conditions and include the invasion of taller species that are better light competitors. T. montanum is a poor light competitor and maintains larger populations in mown or grazed habitats that keep taller invaders out. This species also faces the double whammy of fragmented habitats resulting in isolated populations. These isolates have lower reproductive output likely due to greater inbreeding and less genetic transfer, via pollinators, among different populations.

I always think of Trifolium species as being particularly common and widely distributed, but there are some that are threatened and potentially tell us about the threats faced by imperiled plant populations. In fact, while a number of North American Trifolium species have successfully invaded North America, but T. montanum is not, according to the USDA Plants Database. These results reveal that these negative effects affect plants at different stages of their life cycle (growth to maturity vs. recuitment) and that log-term persistence of these populations requires management activities that ameliorate both of these effects.

SCHLEUNING, M., NIGGEMANN, M., BECKER, U., & MATTHIES, D. (2009). Negative effects of habitat degradation and fragmentation on the declining grassland plant Trifolium montanum Basic and Applied Ecology, 10 (1), 61-69 DOI: 10.1016/j.baae.2007.12.002

A roadmap to generalized linear mixed models

In a recent paper in TREE, Ben Bolker (from the University of Florida) and colleagues describe the use of generalized linear mixed models for ecology and evolution. GLMMs are used more and more in evolution and ecology given how powerful they are, basically because they allow the use of random and fix effects and can analyze non-normal data better than other models. The authors made a really good job at explaining what to use when. Despite the fact that you need more than basic knowledge of stats to fully understand this guide, I think that people should take a look at it before starting to plan their projects, since it outlines really well all the possible alternatives (and challenges) that one can have when analyzing data. This article also describes what is available in each software package; this is really useful since is not obvious with program in SAS or R you need to use when dealing with some specific GLMMs.

Bolker, B., Brooks, M., Clark, C., Geange, S., Poulsen, J., Stevens, M., & White, J. (2009). Generalized linear mixed models: a practical guide for ecology and evolution Trends in Ecology & Evolution, 24 (3), 127-135 DOI: 10.1016/j.tree.2008.10.008

Salamaders and climate change -impending extinctions?

By the now the evidence of a global frog decline, perhaps even an extinction crisis, has been well documented. But what about salamanders? They are normally less abundant and less-studied compared to frogs, but is there evidence of the same general pattern of declining population sizes? According to Sean Rovito and colleagues, the answer is unfortunately yes. They repeated a plethodontid (lungless) salamander survey done in the 1970’s in Central America and found that many species have declined. In fact they failed to find a couple of previously very abundant species. They also found that species declines were phylogenetically non-random and so these declines may result in the loss of whole clades of species, meaning that the evolutionary history of these salamanders is at risk.

The authors attempted to determine the cause of these declines and found that neither habitat loss or the chytridiomycosis fungal disease implicated in other declines explained these salamander declines. The authors hypothesize that these declines are a direct result of climate change –namely changing temperature and humidity. If so, we may be witnessing some of the first extinctions that are directly caused by climate change.

S. M. Rovito, G. Parra-Olea, C. R. Vasquez-Almazan, T. J. Papenfuss, D. B. Wake (2009). Dramatic declines in neotropical salamander populations are an important part of the global amphibian crisis Proceedings of the National Academy of Sciences, 106 (9), 3231-3236 DOI: 10.1073/pnas.0813051106

Post script:
We had a comment questioning the use of climate change as an explanation and here is my response.

Science works by finding parsimonious explanations, until through experimentation or observation another, better explanation emerges. The previous explanations of habitat loss or fungal infections were not supported. These habitats, known as cloud forests, are very humid. The lungless salamanders have no lungs and instead breath through their skin, which must be kept moist. These forest are becoming drier, hence the probable connection. Here's a quote from the paper:

"Pounds et al. (25) used modeling to show that largescale warming led to a greater decrease in relative humidity at Monteverde compared to that caused by deforestation. Species of cloud forest salamanders that can still be found rely at least
in part on bromeliads. Bromeliads depend on cloud water deposition and are predicted to be articularly vulnerable to climate change (26, 27)."

Doesn't sound like "magic" to me, rather a robust hypothesized mechanism worthy of more testing. Given that species are going extinct, it is important to suggest likely mechanisms, providing an impetus for more research.

For those that think that scientists use climate change as boogey man to scare up more research funding (i.e., Crichton), please read the science. You'll discover honest, hardworking folks that are trying to understand this changing world and whose research can only benefit you , me and the salamanders.