Biodiversity and ecosystem functioning – without fungi?

Different subfields of ecology have a propensity to remain remarkably isolated – researchers in aquatic systems independently develop hypotheses that already exist in some form in other systems, and vice versa. Population ecology and community ecology, despite their obvious relevance to each other, are rarely integrated. There is a tendency – resulting from limits on our time, experience, and possibly imagination – to stay within whatever box we’ve defined for ourselves.

Historically, it seems that biodiversity and ecosystem functioning has lost sight of the progress made in classical ecology in understanding the mechanisms behind species coexistence (and all the functional implications that follow). Studies of ecosystem functioning often vaguely reference concepts such as “niche partitioning”, which would hardly be explicit enough for most papers on coexistence. Fortunately, there are periodically attempts to unifying ecological knowledge.

One of the most important contributions to understanding coexistence is Chesson’s (2000) framework of equalizing and stabilizing effects. Unlike previous approaches to species interactions, which tended to reference these vaguely-defined “niche differences”, Chesson proposed that species interactions depended on both fitness differences (differences in absolute growth rates after niche differences are controlled for) and niche differences (ecological differences between species which cause intraspecific competition to exceed interspecific competition). He also suggested rigorous methods to quantify these concepts. This framework has been applied both to the obvious questions of species coexistence and diversity maintenance, as well as predator-prey relationships (2008) and the phylogenetic structure of communities (2010).

In a recent paper, Ian Carroll et al. apply this framework to the search for the mechanisms behind biodiversity and ecosystem functioning. They point out that the questions in studies of ecosystem functioning are directly analogous to Chesson’s concepts – selection effects result from fitness or competitive differences between species, while complementarity relates to the partitioning of resources, or niche differences between species. The added benefit is that Chesson has provided clear definitions for these concepts.

While this may not be world-altering, it’s encouraging. Anytime different areas of ecology intersect, both benefit. Of course there are difficulties – no doubt the question of how to measure niche differences and fitness differences will be contentious (as attempts to translate ecological theory into ecological methodology often are) - but the possibility that a few general ecological concepts explain diverse observations is worth pursuing.

Biodiversity and ecosystem functioning - only with fungi

Once again scientists have come to an age-old conclusion: fungus is behind all of life’s great mysteries. It's responsible for curing strep throat, delicious veggie burgers, that unique musk emanating from your gym bag, the colour-morphing walls at last night’s party and now, biodiversity and ecosystem functioning.

The world of biodiversity and ecosystem functioning (BEF), like many other high-profile disciplines of science, has often been bogged down by controversy. In such situations, we often spend a disproportionate amount of time focusing on the controversy instead of actually advancing the science itself (sound familiar?)

There have been several posts about BEF on this blog in the last few months, but briefly and oversimplified, here's how it works. Ecosystem functions are things like productivity, nutrient cycling and decomposition. Ecosystems that contain many species produce higher levels of these functions than monocultures do. The controversy here surrounds the cause of this phenomenon. In the 1990s, researchers originally disagreed over whether the relationship they observed was due to complementarity (different species partitioning resources) or selection effects (the higher chance of a really productive species being included in a community with many species). The question was largely settled a few years ago; selection effects do exist, but most of the relationship is driven by complementarity. Nonetheless, many biologists who are only tangentially familiar with this area of research are unaware of the consensus and continue to believe that the issue remains unresolved. Some still dismiss the whole field of BEF because of selection effects. I guess people just love a controversy.

The result of all this is that the ecologists studying these relationships have had to spend an undue amount of time parsing their results into selection and complementarity and discussing the two phenomena. They have even come to refer to these as the “mechanisms” behind BEF. And this is where we start to have a problem. Selection and complementarity are not mechanisms - they are symptoms of mechanisms. They do not tell us what is actually causing the positive effect that biodiversity has on ecosystem functioning, only what the shape of the relationship is. In fact, very few studies have actually looked for true mechanisms that explain the effects that we have repeatedly observed.

But this week I read a new paper in Ecology Letters that actually did find a mechanism, and it wasn’t one that we expected. John Maron and his coauthors at the universities of Montana and British Columbia found that belowground fungi were causing plant productivity to increase with diversity.

In an impressively complete experiment, Maron et al. put together a classic BEF setup of many plots containing varying levels of plant diversity and then measured plant biomass. But this time they added a twist; they applied fungicide to the soil in some of these plots. The result was that in the absence of fungi, the common BEF relationship disappeared. The low diversity plots became much more productive, while productivity at high diversity only increased slightly. The authors explained their results by the fact that fungi can be both species-specific and density-dependent, so as plant diversity increases, the fungi’s negative impact on plant productivity diminishes. And for good measure, they of course also ruled out a significant selection effect in their results.

So what does this all mean? Well for one thing, it means that we now have at least one good mechanistic explanation for that black box that we’ve been calling “complementarity” for years. But perhaps more importantly, it means that the link between biodiversity and ecosystem functioning is now more real than ever. If plant species go extinct, the remaining ones will be more susceptible to fungal pathogens and productivity will decline. So let’s try to not let that happen, k?

Maron, J. L., Marler, M., Klironomos, J. N. and Cleveland, C. C. , Soil fungal pathogens and the relationship between plant diversity and productivity. Ecology Letters, DOI: 10.1111/j.1461-0248.2010.01547.x

The effects of forest fragmentation after 30 years

Large-scale alteration of nature landscapes has had profound implications for biological diversity. The single biggest contributor to the current extinction crisis is the wholesale destruction of habitats. As habitats are destroyed, formerly contiguous landscapes become fragmented into smaller patches. But what exactly the effects of fragmentation are, independent of habitat destruction, is not always so clear (e.g., Simberloff 2000. What do we really know about fragmentation? Texas Journal of Science 52: S5-S22).

The biological dynamics of forest fragments project (BDFFP) in the Amazon, was started in 1979 and created 11 tropical forest patches ranging from 1 to 100 ha in size. The dynamics of these fragments have been consistently monitored and compared to plots in intact forest. This experiment represents the world's largest, longest-running fragmentation experiment and has told us more about fragmentation then any other study system. In a recent publication by William Laurance and many colleagues involved in this project, they summarize 30 years of data and show how fragmentation affects ecological patterns and processes.
Fragments turn out to be very dynamic and defined by change, compared to interior plots. They have higher tree mortality and are much more susceptible to weather events such as storms or droughts. The effects are especially pronounced at the edges of these fragments. The edge community face high mortality but also have higher tree density. Faunal communities in fragments and especially near edges are depauperate.

One interesting aspect highlighted by this 30 years of research is that the edge effects are strongly influenced by what is happening around the fragments. The fragment edge effects are sensitive to the composition of the inter-patch matrix, giving managers the opportunity to influence fragment diversity and health by managing the matrix in ways that support fragments. Because of over 30 years of perseverance of the researchers involved, this experiment give scientists, managers and policy-makers information to help manage an increasingly fragmented world and to find ways to reduce to negative impacts of habitat destruction.

Laurance, W., Camargo, J., Luizão, R., Laurance, S., Pimm, S., Bruna, E., Stouffer, P., Bruce Williamson, G., Benítez-Malvido, J., & Vasconcelos, H. (2010). The fate of Amazonian forest fragments: A 32-year investigation Biological Conservation DOI: 10.1016/j.biocon.2010.09.021

Carnival of Evolution!

The 29th installment of Carnival of Evolution is here, hosted by Byte Size Biology. Check out recent evolutionary musings and rants from around the blogoshpere.

Grassland diversity increases stability across multiple functions

As ecological systems are altered with cascading changes in diversity, the oft-asked question is: does diversity matter for ecosystem function? This question has been tested a multitude of times, with the results often supporting the idea that more diverse assemblages provide greater functioning (such as productivity, nutrient cycling, supporting greater pollinator abundance, etc.). Besides greater functioning, scientists have hypothesized that more diverse systems are inherently more stable. That is, the functions communities provide remain more constant over time compared with less diverse systems, which may be less reliable.

While the relationship between diversity and stability has been tested for some functions, Proulx and colleagues examined the stability of 42 variables over 7 years across 82 experimental plots planted with either 1, 2, 4, 8, 16 or 60 plant species in Jena, Germany. They examined patterns of variation (and covariation) in the functions and found that many show lower variation over time in plots with more plant species. Greater stability was found at many different trophic levels including plant biomass production, the abundance and diversity of invertebrates and the abundance of parasitic wasps -which indicate more complex food webs. They also found greater stability in gas flux, such as carbon dioxide. Despite the greater stability in these measures of above-ground functions, below ground processes, such as earthworm abundance and soil nutrients, were not less variable in high diversity plots.

How ecosystems function is of great concern; these results show that more diverse plant communities function more stably and reliably than less diverse ones. The next step for this type of research should be to address what kind of diversity matters. A greater number of species means more different kinds of species, with differing traits and functions. What aspect of such functional differences determine stability of ecosystem function?

This is an exciting paper that continues to highlight the need to understand how community diversity drives ecosystem function.

Proulx, R., Wirth, C., Voigt, W., Weigelt, A., Roscher, C., Attinger, S., Baade, J., Barnard, R., Buchmann, N., Buscot, F., Eisenhauer, N., Fischer, M., Gleixner, G., Halle, S., Hildebrandt, A., Kowalski, E., Kuu, A., Lange, M., Milcu, A., Niklaus, P., Oelmann, Y., Rosenkranz, S., Sabais, A., Scherber, C., Scherer-Lorenzen, M., Scheu, S., Schulze, E., Schumacher, J., Schwichtenberg, G., Soussana, J., Temperton, V., Weisser, W., Wilcke, W., & Schmid, B. (2010). Diversity Promotes Temporal Stability across Levels of Ecosystem Organization in Experimental Grasslands PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0013382

Protecting biodiversity one task at a time: have your say

The fact that the Earth is in the midst of a biodiversity crisis has been repeatedly acknowledged by world governments. The greatest pronouncement was is 2002 with the '2010 Biodiversity Target' where many of the largest economies signed a pledge to halt biodiversity loss by 2010. Yet it is now 2010 and species are continuing to go extinct and habitats are continuing to be destroyed or degraded. But it shouldn't be a surprise that non-binding governmental proclamations fail to produce substantial results. Yet the reality is that we need to do something, inaction only worsens the legacy of biological deficit for future generations.

Maybe the best way forward is not more international governmental summits, but rather focusing on small scale, achievable short term goal. Guillaume Chapron started the Biodiversity 100 campaign, hosted by the Guardian (see story here), which seeks out public and professional input into the 100 immediate and achievable projects or ideas that will help protect biodiversity. The idea is to be able to go to governments and international agencies with this list and get them to make specific pledges to carry out these tasks.

There is till time to participate! If you have an idea of an action to protect biodiversity, fill out the web form. There are already a plethora of great suggestions, from protecting specific habitats to stemming population growth. This list is important because it includes the voices of the international public citizenry and that of scientists. More than that though, there will be a concrete list of tasks (ranging from very local to very global) that citizen groups can use to sustain pressure on governments.

Enhanced biodiversity-ecosystem function relationships in polluted systems

*note: this text was adapted from an Editor's Choice I wrote for the Journal of Applied Ecology.

In this era of species loss and habitat degradation, understanding the link between biodiversity and functioning of species assemblages is a critically important area of research. Two decades of research has shown that communities with more species or functional types results in higher levels of ecosystem functioning, such as nutrient processing rates, carbon sequestration and productivity, among others. This research has typically used controlled experiments that standardize environmental influences and manipulate species diversity. However, a number of people have hypothesized that biodiversity may be even more important for the maintenance of ecosystem functioning during times of environmental stress or change rather than under stable, controlled conditions. It is during these times of environmental change that preserving ecological function is most important, as changes in function can have cascading effects on other trophic levels, compounding environmental stress. Therefore, explicitly testing how biodiversity affects function under environmental stress can help to inform management decisions.

Image from Wikimedia commons

In a recent paper in the Journal of Applied Ecology, Li and colleagues examine how algal biodiversity influences productivity in microcosms with differing cadmium concentrations. Cadmium (Cd) is a heavy metal used in a number of products and industrial processes, but it is toxic and Cd pollution is a concern for human populations and biological systems, especially aquatic communities. This is especially true in nations currently undergoing massive industrial expansion. In response to concerns about Cd pollution effects on aquatic productivity, Li et al. used algal assemblages from single species monocultures to eight species polycultures grown under a Cd-free control and two concentrations of Cd, and measured algal biomass.

Their results revealed that there was only a weak biodiversity-biomass relationship in the Cd-free teatment, which the authors ascribed to negative interactions offsetting positive niche partitioning. In particular, those species that were most productive in their monocultures were the most suppressed in polycultures. However, in microcosms with Cd present there were positive relationships between diversity and biomass. They attribute this to a reduction in the strength of competitive interactions and the opportunity for highly productive species to persist in the communities.

While a plethora of experiments generally find increased ecosystem function with greater diversity, Li et al.’s research indicates that the effect of biodiversity on function may be even more important in polluted systems. If this result can be duplicated in other systems, then this gives added pressure for management strategies to maintain maximal diversity as insurance against an uncertain future.

Li, J., Duan, H., Li, S., Kuang, J., Zeng, Y., & Shu, W. (2010). Cadmium pollution triggers a positive biodiversity-productivity relationship: evidence from a laboratory microcosm experiment Journal of Applied Ecology, 47 (4), 890-898 DOI: 10.1111/j.1365-2664.2010.01818.x

Reinterpreting phylogenetic patterns in communities

Examining the phylogenetic structure of a community in order to understand patterns of community assembly has become an increasingly popular approach. A quick web search of “community”, “phylogenetics”, and “ecology” finds several hundred papers, most written in the last ten years.

Eco-phylogeneticists examine how patterns of evolutionary relatedness within communities may reflect the processes structuring those communities. In particular, a commonly tested hypothesis is the competition-relatedness hypothesis, which suggests that more closely-related species having more similar niches and therefore stronger competitive interactions, making coexistence between them less likely. As a result, if competition is important, communities may exhibit phylogenetic overdispersion, with species being less related on average than if drawn randomly from the regional species pool. The contrasting pattern, phylogenetic clustering, where species tend to be more closely related than expected, is often interpreted as being the result of strong environmental filtering, such that only a closely related group of species, best adapted to that environment, surviving in the community.

Evidence for the competition-relatedness hypothesis has been mixed, and since most tests of this hypothesis focus on patterns in observed data, conclusions about the underlying mechanism driving community phylogenetic patterns are rarely testable, and yet widely made.

In Mayfield and Levine (2010, Ecology Letters), the authors critique the current ecological justification for the competition-relatedness hypothesis, noting that it does not agree with a more current view of the processes driving species coexistence. As established by Chesson (2000, Annual Review of Ecology and Systematics), coexistence can involve both stabilizing forces (niche differences between species), and equalizing forces (fitness differences between species). In a simplistic example, plants using different soil types (niche differences) may coexist, while plants with similar high growth rates may exclude those species with lower growth rates (fitness differences). The final community should reflect the interplay of both these processes.

The implication of this view of species coexistence is that there is no preconceived phylogenetic pattern which should reflect competition: if species with the highest heights are competitively superior and exclude other species (coexistence driven by fitness differences), and height is a phylogenetically conserved trait, the community will appear to be phylogenetically clustered. Traditionally, a clustered pattern would not be considered to indicate the effects of competition. In fact, Mayfield and Levine show that the expected phylogenetic pattern depends entirely on whether niche and/or fitness differences are important and/or related to phylogenetic distance.

This suggest that conclusions in past studies may need to be reinterpreted. It also adds to the list of assumptions about evolutionary relatedness and ecological function which need to be tested: for example, how do niche and fitness differences tend to change through time? Do they tend to be conserved among closely related species? Does one or the other tend to dominate as a driver of coexistence in different systems? If nothing else, we need to be careful about making generalizations which don’t account for the differing evolutionary history, geographical location, and ecological setting that communities experience, when interpreting observed patterns in those communities.

Organic farming and natural enemy evenness

The basic reality of agricultural activity is that it reduces biological diversity, and these reductions in diversity potentially impact ecosystem services. But do some agricultural practices impact these services less than others? In a recent paper in Nature by David Crowder and colleagues, the question of how organic versus conventional farming affects predator and herbivore pathogen diversity and how this cascades to pest suppression. They show through a meta-analysis, that organic farms tend to support greater natural enemy evenness, and they hypothesize that greater evenness of enemies should better control pest populations, resulting in larger, more productive plants.

Picture from wikipedia

This result in itself is interesting, but they also carried out an elegant enclosure experiment where they manipulate the evenness of insect predators and pathogens and measure potato plant size. They found that even communities had the lowest herbivore densities and saw the greatest increases in plant biomass. Conversely, very uneven communities, typical of conventional farms, had the largest pest populations resulting in lower plant biomass accumulation.

While, multiple farming strategies are needed for adequate agricultural production, there are strong arguments for organic farms to be a important part of agricultural practice. These results show that organic farms have cascading effects on pest predators and pathogens and show that enemy evenness, as opposed to richness, has important ecosystem service consequences. To quote myself, evenness is a critical component of biodiversity, and much research has emphasized species richness, maybe at the detriment of studying evenness.

Crowder, D., Northfield, T., Strand, M., & Snyder, W. (2010). Organic agriculture promotes evenness and natural pest control Nature, 466 (7302), 109-112 DOI: 10.1038/nature09183

New Carnival of Evolution

Check out the July edition of the Carnival of Evolution written by Hannah Waters at Culturing Science.

Happy Year of Biodiversity

It’s ironic that during the International Year of Biodiversity, the US is experiencing an environmental disaster on a massive scale. Unfortunately, this disaster is just another failure in environmental protection, part of a long series of failures which seem to characterize this Year of Biodiversity. Even as the political will behind the 2010 biodiversity targets seems to have waned (and most indicators suggest that declines in diversity are unchecked), evidence continues to mount for the functional value of biological diversity.

This week’s issue of Nature features a couple of pieces focusing on biodiversity through a political or economic lens. Although the economic benefits and services provided by species-level diversity has been well illustrated, in “Population diversity and the portfolio effect in an exploited species”, Schindler et al. (Nature, 465, 609-612) new evidence that at even finer divisions than the species, diversity plays an important role. In this case, they find that genetic diversity at the population level is an additional and significant contributor to ecosystem stability. Schindler et al. examine the effects of hundreds of locally-adapted populations of sockeye salmon on the valuable salmon fishery in the Bristol Bay area of Alaska. They suggest that the portfolio effect (or the robustness of biodiversity to variable conditions – like a diverse financial portfolio) can function at the population level as well as the species level. High levels of intra-specific diversity can produce temporal variation among populations in response to environmental variability, resulting in catches that are more stable year-to-year, and making fishery closures less likely, a clear economic benefit.

Populations are declining at an even faster rate than species themselves: the more we understand the importance of conserving diversity at multiple biological scales (ecosystem, species, population, even the individual?), the more complicated and onerous the task of conserving diversity becomes.

In the same issue of Nature is an editorial on the possibility of an IPCC-like panel for biodiversity. At this very moment (give or take a few time zones), government representatives from all over the world are deciding whether or not to create this panel. So far, they have a catchy name for it, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), which hopefully hasn’t been written in stone. But they also have a strong recognition of the inextricable links between biodiversity, ecosystem services and human wellbeing – links that are highlighted in the Schindler et al. article. Furthermore, an explicit goal of IPBES is to address the currently tangled state of biodiversity organizations, conventions and programs by forming a unified front of sound biodiversity policy and science. The Convention on Biological Diversity had set a target of halting biodiversity loss by 2010 and we have failed spectacularly. Is IPBES the solution?

Wanted: an IPCC for biodiversity. Nature, 465, 525-525

Schindler, D.E., Hilborn, R., Chasco, B., Boatright, C.P., Quinn, T.P., Rogers, L.A. & Webster, M.S. Population diversity and the portfolio effect in an exploited species. Nature, 465, 609-612

By Nick Mirotchnick and Caroline Tucker

Another reason why a new publishing model is needed...

The finances and ethics of scientific publishing are complex, and there is an inherent tension between commercial publishers and academics and their institutions. On the one hand, we as scientists are (most often) using public money to carry out research, usually in the public interest, and then we typically publish in for-profit journals that restrict public access to our publications. Authors seldom see any of the financial return from publisher profits. On the other hand, publishers provide a level of distribution and visibility for our work, which individual authors could not match. In previous posts I have discussed Open Access publications, but there is another reason to consider other publication models. Recently Nature Publishing Group notified the University of California system of an impending 400% increase in the cost for their publications. The UC administration has responded with an announced plan to boycott NPG publications. The announcement rightly points out a 400% increase is not feasible given the current plight of library budgets, especially in California, and that scientists in the UC system disproportionately contribute to publishing, reviewing and editing NPG publications and thus are the engine for NPG profits. (See a nice story about the boycott in The Chronicle of Higher Education)

This is just the latest symptom of the growing tension between publishing and academia, and is a stark reminder that other publishing models need to actively supported. Perhaps the UC system could invest in open access publishers in lieu of NPGs outrageous costs? Something has to give, and perhaps the UC boycott will remind libraries that they hold the purse strings and could be the greatest driving force for change.

Experimental test of Darwin's naturalization hypothesis

Among the numerous and still informative ecological predictions made by Darwin, one posits that when species are introduced into regions where they were not formerly found, the most successful tend to not have close relatives already occupying the region. This is known as Darwin's Naturalization Hypothesis, and his logic was that among close relatives, where ecological requirements should be most similar, the struggle for existence is most severe. Thus the modern formulation is that invader success is influenced by the amount of time since two species shared a common ancestor (usually called phylogenetic distance). Tests of this hypothesis have been primarily done on large species inventories, with results from different studies either supporting or refuting it. In a new study by Lin Jiang and colleagues published in the American Naturalist, they cleverly use bacteria with known relatedness to test this hypothesis.

They used four species of bacteria: Bacillus pumilus, B. cereus, Frigoribacterium sp. and Serratia marcescens as residents in every possible 1, 2, 3 and 4-species communities and invaded them with a subspecies of S. marcescens. What they found was that the invader density was highly significantly related to phylogenetic distance, so that the invader reached its greatest density when communities contained only distantly-related species.

Though these types of laboratory experiments are simplistic (I too use these systems), they offer insights into particular mechanisms, which may otherwise be difficult to detect in noisier systems.

Jiang, L., Tan, J., & Pu, Z. (2010). An Experimental Test of Darwin’s Naturalization Hypothesis The American Naturalist, 175 (4), 415-423 DOI: 10.1086/650720

The successful launch of MEE

Usually, I view the release of a new journal with some skepticism. There are so many journals and it feels like academics are over-parsing fields, isolating researchers that should be communicating. However, sometimes a journal comes along and it is obvious that there is a need and the community responds to its arrival. Such is the case with the British Ecological Society's newest journal, Methods in Ecology and Evolution, started by Rob Freckleton. The idea that a journal would be dedicated to methods papers is a great idea. This era of ecology and evolution is one that is defined by rapid advances in experimental, technological and computational tools and keeping track of these advances is difficult. Having a single journal should make finding such papers easier, but more importantly provides a home for methodological and computational ecologists and evolutionary biologists, which will hopefully spur greater communication and interaction, fostering more rapid development of tools.

Two issues have been published and they have been populated by good, entertaining articles. I especially enjoyed the one by Bob O'Hara and Johan Kotze on why you shouldn't log transform count data. As a researcher, I've done this (instead of using a GLM with proper distribution) and as an editor, I've allowed this, but it has always felt wrong somehow, and this shows that it is.

The early success of the journal is not just the product of the good papers it has already published, but also because of the savvy use of electronic communication. They Tweet on Twitter, link fans through Facebook, blog about recent advances in methods from other journals and post podcast and videocast interviews with authors. These casts give readers access to authors' own explanations of how their methods can be used.

I am excited about this new journal and hope it has a great impact on the publication of methodological papers.

Picante's coming out party

This past decade has seen a rapid expansion of the use of evolutionary phylogenies in ecological studies. This expansion is largely due to the increased availability of phylogenies, but has resulted in new types of hypotheses and statistics aimed to test the phylogenetic patterns underpinning ecological communities. The main computational tool used has been phylocom, created by Cam Webb, David Ackerly and Steve Kembel, which has its own binaries to be installed on one’s computer. However, a new R package, picante has been created by Steve Kembel and colleagues which runs many of the same routines as in phylocom, but in the R framework, allowing one to tie these analyses in better with other, non-phylogenetic tests. Picante also has a number of features and tests not found in phylocom, including tests of phylobetadiversity and phylogenetic signal using Blomberg’s K.

Thanks Steve for all your hard work and for making these tests available to everyone.

Kembel, S., Cowan, P., Helmus, M., Cornwell, W., Morlon, H., Ackerly, D., Blomberg, S., & Webb, C. (2010). Picante: R tools for integrating phylogenies and ecology Bioinformatics DOI: 10.1093/bioinformatics/btq166

Niche or Neutral? Why size matters.

Metacommunity dynamics (i.e. the effects of dispersal among connected communities) have become an increasingly common lens through which to explain community structure. For example, competition-colonization models explain the coexistence of superior and inferior competitors as the result of a trade-off in colonization and competitive ability. Species are either superior competitors, with high probabilities of establishing in patches, but low ability to move between patches, or superior colonizers, which have tend to lose in competitive interactions but can travel easily between patches. Under this framework, the ability of superior colonizers to reach and maintain populations in patches where their superior competitors are absent allows them to avoid extinction.

One problem with these types of models is that they rarely acknowledge the importance of ecological drift – that is, that chance events also affect species interactions. This despite the fact that we know that in “real life”, chance events likely play a major role in producing assemblages different than those we might predict based on theory. One of the strengths of the Hubbell’s neutral model is that it recognizes and embraces the importance of randomness.

A recent paper by Orrock and Watling (2010) examines how chance events can alter the predictions of the classic competition-colonization model. Orrock and Watling show that the size of communities in a metacommunity (which is assumed to correlate with the strength of ecological drift) determines whether community dynamics are niche-structured or neutral in nature. In large communities, predictions agree closely with those of the classic competition-colonization model, and niche-based interactions (i.e. competitive hierarchies) dominate. It’s in small communities that things get interesting: ecological drift becomes more important, so that differences in competitive ability between species are effectively neutralized. As a result, small communities begin to resemble neutral assemblages in which species abundances don’t relate to differences in competitive ability. An interesting consequence of this outcome is that species who are poor competitors but good colonizers have an additional refuge – simply by escaping to small communities, even if these communities contain superior competitors, they can persist in a metacommunity.

Beyond the theoretical implications of this model, the applied implications are what really matter. Habitat destruction and fragmentation are an growing problem due to human activities. Habitat patches are often smaller, and of lower quality, decreasing the size of the community each patch can support. Even if these patches are still connected and functioning as a metacommunity, species which rely on their strong competitive ability for persistence will lose this advantage as assemblages become increasingly neutral. Under this model, community diversity declines even more as habitat is lost than in the traditional competition-colonization model, and superior competitors face even greater extinction risk than previously predicted.

Since in reality, metacommunities are likely to consist of patches of different sizes, rather than all large or all small patches, the predictions here remain to be extended to more realistic metacommunities. However, Orrock and Watling have produced a useful model for understanding how ecological drift can affect diversity in a metacommunity and alter the expectations of traditional competition-colonization models.


Orrock, J.L. and Watling, J.I. (2010) Local community size mediates ecological drift and competition in metacommunities. Proc. R. Soc. B.

Teaching a quoll that cane toads are bad

Often, species become endangered because of multiple stressors, with habitat destruction taking the prize as the most egregious. However, often what pushes a species into extinction is not the main driver of endangerment. For example, passenger pigeon numbers were decimated by unabated hunting, but the proximate cause of extinction was likely an inability to thrive in low densities. Yet, seldom is the case where a known single species interaction is the primary cause of engangerment and maybe extinction. The northern quoll, Dasyurus hallucatus, is an endangered marsupial predator in Australia. The current major threat to the northern quoll is the invasion of toxic can toads. Quolls, being predators of small mammals, birds, reptiles and amphibians, readily attacks cane toads, which are toxic to quolls. Quoll populations have disappeared from areas invaded by cane toads, and extinction seems almost inevitable.

Given that the spread of cane toads into the remaining quoll habitats is inevitable, research, led by Stephanie O'donnell in Richard Shine's lab at the University of Sydney and published in the Journal of Applied Ecology, is underway to train quoll's to avoid cane toads. These researchers feed a subset of captive quolls dead toads laced with thiabendazole, a chemical that induces nausea. They then fitted individuals with radio collars and released these toad-smart quolls as well as toad naive ones. Some toad-naive quolls died quickly, after attacking cane toads. Only 58% of male naive quolls survived, while 88% of toad-smart males survived. While females seemed less likely to attack toads, 84% of naive females survived and 94% of toad-smart females survived!

See the video of a toad-smart quoll deciding not to eat a cane toad, its pretty cool.

O’Donnell, S., Webb, J., & Shine, R. (2010). Conditioned taste aversion enhances the survival of an endangered predator imperilled by a toxic invader Journal of Applied Ecology DOI: 10.1111/j.1365-2664.2010.01802.x

Plant rarity: environmental or dispersal limited?

In order to promote the persistence and possible spread of extremely rare plant species, ecologists need to know why a species is rare in the first place. In 1986, Deborah Rabinowitz identified seven forms of rarity, where rarity could mean several things depending on range size, habitat specificity and population sizes. When considering rarity, it often feels intuitive to look for environmental causes for these different forms of rarity. Habitat alteration is an obvious environmental change that affects abundance and distribution, but are rare species generally limited by habitat or resource availability? The alternative cause of rarity could just be that sufficient habitat exists, but that the rare species is simply unable to find or disperse to other sites. An extreme example of this would be the Devil's Hole pupfish which exists at only a single pool. It can survive elsewhere (such as in artificial tanks) but natural dispersal is impossible as its pool is in a desert.

Photo taken by Kristian Peters and available through GNU free documentation license

In a recent paper by Birgit Seifert and Markus Fischer in Biological Conservation, they examine whether an endangered plant, Armeria maritima subsp. elongata, was limited because of a lack of habitats or if it was dispersal limited. They collected seeds from eight populations and experimentally added these seeds to their original populations and to uninhabited, but apparently appropriate sites. They found that seeds germinated equally well in inhabited and uninhabited sites and seedlings had similar survivorships. They found that variation in germination rates were likely caused by originating population size and that low genetic diversity and inbreeding reduce viability.

These results reinforce two things. First is that conserving species may only require specific activities, such as collect and distributing seeds. Here ideas like assisted migration seem like valuable conservation strategies. Secondly, we really need to be doing these simple experiments to better understand why species are rare. If we fail to understand the causes of rarity, we may be wasting valuable resources when try to protect rare species.

Seifert, B., & Fischer, M. (2010). Experimental establishment of a declining dry-grassland flagship species in relation to seed origin and target environment Biological Conservation DOI: 10.1016/j.biocon.2010.02.028

Predicting endangered carnivores: the role of environment, space and phylogeny

For conservation biology, there are several research thrusts that are of critical importance, and one of these is to find predictors of species' extinction risk. Oft-cited is the particular susceptibility of large-bodied organisms, with their large ranges and slow reproductive rates. But there should be other predictors too, especially within larger mammals. In a forthcoming paper in Global Ecology and Biogeography, Safi and Pettorelli use just a few variables to predict extinction risk in carnivores.
They quantified species extinction risk according to the IUCN risk assessments and asked how well three attributes explained variation in extinction risk. They quantified the environmental characteristics of the species' ranges (temperature, precipitation, etc.), spatial distances between species' ranges and the phylogenetic distances among species. Overall, spatial and phylogenetic distances were good predictors of threat status -generally predicting between 21-70% of variation in extinction risk, whereas the environmental variables were weaker predictors. Full models incorporating all three variables (and accounting for their covariance), were able to explain upwards of 96% of the variation in extinction risk!

Although these variables do not represent causal mechanisms of extinction risk -rather they are correlative, they do provide conservation biologists with a rapid assessment tool to evaluate extinction risk. These tools should be particularly important in cases were population data are lacking and immediate pragmatic decisions are required.

Safi, K., & Pettorelli, N. (2010). Phylogenetic, spatial and environmental components of extinction risk in carnivores Global Ecology and Biogeography DOI: 10.1111/j.1466-8238.2010.00523.x

Low impact blogging

As a form of communication, blogging (and all that other stuff on the internet) is fairly environmentally friendly. Trees are not cut down to produce paper to print our posts, fuel-hungry trucks are not used to deliver these articles and stories to our many(!) readers and there is no trash to add to landfills. However, there is still the unappreciated cost associated with energy consumption for all the hours of researching, writing, and being read. The energy for all this electronic activity mainly comes from fossil fuels, meaning that my blogging has a carbon footprint.

Not anymore. No, we did not go nuclear. Rather, the ingenious people behind Mach's grun have started a great program. For writing this post about them, their 'make it green' campaign and the Arbor Day Foundation will plant a tree in Plumas National Forest in northern California. In 2007, a devastating forest fire destoyed 65,000 ha. By choosing to blog green, at least one more tree is planted. I will feel better knowing that there will be tree exhaling oxygen for our blog.

Ecology and industry: bridging the gap between economics and the environment

Applied ecology is the science of minimizing human impacts and of supporting ecological systems in an economic landscape. Often though, applied ecologists work in isolation from those economic forces shaping biological landscapes, not really knowing what businesses would like to accomplish for habitat protection or sustainability. At the same businesses are seldom aware of the knowledge, tools and insight provided by ecologists. And perhaps, greater interaction could help turn ecology into a science with direct impact into how human activities proceed and how we manage the impacts of those activities.

This is the premise of a paper by Paul Armsworth and 15 other authors on the ecological research needs of business, appearing in the Journal of Applied Ecology (for an interview with Paul, by yours truly, please go to the podcast, and I should point out that I am an Editor with this journal). The authors include academics, NGOs and industrial representatives, and they've come together to analyze patterns of cooperation and to discuss ways forward.

They reviewed papers appearing in the top applied ecology journals and grant proposals to the National Environmental Research Council (NERC) in the UK to measure the degree and type of interaction between ecologists and different industries. Ten to 15 percent of publications in applied journals showed some business involvement -mostly from the traditional biological resource industries (farming, fishing and forestry). Further, 35% of NERC proposals included some business engagement, but only 1% had direct business interaction.

Further, the authors reported on a workshop where ecologists and business representatives discussed a number of topics. This included how to minimize negative biodiversity impacts and for industries, such as mining, to consider ecosystem function, and how to develop new ecologically-based economic opportunities, such as insurers managing environmental risk. While there were some challenges identified (such as differing time frames of business needs versus scientific research), the authors note the positive atmosphere and the spirit of collaboration.

The research in this paper should be emulated elsewhere. A better understanding of business needs and desires can only inform and offer opportunities for applied ecological research. Top-down governmental regulation can only take conservation and ecosystem management so far and those who are directly involved in altering and managing ecosystems must articulate goals and desires in order to successfully apply ecological principles to biodiversity protection in an economic landscape.

Armsworth, P., Armsworth, A., Compton, N., Cottle, P., Davies, I., Emmett, B., Fandrich, V., Foote, M., Gaston, K., Gardiner, P., Hess, T., Hopkins, J., Horsley, N., Leaver, N., Maynard, T., & Shannon, D. (2010). The ecological research needs of business Journal of Applied Ecology, 47 (2), 235-243 DOI: 10.1111/j.1365-2664.2010.01792.x

Competitive coexistence, it's all about individuals.

Understanding how species coexist has been the raison d'etre for many ecologists over the past 100 years. The quest to understand and explain why so many species coexist together has really been a journey of shifting narratives. The major road stops on this journey have included searching for niche differences among species -from single resources to multidimensional niches, elevating the role for non-equilibrial dynamics -namely disturbances, and assessing the possibility that species actually differ little and diversity patterns follow neutral process. Along this entire journey, researchers (especially theoreticians) have reminded the larger community that that coexistence is a product of the balance between interactions among species (interspecific) and interactions among individuals within species (intraspecific). Despite this occasional reminder, ecologists have largely searched for mechanisms dictating the strength of interspecific interactions.

Image used under Flickr creative commons license, taken by Tinken

In order for two species to coexist, intraspecific competition must be stronger than interspecific -so sayeth classic models of competition. While people have consistently looked for niche differences that reduce interspecific competition, no one has really assessed the strength of intraspecific competition. Until now that is. In a recent paper in Science, Jim Clark examines intra- vs interspecific interactions from data following individual tree performances, across multiple species, for up to 18 years. This data set included annual growth and reproduction, resulting in 226,000 observations across 22,000 trees in 33 species!

His question was actually quite simple -what is the strength of intraspecific interactions relative to interspecific ones? There are two alternatives. First, that intraspecific competition is higher, meaning that among species differences only need to be small for coexistence to occur; or secondly, that intraspecific competition is lower, requiring greater species niche differences for coexistence. To answer this he looked at correlations in growth and fecundity between individuals either belonging to the same or different species, living in proximity to one another. He took a strong positive correlation as evidence for strong competition and a negative or weak correlation as evidence for resource or temporal niche partitioning. What he found was that individuals within species were much more likely to show correlated responses to fluctuating environments, than individuals among species.

This paper represents persuasive evidence that within-species competition is generally extremely high, meaning that to satisfy the inequality leading to coexistence: intra > inter, subtle niche differences can be sufficient. These findings should spur a new era of theoretical predictions and empirical tests as our collective journey to understanding coexistence continues.

Clark, J. (2010). Individuals and the Variation Needed for High Species Diversity in Forest Trees Science, 327 (5969), 1129-1132 DOI: 10.1126/science.1183506

Check out the carnival of evolution and be sure to vote for your favorite blogs

Be sure to check out this month's Carnival of Evolution (number 21) posted at Mauka to Makai. The Carnival is a monthly digest of recent evolutionary musings from around the blogosphere. This month's edition includes a number of interesting posts, as well as one of our posts on what evolution offers conservation.

Also, Research Blogging has announced finalists for various blogs awards. If you are eligible, please vote, there are a lot of great blogs vying for these awards. Also, The EEB and Flow is among the finalists for best biology blog. And to the people we nominated us, thanks again for nominating our blog.

New Tool Reveals Where Ticks Eat Breakfast

You have a much greater chance of getting sick from a tick bite today than you did 30 years ago. But a new tool might allow researchers to better understand why more ticks are making people sick.

“If you’re a health inspector and a bunch of people get food poisoning, the first thing you’d want to know is where they ate last. If you’re a disease ecologist and a bunch of ticks have a pathogen, the first thing you’d want to know is where the ticks ate last,” said Brian Allan, a post-doctoral researcher at the Tyson Research Station in St. Louis.

Allan led a team of researchers in developing a novel technology that probes the genetic contents of ticks’ gut. The tool can determine which wildlife species provided the tick’s last meal and which pathogens came along with that meal.

In the first study to use the new technology, Allan and his colleagues focused on several rapidly emerging diseases transmitted by the lone star tick. These include two pathogens responsible for a potentially fatal bacterial infection known as ehrlichiosis [ur-lick-ee-oh-sis]. In Missouri, over 200 cases of ehrlichiosis were documented last year.

Allan et al.'s study showed that about 80 percent of pathogen-positive ticks had fed on white-tailed deer. They also found that squirrels and rabbits were capable of infecting ticks at a higher rate than deer. However, since the lone star tick feeds on squirrels and rabbits less frequently, they account for a smaller percentage of infection.

Allan and his colleagues hope that the technique will shed light on theoretical questions in the field of ecology. They are especially interested in testing whether biodiversity is good for your health, a hypothesis known as “the dilution effect.”

Allan, B. F., L. S. Goessling, G. A. Storch, and R. E. Thach. 2010. Blood meal analysis to identify reservoir hosts for Amblyomma americanum ticks. Emerging Infectious Diseases 16: 433-440. DOI: 10.3201/eid1603.090911

How can evolution inform conservation decisions?

First of all, let me apologize for the lack of blog posts over the past 2 weeks, I've been busy visiting the Olympics and reading a couple of hundred blogs, judging them for the Research Blogging awards.

The conservation of biological diversity is a major imperative for biologists. International agreements such as the Convention on Biological Diversity and intergovernmental exercises, such as the Millennium Ecosystem Assessment, call upon scientists to provide evidence on the current state of biological diversity and to evaluate solutions for reducing diversity and ecosystem function loss. Critical to these efforts have been the work of ecologists, conservation biologists and ecological economists. However, seemingly missing from the conversation about the state of biodiversity knowledge has been evolutionary biologists. Are they primarily concerned with describing historical processes and mechanisms of biological change, or do they have substantive knowledge and ideas that should be viewed as a critical component of any scheme to conserve biological diversity?

In a recent paper in Evolution, Hendry and a number of coauthors convincingly make the case that evolutionary biology is a necessary component for conservation. Evolution offer four key insights that should inform conservation and policy decisions. First, they point out that evolutionary biologists are in the business of discovering and documenting biodiversity. They are the primary drivers behind long-term, sustained biological collections, because they need to know what exists in order to better understand evolutionary history. With millions of species awaiting scientific discovery, their efforts are critical to measuring biodiversity. But not only are they discovering new species and enumerating them, they are uncovering their evolutionary relationships, which gives conservationists better information about which species to prioritize. What Vane-Wright famously called 'the agony of choice', with limited resources, we need to prioritize some species over others, and their evolutionary uniqueness ought to be a factor. More than this, evolutionary biologists have developed pragmatic tools for inventorying and sharing data on biodiversity at all levels, from genes to species, which is available for prioritization.

The second key insight is that by understanding the causes of diversification, we can better understand and predict diversity responses to environmental and climatic change. By understanding how key functional traits evolve, we can develop predictions about which species or groups of species can tolerate certain perturbations. Further, research into how and why certain evolutionary groups faced extinction can help us respond to the current extinction crisis. For example, the evolutionary correspondence between coevolved mutualists, such as plants and pollinators, can be used to assess the potential for cascading extinctions. These types of analyses can help identify those groups of related species, or those possessing some trait, which make species more susceptible to extinction.

Thirdly, evolution allows for an understanding of the potential responses to human disturbance. Evolutionary change is a critical part of ecological dynamics, and as environment change can result in reduced fitness, smaller population sizes and extinction, evolution offers an adaptive response to these negative impacts. Knowing when and how populations can evolve is crucial. Evolutionary change is a product of genetic variation, immigration, population size and stochasticity, and if the ability to evolve to environmental change is key for persistence, then these evolutionary processes are also key.

Finally, evolutionary patterns and processes have important implications for ecosystem services and economic and human well-being. Both genetic and evolutionary diversity of plant communities has been shown to affect arthropod diversity, primary productivity (including work by me) and nutrient dynamics. Thus understanding how changes in diversity affect ecosystem processes should consider evolutionary processes. Further, exotic species are often cited as one of the major threats to biodiversity, and evolutionary change in exotics has been shown to increase exotic impacts on native species.

All together, these key reasons why evolution matters for conservation, mean that developing sound management plans requires considering evolution patterns and processes. We can use evolution to our benefit only if we understand how evolution shapes current dynamics. The challenge to evolutionary biologists is the same as it was for ecologists perhaps 15 to 20 years ago, to present their understanding and conservation ideas to a broader audience and to engage policy makers. To this end, the authors highlight some recent advances in incorporating evolutionary views into existing biodiversity and conservation programmes –most notably into DIVERSITAS.

Just like ecological processes and dynamics cannot be fully understood without appreciating evolution ancestry or dynamics, developing an extensive, expansive conservation strategies must take into account evolution. I hope that this paper signals a new era of a synthesis between ecology and evolution, which produces precise, viable conservation strategies.

Hendry, A., Lohmann, L., Conti, E., Cracraft, J., Crandall, K., Faith, D., Häuser, C., Joly, C., Kogure, K., Larigauderie, A., Magallón, S., Moritz, C., Tillier, S., Zardoya, R., Prieur-Richard, A., Walther, B., Yahara, T., & Donoghue, M. (2010). EVOLUTIONARY BIOLOGY IN BIODIVERSITY SCIENCE, CONSERVATION, AND POLICY: A CALL TO ACTION Evolution DOI: 10.1111/j.1558-5646.2010.00947.x

Research blogging awards; and thanks

Hi all, nominations for Research Blogging's annual awards will close Feb. 11, so be sure to nominate any research blogs you think deserve consideration. The top prize is $1000, and there are several smaller, field-specific awards as well. A panel of judges (with me being a member) will create a short list of blogs for each category and registered users on Research Blogging will be able to vote for the winners.

And a thank you to whoever nominated the EEB and Flow.

Predator-human conflict: the emergence of a primordial fear?

There is something terrifying and at the same time captivating about the idea of a large, wild, mysterious predator. The very idea that a large predator is near by makes us feel vulnerable. Every year, news stories about wild animal attacks appear in numerous publications and on many television shows. Human death at the fangs or claws of a wild beast is at the heart of many legendary stories and probably sown into the fabric of our being by millennia of ever present risk from large predators. This characteristic of our human experience, I think, dictates our response to animal attacks. Stories of animal attacks are usually concluded with statements about having or attempting to track down and destroy the guilty animal.

Such is the case for three recent animal attacks in Canada. In late October, 2009 in Nova Scotia, a raising 19-year old folk singer was killed by a couple of coyotes while hiking. It is difficult to find meaning in such a horrendous death, but the narrative, told by reporters, was essentially to rest assured that one of the coyotes had been killed and the other was being tracked and would be destroyed. There were two cougar attacks in early January, 2010 in British Columbia, that basically ended with the same reassurance. In the first, a boy was attacked and his pet golden retriever courageously saved his life. A police officer arrived a shot the cougar which was mauling the dog -an obviously legitimate response, and the news story again reassures us that the animal was destroyed. And don't worry the hero dog survived. In the second cougar attack, another boy was attacked, and this time his mother saved his life. But again the story narrative ended by reassuring us that the guilty cougar, and another cat for good measure, were destroyed the next day.

After reading these stories, I asked myself two things. Why is our response to destroy predators that attack? And why do we need to be reassured that this has happened? In defence of the predators, they are just doing what their instincts tell them to do, and most often their only mistake is that they selected their prey poorly. But the reality is that there are only 2-4 cougar attacks per year and only 18 fatalities over the past 100 years. Why do we fear such a low probability event? In contrast, automobile accidents are the leading cause of death in children under 12 in North America. Thousands of people die, and millions injured in car accidents every year in North America. Recently, in Toronto, were I live, 10 pedestrians were killed in 10 days, yet my heart doesn't race when I cross a street. If our fears and responses to human injury and death reflected the actual major risks, we would invoke restrictive rules regarding automobile use.

We believe that we can live with nature in our backyard. But when that close contact results in an animal attack, human fear seems to dictate an irrational response. Do we really expect predators to obey our rules? Can we punish them enough to effectively tame them? We cannot, and I hope that our approaches to dealing with human-animal conflict can better deal with animal attacks, in a way that does not subjugate large predators to whims of our fears.

The evolution of a symbiont

The evolution of negative interactions seems like a logical consequence of natural selection. Organisms compete for resources or view one another as a resource, thus finding ways to more efficiently find and consume prey. However, to me, the natural selection of symbiotic or mutualistic interactions has never seemed as straight forward (expect maybe the case where one species provides protection for the other, such as in ant-plant mutualisms). A specific example is the rise of nitrogen-fixing plants, who supply nutrients to bacteria called rhizobia capable of converting atmospheric nitrogen into forms, such as ammonia, usable to the plant host. Not only has this symbiosis evolved, but has seemed to evolve in very evolutionarily distinct lineages. The question is, what are the mechanisms allowing for this?

In a recent paper, Marchetti and colleagues answer part of the question. They experimentally manipulate a pathogenic bacteria and observe it turning into a symbiont. They transferred a plasmid from the symbiotic nitrogen fixing Cupriavidus taiwanensis into Ralstonia solanacearum and infected Mimosa roots with it. Plasmid transfer among distinct bacteria species is common and referred to horizontal genetic transfer (as opposed to vertical, which is the transfer to daughter cells). The presence of the plasmid caused R. solanacearum to quickly evolve into a root-nodulating symbiont. Two regulatory genes lost function, and this caused R. solanacearum to form nodules and to impregnate Mimosa root cells.

This extremely novel experiment reveals how horizontal gene transfer can supply the impetus for rapid evolution from being a pathogen to a symbiont. More importantly it reveals that sometimes just a few steps are required for this transition and how distantly-related bacterial species can acquire symbiotic behaviors.

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