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

To intervene or not to intervene: this is a real question

Should land managers actively manipulate the structure and function of ecosystems within protected areas? Is intervention appropriate to protect or maintain native biodiversity and natural processes in areas such as national parks and wilderness areas? These are the questions that stem from a new paper by Richard Hobbs and others in Frontiers in Ecology and the Environment. US national parks and wilderness areas have legislative mandates to maintain ‘naturalness’, but what does this mean in the context of dynamic ecosystems with current and future changes including invasions by nonnative organisms and climate change?

Hobbs and his colleagues challenge concepts of naturalness and propose several ‘guiding principles’ for stewards of national parks and wilderness. They suggest that more useful concepts for managing protected areas relate to ecological integrity and resilience. Concepts of ecological integrity have been adopted by Parks Canada and relate to maintaining ecosystem components. Resilience concepts focus on the ability of a system to “absorb change and persist” without undergoing a “fundamental loss of character”. While maintaining ecological integrity in the face of global changes may - by definition - require protection of species, maintaining ecological resilience tends to focus more attention on ecosystem function “over preserving specific species in situ”.

Rather than protecting an area to maintain naturalness, focusing on ecological integrity and resilience acknowledges that a diversity of approaches - from non-intervention to actively managing systems - may be required. The flexibility in this view, demands that conservation planning span gradients of land uses across landscapes. Management objectives and success need to be re-evaluated in an adaptive and experimental framework, which requires careful and robust monitoring.

At The Wilderness Society and specifically here in Montana, these very questions are being wrestled with in terms of forest restoration, fire management, and climate change. Current forest conditions have been shaped by historic logging practices and fire suppression leading to altered structure and function – including increasing the severity of fires. Through active management, including removing small diameter trees and lighting prescribed fires, managers hope to restore forests and fire intensities to conditions more closely resembling those that historically occurred. Much of the research on restoration was conducted in dry forests in the American Southwest where low-severity fires occurred across large areas. However, in the Northern Rockies, many forests were shaped by a ‘mixed severity’ fire regime, where fires crept along the forest floor in some areas and torched trees in others. In many cases, these forests have not been fundamentally altered and need only the return of fire to restore their resilience. In other cases, forests are recovering from past logging practices and may benefit from thinning to restore a fire-resilient structure.

To return to the paper at hand: what is the appropriate level of intervention to maintain ecological integrity and resilience given past forest management and future climate change? If the current forest lacks integrity (novel stand structure) and resilience under a predicted climate of warmer, drier conditions, what is the appropriate level of management? While The Wilderness Society continues to work with diverse partners to answer these questions, one thing is clear: whatever actions take place, they need to be conducted with humility in an experimental framework that includes sufficient ecological monitoring. For the ‘experiment’ to be most helpful, we should maintain adequate hands-off “controls” along with the “treatments” to allow us to gauge the effects of intervention.

Richard J Hobbs, David N Cole, Laurie Yung, Erika S Zavaleta, Gregory H Aplet, F Stuart Chapin III, Peter B Landres, David J Parsons, Nathan L Stephenson, Peter S White, David M Graber, Eric S Higgs, Constance I Millar, John M Randall, Kathy A Tonnessen, Stephen Woodley (2009) Guiding concepts for park and wilderness stewardship in an era of global environmental change. Frontiers in Ecology and the Environment e-View.
doi: 10.1890/090089
http://www.esajournals.org/doi/abs/10.1890/090089

Timing is everything: global warming and the timing of species interactions

While an obvious affect of climate change will be changes in the distributions or range sizes of species, more insidious and likely more consequential will be how species interactions are affected by changes in the timing of growth and reproduction. These changes in an organism's life cycle, or phenology, can create mismatches between an organism's need and resource availability or the readiness of coevolved partners -such as plants and pollinators.

In an 'Idea and Perspective' paper in Ecology Letters, Louie Yang and Volker Rudolf set out a new framework to examine the effects of phenological shifts on species interactions. They argue that one cannot understand or predict the fitness consequences of a phenology shift without knowing how interacting species' phenologies are also influenced by environmental changes. The consequences of phenological shifts are changes in fitness, and the question is: how would one go about assessing the fitness effects of phenological changes on interactions? This is where this paper really hits its stride. Yang and Rudolf set out a new conceptual framework for studying the fitness consequences of phenological shifts. They make the case that an experimental approach is required to test the three likely scenarios. The first is that there are no changes in phenology -that is, measuring the fitness levels of the two interacting species under stable conditions. Second, you induce an experimental shift in the timing of one of the species. For example, in a plant-herbivore interaction, germinate the plant earlier and when the herbivore normally has access to the plant, the plant will be older. What are the fitness changes associated with this shift? Finally, you can shift the timing of the other species relative to the first. In our example, the herbivore has access to younger plants and again are there fitness consequences?

Yang and Rudolf call the full combination of possible fitness effects, across a number of timing mismatches, 'the ontogeny-phenology landscape'. By mapping fitness changes across this ontogeny-phenology landscape, researchers can offer better predictions, on top of just changes in range size or habitat use, about the possible affects of climate change. The obvious question, and Yang and Rudolf acknowledge this, is how to extend two-species ontogeny-phenology to multi-species communities. Of course, extending two-species interactions to communities is a question that plagues most of community ecology, but I think the solution is that researchers who know their systems often have intuition about the major players, and thus those species where phenology shifts should have disproportionate effects on other species. Such species could be the place to start. Another strategy would be a food web type approach, where species are lumped into broader trophic groups and we ask how shifts in certain trophic groups affect other groups.

Regardless of how to extend this framework to multispecies assemblages, I see this paper as likely to be very influential. It gives researches a new focus and framework, where specific predictions about climate change can be made.

Yang, L., & Rudolf, V. (2010). Phenology, ontogeny and the effects of climate change on the timing of species interactions Ecology Letters, 13 (1), 1-10 DOI: 10.1111/j.1461-0248.2009.01402.x

Plant genotypic diversity supports pollinator diversity

Research over the past 20 years has shown that plant communities with greater diversity maintain higher productivity, greater stability and support more diverse arthropod assemblages. More recently, several experiments have shown that interspecific diversity (namely genotypic differences) also affects community functioning. Pollination is often considered an essential function, and does plant genotypic diversity affect pollinator diversity and frequency?

In a recent paper in PLoS ONE, Genung and colleagues test whether plant genotypic diversity affects pollinator visits. They use an experimental system set-up by Greg Crutsinger that combines multiple genotypes of the goldenrod, Solidago altissima, and record pollinator visits over two years. Experimental plots contained 1, 3, 6, or 12 genotypes of S. altissima. After accounting for differences in abundance, Genung et al. show that as genotypic diversity increases, both pollinator richness and number of visits to the plot significantly increase. This increase is greater than expectations of randomly simulated assemblages combining proportional pollinator visits from monocultures.

The previous research at the species-level has made a persuasive rationale to protect species diversity in order to maintain ecosystem functioning. Now, research like this is making a case that there are consequences for not explicitly considering genetic diversity in conservation planning and habitat restoration.

Genung, M., Lessard, J., Brown, C., Bunn, W., Cregger, M., Reynolds, W., Felker-Quinn, E., Stevenson, M., Hartley, A., Crutsinger, G., Schweitzer, J., & Bailey, J. (2010). Non-Additive Effects of Genotypic Diversity Increase Floral Abundance and Abundance of Floral Visitors PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008711

Double or nothing

As I finished my undergrad career and started thinking about graduate school, I was totally infatuated with the chromosomal speciation of treefrogs in the genus Hyla. Hyla versicolor and H. chrysoscelis, the 'gray treefrogs', have similar geographic distributions and look almost identical - except that one is a tetraploid version of the other. The increase in genome size is associated with a slight increase in cell size, which has trickle-down effects into physiology, the sound of their call, and other ecological factors, and of course they are reproductively isolated. As it turns out, Margaret Ptacek and colleagues were unraveling this mystery at the genetic level just as I was learning of it, and while I was disappointed not to be able to explore this for my graduate work, Margaret made up for it by paying for all the drinks when I visited Clemson a few years back.

So it was with considerable interest that I stumbled across one of the first tables of contents of the new year, in BMC Evolutionary Biology. Two co-occurring populations of the diatom Ditylum brightwellii, it turns out, differ in genome size. In this case, the belief is that there is a single taxonomic species harboring a very recent genome duplication polymorphism (which are likely cryptic species). Of course, a species by any other name... well, that's the problem isn't it? In the world of diatoms, according to Koester and colleagues, the 'barcode' standard is to use the 18S rDNA gene sequences and silica cell wall morphology in diagnosing species. However, already armed with evidence that two substantially distinct populations could be identified with the more rapidly-evolving ITS gene region, these researchers explored how differences in reproductive rates and size distributions might be associated with genome size.

See, diatoms are the petri dishes of the natural world. In order to reproduce, each side of the interlocking silica case separates and generates a new nested case. One of the offspring of this fission will be the same size as the parental individual, the other will be slightly smaller - the smaller of the two original cell walls, with an even smaller one nested within. At least that is how I understand it. Over time, these clonal lineages reduce substantially in size, and cell size is eventually limited by genome size; sexual reproduction then allows them to regain a larger cell size and the process repeats. So, the life history of this species requires an interesting interaction among the genome (which places a lower bound on cell size, and a lower bound on reproductive rate) and the population.

In Ditylum, Koester et al. were able to show that there are not only two very distinct genetic lineages, but that the one that is regionally localized to Puget Sound appears to have been generated through genome duplication. That is, there is a cosmopolitan species, and an offshoot lineage that was formed through some form of genome duplication, with concomitant changes in cell size, rates of population growth, and reproductive isolation. Koester et al. conclude that these lineages are cryptic species, and that this form of isolation may be common in marine diatoms.

More generally, this shows another way in which our understanding of biodiversity is changing rapidly thanks to molecular diversity analysis. The latest term to be coined by John Avise, biodiversity genetics, reflects the fact that we must now consider all of the new ways in which this technology can accelerate the rate of discovery in our natural world. Taxonomists trained in the morphology and phenotypic diversity of life are few; certainly too few to keep up with growing scientific collections, and the bottleneck in describing species can be a difficult one for management and conservation. The '18S or bust' approach in diatoms may be one standard that will change as more studies like this one, out of Armbrust's lab at Washington, illuminate how dynamic biological diversity can be.

Predicting invader success requires integrating ecological and land use patterns.

Disclaimer, this was modified from an editorial I wrote for the Journal of Applied Ecology.

In the quest to understand species invasions, we often try to link the abundance and distribution of invaders to underlying ecological processes. For example, oft-studied are the links between exotic diversity and native richness or environmental heterogeneity. Seemingly independently, research into how specific land use or management activities affect invasion dynamics is also fairly common. While both research strategies are of fundamental importance, not often recognized, or at least explicitly studied, is that both ecological patterns and management activities simultaneously affect invasion success. Thus a truly integrative approach to understanding invader success must take into account variation in ecological communities and abiotic resource avalibility as well as land use patterns at multiple spatial scales. Such an approach is necessary if ecologists wish to predict potential invader abundance, spread and impact.

Diez et al. Examine how environmental and management heterogeneity interact to influence patterns of Hieracium pilosella (Asteraceae) inasions in the South Island of New Zealand. The spread of H. Pilosella in New Zealand is threatening native habitats (tussock fields) and the livestock grazing industry. Diez et al. Asked how environmental and management regimes affect H. Pilosella abundance and distribution across six large farms on the South Island. This is an interesting and important question, not just because they are examining how human-caused and ecological variation interact to affect H. Pilosella dynamics, but also because these sources are heterogeneity are realized at different spatial scales.

Diez et al. show that the abundance and distribution of H. Pilosella was significantly affected by the interaction of habitat type (i.e., short vs. tall tussocks) and farm management strategies (i.e., fertilization and grazing rates). At larger scales, H. Pilosella was more abundant in tall tussock habitats and was unaffected by fertilization, while in short tussocks, it was less abundant in fertilized patches. At small scales, H. Pilosella was less likely to be found in short tussocks with high exotic grass cover and high productivity (measured as site soil moisture and solar radiation). Conversely, in tall tussocks, H. Pilosella was more likely to be found on sites with high natural productivity. Diez et al. were able to tease these complex causal mechanism apart by using Bayesian multilevel linear models, for which they included example R code in an online appendix.

While it is a truism in ecology to say that heterogeneity affects ecological patterns, this paper deserves mention because they convincingly show that the spread of noxious exotic plants in a complex landscape, can potentially predicted by understanding the invader success in different habitat types and land management strategies. In their case they show how human activities, which were not designed to affect H. Pilosella, can strongly affect abundance in different habitat types. This type of approach to understanding invader dynamics can potentially arm managers with the ability to use existing land use strategies to predict how and where further invader targeting would be most useful.


Diez, J., Buckley, H., Case, B., Harsch, M., Sciligo, A., Wangen, S., & Duncan, R. (2009). Interacting effects of management and environmental variability at multiple scales on invasive species distributions Journal of Applied Ecology DOI: 10.1111/j.1365-2664.2009.01725.x