Best job site, ever

For those ecologists and evolutionary biologists actively on the academic job market, there are a number of sources to get job ads (such as Science careers). But growing in popularity and by far the best job resource is the ecology job wiki. This site is a user modified site (as wikis are) where people list current job postings. But more than this people can actively discuss specific jobs, frustrations, updates, strategies, etc. For example, once a position starts interviewing, often an update will appear on the wiki informing all that interviewees have been selected Thus alleviating the feeling of limbo that we have when information is scarce. While it may not be entirely comprehensive in that not every single advertised job will appear, it does offer more information and the opportunity to share with others.

Good luck job hunters! Hopefully the job wiki is useful.

Researcher spotlight: Tadashi Fukami

Increasingly, ecological explanations for extant community patterns are relying on dynamics operating across multiple spatial and temporal scales, linking small and large scales, and the here and now with evolutionary history. The traditional boundaries of sub-disciplines are blurring. I think that few other young scientists straddle these boundaries as successfully as Tad Fukami, and new assistant professor in the Department of Biology at Stanford University. Tad uses a broad array of theoretical and experimental approaches to understand how ecological communities are put together. From laboratory microcosms to rat-infested islands, and from the computer to remote locations, he is able to pull together disparate pieces of information into a central narrative about the assembly of communities.

I asked him why the question of community assembly interested him so much, and he gives much credit to his advisors, Jim Drake (also my PhD advisor) and Dan Simberloff both in the Department of Ecology and Evolutionary Biology at the University of Tennessee. But more than this, he says that:

“you need to look into the historical background of species interactions to understand the apparently inexplicable variation in the way species interact and the way communities are structured by the interactions.”

and certain aspects of this research obviously excite him. He goes on to say:

“One particularly intriguing thing is the great effect that small chance events that cause variation in early immigration history can have on long-term community development.”

Most ecologists gain their expertise by coming to understand and appreciate the details and intricacy of particular organisms or ecosystems. But Tad is especially noted for his use of an amazingly broad assemblage of systems and methods. I asked him why he used so many different systems, and how he chose those to test his ideas. He said that his work has benefitted from many exciting collaborations and that he has:

“been very lucky to meet many great people who have expertise on specific organisms and systems that a person with diffuse interests like me doesn't have.”

But I think that there may be something deeper and more reassuring. That is, the fact that one could study a multitude of systems, testing the basic dynamics of community assembly, means that there are regularities in how communities are assembled. That you can study stochastic historical events in bacterial microcosms and inform your understanding of plant succession means that while we individually take on these, at times, daunting research projects, our collective understanding of ecological processes are threaded together in a great fabric. And no one is a microcosm of this more than Tad Fukami.

Key recent papers

Fukami, T., Beaumont, H. J. E., Zhang, X.-X. & Rainey, P. B. (2007) Immigration history controls diversification in experimental adaptive radiation. Nature 446: 436-439.

Fukami, T., Wardle, D. A., Bellingham, P. J., Mulder, C. P. H., Towns, D. R., Yeates, G. W., Bonner, K. I., Durrett, M. S., Grant-Hoffman, M. N. & Williamson, W. M. (2006) Above- and below-ground impacts of introduced predators in seabird-dominated island ecosystems. Ecology Letters 9: 1299-1307.

Fukami, T., Bezemer, T. M., Mortimer, S. R. & Van der Putten, W. H. (2005) Species divergence and trait convergence in experimental plant community assembly. Ecology Letters 8: 1283-1290.

Mutualistic networks for beginners

Research on the role of positive interactions in ecology has been increasing rapidly in the last 15 years or so. An example of this is the study of mutualistic networks, which are among the most exciting and fast-moving areas of ecology. In the last few years a number of really amazing papers have shown that studying these networks can really increase our understanding of natural systems. In a recent review papers in Frontiers in Ecology and the Environment Jordi Bascompte describes briefly but thoroughly the history and current state of this field of research. Starting with observations by Charles Darwin, he describes the importance of positive interaction and how during many decades research had been focused on single plants or pollinator, or highly coevolved interactions which has produced fundamental information. However, now with this network approach a lot can be learn about their stability and effects of species extinctions, among many other aspects. A very interesting comparison that is made is with the Internet. Apparently, a lot has been learn from this human made network, where studies have shown that networks are more stable and resistant to random attacks if they are heterogeneous (some part of the network being much more connected than most) that if they are homogeneous (all nodes being equally important / connected). The internet is actually a heterogeneous network, and so are the mutualistic networks. Bascompte also mentions the role of non-reductionist approach to science in the study of this highly complex networks since studying the parts of the network doesn’t allow researches to fully understand its behavior (e.g. you can know a lot about pairs of interactive species, but it has been proven that it will not tell you about the stability of the network to say, the extinction of same of its members). Also, he highlights the role of multidisciplinary approaches to complex problems, since the study of mutualistic networks has relayed heavily on research from other areas of science.

Jordi Bascompte (2009). Mutualistic networks Frontiers in Ecology and the Environment DOI: 10.1890/080026

However you skin them, cats have important ecosystem consequences

For disclosure’s sake, I was the editor who handled this paper, and much of this post comes from an editorial I wrote for this paper.

Islands experience the greatest impacts from the invasion of non-indigenous species and are also at the forefront of efforts to eradicate problematic species and mitigate negative impacts. Bergstrom et al. elegantly studied the habitat and ecosystem consequences from the eradication of feral cats from Macquarie Island, a subantarctic island and a world heritage site administered by the state of Tasmania, Australia. This island has undergone a series of invasions and both cats and rabbits were introduced in the 19th century. Cat predation resulted in drastic declines in seabird populations, likely causing two extinctions, and thus a cat eradication programme began in 1985 with the last cat killed in 2000. The authors recognized that the feral cats had become fully ingrained in the island food web, and they show that despite the introduction of the Myxoma virus prior to the cat eradication, rabbit populations exploded after the cat removal. These large rabbit populations caused pervasive vegetation changes. The authors sampled plots before and after the eradication and found that vegetation in these plots shifted from large, long-lived plants to smaller, faster growing species, some of which are themselves non-indigenous to the island. Further, satellite imagery revealed that more than one-third of island has since undergone vegetation change, likely resulting in large-scale habitat alterations.

What these results show us is that the consequences of species eradication may be complex with unintended results. Non-indigenous predators and meso-predators can become important components of island food webs –so important that their subsequent removal can have repercussions felt throughout the entire food web. While trying to protect seabird populations is undoubtedly worthy of management action (including eradication programmes), adequately predicting ecosystem-level consequences should be the basis directing such activities. Planning for such management activities must include information gained through experimentation, modeling and natural history. By using all available tools and knowledge, management activities can have a better chance of succeeding and harmful unintended consequences minimized.

Dana M. Bergstrom, Arko Lucieer, Kate Kiefer, Jane Wasley, Lee Belbin, Tore K. Pedersen, Steven L. Chown (2009). Indirect effects of invasive species removal devastate World Heritage Island Journal of Applied Ecology, 46 (1), 73-81 DOI: 10.1111/j.1365-2664.2008.01601.x

Who is Naïve, the invaders or the natives?

Why some species can invade natural ecosystems and many others cannot, is a question that doesn’t have an answer. Many ideas have been proposed to explain this, with relative success, but very low predictability. Most of the ideas have been focused on the factors that promote invasion (i.e. why successful invaders are successful). In a recent ideas paper Koen Verhoeven and collaborators propose a different approach. They ask the question, how ecological mismatches between natives and exotics can explain invasion? They propose a series of predictions based on plant defenses and plant enemies (herbivores, pathogens). They propose that the mismatches between exotic plants and their new enemies could explain their success or failure. For example, if a plant presents a new type of toxic chemical compound that the local herbivores have never encounter and cannot deal with, it would be a clear advantage for the plant (this is related to the novel weapons idea). On the other hand, if the plant has defenses that need to be trigger by a particular enemy (for example an induced defense triggered by a specific chewing insect) that could be a disadvantage for it. They propose that biotic resistance (when the native community resist the invasion) and enemy release (when an exotic invades due to experiencing less pressure by enemies than in its native range) are not oppose ideas but could be the different outcome of these mismatches.

This paper propose a very interesting approach to study some cases of successful and failed invasions, and I look forward for empirical tests of this idea.

Koen J. F. Verhoeven, Arjen Biere, Jeffrey A. Harvey, Wim H. van der Putten (2009). Plant invaders and their novel natural enemies: who is naïve? Ecology Letters, 12 (2), 107-117 DOI: 10.1111/j.1461-0248.2008.01248.x

Grazers chew, cereal gets sick

Managing plant disease is a major part modern agricultural practice, so it is important to understand the basic ecological dynamics of plant diseases. Some theoretical studies have found that the prevalence of plant diseases can be affected by the amount of herbivory in a system. Given that human land-use and the removal of top predators from many ecosystems has fundamentally changed the abundance and distribution of many herbivores, the repercussions of herbivory can have important cascading consequences throughout foodwebs –including disease dynamics. In the first experimental study of the interaction between herbivory and plant disease, the forthcoming paper in PNAS by Elizabeth Borer and colleagues, shows that increased exposure to large herbivores (e.g., mule deer) resulted in higher disease prevalence in the plant community. The disease they studied, barley and cereal yellow dwarf virus (shown in the photo), is transmitted by aphids, so herbivory does not cause increased transfer. Rather, herbivores changed community composition resulting in higher abundances of very susceptible species, creating a feedback where higher abundances resulted in higher infection rates due to a larger pool of potential hosts near by. These results are important for two reasons. First, this particular virus is an important agricultural disease. Secondly, we need to take a whole-community approach to understanding disease dynamics because these dynamics are not only a property of host-vector-pathogen interactions, but are subject to direct and indirect effects from interactions with other community members.

E. T. Borer, C. E. Mitchell, A. G. Power, E. W. Seabloom (2009). Consumers indirectly increase infection risk in grassland food webs Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0808778106

Fisheries and food webs: a whole system approach to cod recovery

The collapse of cod fisheries around the world is a breathtaking example of over exploitation and poor planning. But with reduced fishing pressure why have cod populations shown such slow or stagnant population recovery? This has been an extremely active area of research for fisheries scientists. In a recent paper by Casini and colleagues in the Proceedings of the National Academy of Sciences, they found that over-fishing of cod in the Baltic Sea has led to a regime shift, where a small planktivorous fish called sprat now dominate the system. But its not just that there is a new dominant, sprat seem to really change how the ecosystem operates, to the detriment of cod recovery. When the ecosystem was cod dominated, zooplankton abundance was unrelated to sprat abundance but did appear to be dependent on hydrological environmental variables. In the new sprat-dominated system zooplankton numbers are negatively related to sprat abundance and the environmental controls of zooplankton abundance do not appear to be important. So why is this bad for cod recovery? Adult sprat compete with larval and juvenile cod for zooplankton and sprat consume cod eggs. The authors suggest that a good cod recovery plan will involve managing key aspects of the food web. This paper reveals how a whole food web or ecosystem approach is necessary for understanding population controls of important fisheries species.

M. Casini, J. Hjelm, J.-C. Molinero, J. Lovgren, M. Cardinale, V. Bartolino, A. Belgrano, G. Kornilovs (2009). Trophic cascades promote threshold-like shifts in pelagic marine ecosystems Proceedings of the National Academy of Sciences, 106 (1), 197-202 DOI: 10.1073/pnas.0806649105

Review or publish; the curse of the commons

Need we be concerned about the volume and quality of manuscript reviews for journal submissions? In a recent editorial published in Ecology Letters by Michael Hochberg and colleagues, they answer yes, we should be concerned. They argue that manuscript reviewing is suffering from a tragedy of the commons, where growing submission rates to top journals is overburdening potential reviewers. This overburdening has two causes. First, that researchers tend to send their manuscripts to journals based on impact factors, regardless of the appropriateness of the manuscript for the receiving journal. Second is that authors view negative reviews as stochastic happenstance and in the rush to resubmit do little to improve their manuscript.

While the concerns are real, and the authors do suggest common sense approaches to publishing (i.e., choose appropriate journals and get colleagues to review drafts -something most of my colleagues do), there is little discussion of what incentives could be offered. The curse of the commons is when individual motives do not benefit the greater good, thus incentives could be used to alter motives potentially benefiting the larger community.

A number of journals now offer free access or free color figures in future publications for reviewing or even offering payment. Perhaps the move towards reduced length rapid turn around publications is part of the problem and that we should be valuing longer, more detailed papers (the classic quantity vs. quality problem). Whatever the potential solutions, it is promising to see journals, especially top-ranked ones like Ecology Letters, discussing these issues.

Michael E. Hochberg, Jonathan M. Chase, Nicholas J. Gotelli, Alan Hastings, Shahid Naeem (2009). The tragedy of the reviewer commons* Ecology Letters, 12 (1), 2-4 DOI: 10.1111/j.1461-0248.2008.01276.x

How to plan an experiment that could last 99 years

For a number of reasons, including the fact that most grants only allow for research over a time span of 1-3 years, ecologists and evolutionary biologists usually plan experiments that last few years (with notable exceptions, such as the LTER). A usual approach to study long term phenomena is to take advantage of “natural” experiments. This allows us to understand about processes over long time periods, but usually with limited control on the initial conditions.

In a recent paper by Thomas Bruns and collaborators I learned about another way. They study spores viability of an important genus of ectomycorrhizal fungi, symbiont of Pinaceae: Rhizopogon. Pinaceae (the family of pines and other conifers) need ectomycorrhizal fungi to survive and usually spores and seeds are dispersed independently. It was not known how long their spores can last, which has very important implications, for example for colonization of areas not previously colonized by Pinaceae, or colonization after large scale disturbances, since if seeds cannot find mycorrhizae they have really few chances of survival. Now we know, based on this research that spore banks can be build and last probably decades.

What they did is really interesting, and was inspired on a previous study on seeds. They planted known number of spores of several species of Rhizopogon in terracotta pots, that were later planted into the ground (to mimic natural conditions). They planted 16 replicates, and they plan to open and analyze them later in the century based on the spore viability (for example, if in a few years most spores seem to be not viable that may reduce the expected length of the experiment to increase resolution). This paper found that after 4 years the inoculum potential of these spores seems to be increasing with time. I found the approach used in this experiment really fascinating and I look forward to see what happens in the next years!

Thomas D. Bruns, Kabir G. Peay, Primrose J. Boynton, Lisa C. Grubisha, Nicole A. Hynson, Nhu H. Nguyen, Nicholas P. Rosenstock (2009). Inoculum potential of
spores increases with time over the first 4 yr of a 99-yr spore burial experiment
New Phytologist, 181 (2), 463-470 DOI: 10.1111/j.1469-8137.2008.02652.x

Podcasts

Keeping up with scientific literature is a challenge. Even though is it possible to do a descent job in your super specific area of expertise, it is almost impossible to keep up with literature in general areas of science, such as ecology or evolution, given the hundreds of papers that are published each week. There are many tools that can be used to stay (kind of) updated. One of those are podcasts. If you are reading this blog (and if you frequently read blogs) it is likely that you know a lot about podcasts, but I found remarkable the few people that profits from this awesome resource in academia. There are many nice podcast on science, but few on ecology. The new podcast of Frontiers in Ecology and the Environment is an awesome one, and I hope that other journals start doing the same thing (let me know if they are more!). This ESA podcast, with music by Nick Gotelli (excellent choice by the way, click here for more of his music), is surely one that you want to have in your mp3 player when you go for walk.

Other nice ones (but not specific on ecology or evolution) are the Nature podcast and the Science podcast, and my preferred one, the Scientific American podcast.