Wednesday, December 30, 2009

1st anniversary!

The Eeb and Flow is now a year old. Thanks to all our contributors and we hope readers will continue to find our posts interesting, informative and timely. Hopefully, with sustained effort on our part, we can surpass the 20,000 reads from this year and make 2010 a great year for readers and contributors.


Wednesday, December 16, 2009

Parasite competition enhances host survival

ResearchBlogging.orgContracting a parasite is bad. But is getting colonized by multiple parasitic species worse? This is an interesting and important question. The host is a resource, which can support a limited number of parasitic individuals, and so how does competition affect parasitic species and host mortality?
This was the premise of a recent paper by Oliver Balmer and colleagues, studying trypanosome infection of mice hosts. They engineered two transgeneic strains of the protozoan parasite, Trypanosoma brucei (African sleeping sickness), to fluoresce different colors in order to assess infections. They infected mice with each strain separately and together and measured host survival and parasite density.

They found that when both strains were present, they competitively suppressed each other and that the level of suppression depended on the initial density of each strain. One of the strains was more virulent than the other, and infection by both strains reduced mortality by 15% compared to infection by the virulent strain only. This is due to the suppression of the virulent strain by the low virulent strain.

The authors argue that strain source and intraspecific genetic diversity can have an important effect on host mortality. I would also argue that understanding interspecific interactions and within-host niche differences, would also be critical.

What a cool use of molecular technology to test basic hypotheses about disease ecology.

Balmer, O., Stearns, S., Schötzau, A., & Brun, R. (2009). Intraspecific competition between co-infecting parasite strains enhances host survival in African trypanosomes Ecology, 90 (12), 3367-3378 DOI: 10.1890/08-2291.1

Thursday, November 26, 2009

Understanding wildlife-friendly ecolabels

These days, it seems like nearly everything in the supermarket is good for the environment in one way or another. Over the past decade, more and more companies have started using ecolabels to collect a premium on products that claim to contribute to environmental protection.

But not all ecolabels are created equal. The credibility of their claims varies widely, ranging from environmentally meaningful to downright exploitative.

A recent study by Adrian Treves and Stephanie Jones provides a model for policy-makers and consumers to discriminate between claims.

“In a nutshell, [we] were looking for a way to analyze this cloud of ecolabels out there, all of them claiming to be the best thing for a given species or the best thing for a given ecosystem,” said Treves in an interview.

In the early stages of their research, Treves and Jones realized that wildlife friendly ecolabels can be split along the same lines that have divided debating groups of conservationists. They drew upon these divergent perspectives to partition wildlife friendly ecolabels into three categories.

“Supportive” ecolabels such as Endangered Species Chocolate donate some percentage of revenues to conservation organizations. Verifying the claims for this category is compromised by the transfer of funds to a third-party recipient who is usually not accountable to consumers.

“Persuasive” ecolabels claim to improve production methods in a way that eliminates threats to wildlife, but do not assess actual conservation of wildlife. Although the persuasive category is more transparent and environmentally effective than the supportive one, this type of ecolabel bases its certification requirements on assumptions about threats to wildlife without testing how reduction of perceived threats impacts wildlife. Tuna labeled as Dolphin Safe is an example of a persuasive ecolabel.

“Protective” ecolabels certify wildlife conservation by assessing whether reduction of threats enhances wildlife populations. The Marine Stewardship Council certifies fisheries under a protective ecolabel. This category is the most meaningful to wildlife because it matches the recommendations of the latest conservation science. By following the scientific method, protective ecolabels can verify that they actually help humans and wildlife coexist.

Just as conservation is often pitted against economic interests like agriculture or development, ecolabels must balance a trade-off between consumer confidence and producer incentive.

Protective ecolabels gain the most consumer credibility but also require the greatest verification effort. Proving that producers conserved wildlife is costly, time-consuming, and logistically challenging. Wild animals habitually ignore property boundaries and can die or disperse for reasons unrelated to producer activities. Often, the costs associated with these challenges outweigh the economic incentive of being labeled as “green.”

Treves, A. and S. M. Jones. 2009. Strategic trade-offs for wildlife-friendly eco-labels. Frontiers in Ecology and the Environment. DOI:10.1890/080173

(Image courtesy of kateboydell at flickr under a Creative Commons license)

Wednesday, November 25, 2009

Taking below-ground processes seriously: plant coexistence and soil depth

ResearchBlogging.orgSome of the earliest ecologists, like Eugen Warming and Christen Raunkiaer, were enthralled with the minutia of the differences in plant life forms and how these differences determined where plants lived. They realized that differences in plant growth forms corresponded to how different plants made their way in the world. Since this early era, understanding the mechanisms of plant competition is one of the most widely-studied aspects of ecology. This is such an important aspect of ecology because understanding plant coexistence allows us to understand what controls productivity in the basal trophic level for most terrestrial food webs. There are a plethora of plausible mechanisms for how plants are able to coexist, and most involve above-ground partitioning strategies (such as different leaf shapes) or phenological differences (such as germination or bolting timing). Yet, below-ground interactions among plants as a way to understand competition and coexistence have been making a strong resurgence in the literature lately. This resurgence has been driven by new hypotheses and technologies.In what is probably the best hypothesis test of the role for below-ground niche partitioning, Mathew Dornbush and Brian Wilsey reveal how soil depth can affect coexistence. They seeded 36 tallgrass prairie species into plot that were either shallow, medium or deep soiled, and asked if species richness and diversity were affected after 3 years. They found that species richness significantly increased with increased soil depth, revealing that deeper soils likely had greater niche opportunities for species. Not only did deeper soils harbor greater richness, but compositions were non-random subsets. The species inhabiting shallow soils were a subset of medium soils, and medium a subset of deep. This means that increasing depth opened new niche opportunities, unique from the ones for shallow soils.

This study is the first field-based experiment of soil depth and coexistence, that I know of and the results are compelling. Plant species are segregating below-ground niches, and perhaps we look for other partitioning strategies for species that inhabit the same soil depth.

Dornbush, M., & Wilsey, B. (2009). Experimental manipulation of soil depth alters species richness and co-occurrence in restored tallgrass prairie Journal of Ecology DOI: 10.1111/j.1365-2745.2009.01605.x

Other notable recent papers on below-ground processes:

Bartelheimer, M., Gowing, D., & Silvertown, J. (2009). Explaining hydrological niches: the decisive role of below-ground competition in two closely related species Journal of Ecology DOI: 10.1111/j.1365-2745.2009.01598.x

Cramer, M., van Cauter, A., & Bond, W. (2009). Growth of N-fixing African savanna species is constrained by below-ground competition with grass Journal of Ecology DOI: 10.1111/j.1365-2745.2009.01594.x

Meier, C., Keyserling, K., & Bowman, W. (2009). Fine root inputs to soil reduce growth of a neighbouring plant via distinct mechanisms dependent on root carbon chemistry Journal of Ecology, 97 (5), 941-949 DOI: 10.1111/j.1365-2745.2009.01537.x

Beware of the fake conference

I don't know about other researchers, but I get inundated with e-mails about upcoming conferences from organizations I've never heard of, on topics that, at best, only tangentially relate to my work. I think that most of these are put on by for-profit groups that try to cash in on hot topics. But now there are truly fake conferences that are fronts designed to get your financial information. In a new post by Bob Grant on The Scientist news blog, he relays a detailed example of such a scam conference. He went so far as to contact the venues and speakers listed by the scammers, and of course none of those listed had ever heard of the conference. The ultimate enticement was the offer to pay for travel expenses, and the presumption is that they would offer to reimburse you, but need your bank account information. The evolvability of internet scammers is truly impressive.

Sunday, November 22, 2009

Something fishy

Of the many victories wrought by DNA barcoding - the ability to place an unknown sample in a phylogenetic, and often taxonomic, context using short fragments of DNA sequence data - some of the most useful applications for management have come from the sea. One of the best citation-to-data ratios in this regard belongs to a 2004 study by Peter Marko. This project extended naturally from Marko's molecular ecology course: students purchased samples of "red snapper" from various fish markets, and sequence data from the mitochondrial cytochrome b gene region showed that most of these specimens were not, in fact, Lutjanus campechinus - they were often understudied and probably rare relatives, or in some cases not snapper at all. The conservation implications from this study were huge, and a number of papers have followed suit, looking at a variety of similar systems. If you aren't interested in adding to your list of papers to read, check out the short film based on work done in Steve Palumbi's lab that documents their work to identify shark fins.

In a paper by Lowenstein et al., published last week in PLoS ONE, the focus was on sushi, specifically tuna. The common labeling errors were caught again: there were mismatches between what restaurants called the fish, and what was actually being offered. In some cases, very phylo-distant species are being sold as "tuna", and these species can actually make consumers ill. The story is an interesting one of how fraud develops in samples of organisms that can no longer be visually tied to the species they came from, and the difficulties in protecting consumers from fraud under current regulations. Obviously, the perils of overfishing are becoming quite clear and interested readers should carry their Monterey Bay Aquarium seafood guides or similar (there's even an iPhone app for that!) with them before ordering at restaurants.

A particularly interesting advance in this study was taking the barcoding approach beyond the visual appeal of tree-building and similarity with databased sequence data. One concern about barcoding has been that even when a new clade appears in a phylogeny, taxonomy cannot be updated without some sort of diagnostic characters. It is uncommon for new species (especially of animals) to be described based on DNA sequence data alone, but it is nevertheless the norm to define the character states that uniquely define a species from its relatives. In Lowenstein et al.'s paper, they identified 14 diagnostic DNA substitutions that could be used to uniquely identify all species of Thunnus and suggested that focusing on particular characters within the "barcode gene" (mitochondrial cytochrome oxidase I) will also be necessary for new technologies to accelerate in-the-field identification.

This latter step is of interest for anybody interested in cryptic species, or identifications when other reference material is not available. I hassled one of my former Ph.D. students endlessly as she revised her dissertation because we had been comfortably using a phylogenetic tree to assign unknown individuals to one of three cryptic taxa (in the isopod genus Idotea), but prior to publication we knew that diagnostic characters would be necessary for subsequent work to be readily comparable. And, since the undergraduate evolution lab at the University of Georgia repeats Marko's work on red snapper every few years (the local Kroger now knows not to advertise their special on "red snapper from Indonesia"), perhaps the lab can be extended by having the students generate these characters for the genus Lutjanus as well. I don't seem to have any problem convincing students to do their homework when it involves going out for sushi.

Friday, November 20, 2009

Ross Crozier, evolutionary biologist and conservation biologist

Sadly, one of Australia's leading evolutionary biologists, Ross Crozier passed away suddenly last week (Nov. 12th, 2009). As a Professor at James Cook University, he worked on a plethora of evolutionary issues, from understanding the evolution of sociality in insects to population genetics and molecular phylogenetics. To my mind, his most influential papers were on how we can use patterns of evolutionary history in guiding conservation decisions -the agony of choice. While he promoted the conservation of phylogenetic diversity, per se, his great insight was that even comparing species that are relatively divergent does not mean that they are equally valuable, and we should consider information content as well. That is, a species with 80,000 genes is more valuable than a species with 20,000 genes, since the 80K-gene species has greater information content.

"Differences in the information content of genomes led to the realization that, other things being equal, some organisms have intrinsically higher conservation worth than others." -Ross Crozier

Ross also recently was the handling editor, at Ecology Letters, on a paper of mine and his insights and support were greatly appreciated and helped to improve our manuscript in numerous ways.

Here are my two favorite papers of his.

Crozier, R. H. 1992. GENETIC DIVERSITY AND THE AGONY OF CHOICE. Biological Conservation 61:11-15.

Crozier, R. H. 1997. Preserving the information content of species: Genetic diversity, phylogeny, and conservation worth. Annual Review of Ecology and Systematics 28:243-268.

Thursday, November 19, 2009

Eutrophication and fish depletion add up

The Baltic Sea is the world’s biggest brackish water body. The main threats for this unique ecosystem are eutrophication and overfishing. In coastal ecosystems eutrophication is considered to be the main factor causing the observed regime shift from long living canopy forming macroalgae towards systems dominated by ephemeral filamentous algae. Canopy forming macroalgae build nursery habitat, store nutrients, decline turbidity, and enrich water with oxygen whereas ephemeral algae can build large scale floating mats causing hypoxia and increase turbidity. Loss of top predators is known to cause trophic cascades. In the simplest scenario top predator loss means an increase in mesopredators, a decrease in grazers and thus an increase in algae growth. There is growing evidence that nutrient related algae blooms are not independent of top-down regulation. However, both threats, eutrophication and overfishing, are so far managed independently of each other by focusing either on reducing nutrient loads or defining fishing quotas for threatened species.

In a combined study using field data and evidence of two experimental studies Eriksson et al. show that decline of top-predators and nutrient load have similar and additive effects on the abundance of ephemeral algae. Both factors together increased abundance of ephemeral algae many times! The field data revealed a strong negative correlation between the abundance of fish and ephemeral algae. When fish was depleted high abundances of their prey and at the same time high cover of ephemeral algae was observed. The experiments very nicely proofed these observations. By excluding predatory fish Eriksson et al. show that (i) the abundance of small mesopredators increased, (ii) the smaller gastropod grazers became smaller, and (iii) the net production of ephemeral algae increased. Moreover, the predator effect depended on grazers and habitat complexity. In the absence of grazers predator removal had no effect on algae growth. In the absence of canopy cover, i.e. a proxy for habitat complexity ephemeral algae growth doubled.

This paper makes a strong point that to successfully combat eutrophication the so far unidirectional view on either bottom-up or top-down forces should change towards an integrated approach taking into account both factors.

Britas Klemens Eriksson, Lars Ljunggren, Alfred Sandström, Gustav Johansson, Johanna Mattila, Anja Rubach, Sonja Råberg, Martin Snickars (2009) Declines in predatory fish promote bloom-forming macroalgae. Ecological Applications: Vol. 19, No. 8, pp. 1975-1988. doi: 10.1890/08-0964.1

Tuesday, November 17, 2009

Podcasts from the Center

Looking for interviews with scientists and managers working on important ecology and conservation issues? Luckily, a new project, called the Voyage of the Beagle has recently started archiving interview podcasts. Jai Ranganathan, a postdoctoral associate at the National Center for Ecological Analysis and Synthesis started this site to promote current research and researchers and to make lively conversations about research accessible to everyone. Check it often, three new interviews will be posted every week!

The latest podcasts are fed into our blog roll on the right sidebar.

Monday, November 9, 2009

Emergent linkages in seemingly unconnected food chains

ResearchBlogging.orgFood webs are notoriously complex, and a difficult aspect of ecology is to offer a priori model-derived predictions of food web processes. There are some ecologists, such Neo Martinez and Jordi Bascompte, who have advanced our understanding of the general mechanisms of food web properties and dynamics through tools such as network theory. Such advanced approaches rely on direct interactions among species, or at least indirect interactions that are mediated through changes in abundance of different network players. However, what is missing from our general understanding of food web interactions is the role that behavioral responses can affect patterns of consumption and network connectivity.

Washington State University ecologists, Renée Prasad and William Snyder convincingly show how behavioral responses to predation can fundamentally alter food web interactions and link previously independent predator-prey interactions. They used two spatially independent insect predator-prey links in a novel, factorially-designed experiment. The two food chains consisted of a ground-based one, where ground beetles consume fly eggs and a plant-based one, where green peach aphids feed on the plants and are consumed by lady beetles. Under the ground-based chain only, the ground-based chain plus aphids, or ground-based chain plus lady beetles, the ground beetles consume a high proportion of the fly eggs. However, when both aphids and lady beetles are present, aphids respond to lady beetles by dropping off the plants and the ground beetles switch from consuming fly eggs to aphids. Under this last treatment, very few fly eggs are consumed, fundamentally altering the strength of the linkages in the two food chains and connecting them together.

This research highlights the inherent complexity in trying to understand multispecies systems, where the actors potentially have behavioral responses to other species, changing the nature of interactions. These types of responses may also generally increase the connectedness of such networks, which may result in more stable food webs, but this would need to be empirically tested. Regardless, this type of experiment offers food-for-thought to scientists trying to work general processes into a broad understanding of food web dynamics.

Prasad, R., & Snyder, W. (2009). A non-trophic interaction chain links predators in different spatial niches Oecologia DOI: 10.1007/s00442-009-1486-7

Monday, November 2, 2009

Eco-label Promotes Biodiversity on Farms

At first glance, potato farms might seem like an unlikely candidate for conservation efforts.

But Wisconsin researchers are demonstrating that biodiversity can be restored even in the midst of large-scale farming.

Paul Zedler, professor of Environmental Studies at the University of Wisconsin (UW)-Madison, and his colleagues are working with potato farmers to restore pre-settlement habitats on growers’ lands.

In central Wisconsin, 42,600 acres are devoted to potatoes. Since the landscape is dominated by agriculture, some proportion of farmland must be set aside for conservation to preserve biodiversity in this part of the state.

Restoration is a requirement of the Wisconsin Healthy Grown potato program, a partnership between UW–Madison, the Wisconsin Potato and Vegetable Growers’ Association, and NGOs such as the International Crane Foundation, Defenders of Wildlife, and the World Wildlife Fund.

The groundwork for the Healthy Grown program was laid out in the 1980s, when a group of potato growers voluntarily discontinued use of the high-risk pesticide aldicarb. The farmers turned to UW-Madison researchers for pest-management advice. This grassroots movement eventually drew attention from conservation agencies.

To be certified under the Healthy Grown eco-label, potatoes must be grown under a set of standards that restrict pesticide and fertilizer use. The program was able to draw from an extensive body of UW-Madison research to guide the formulation of these in-field standards. But farmers and environmentalists were interested in doing more.

Since the program's conception, growers had expressed interest in managing their farms as whole ecosystems rather than just focusing on crop production on a field by field basis. At the same time, the NGOs saw the program as an opportunity to bring farmland into regional-scale conservation plans.

Satisfying this interest in developing a conservation standard for the eco-label was challenging for researchers because fewer precedents existed. Even the largest and most well-known eco-label, USDA Organic, does not include a conservation requirement in its certification standards.

Zedler and his colleagues looked to the Nature Conservancy, which had established a system for making strategic conservation decisions and measuring conservation success at sites where the objective is to improve biodiversity on whatever land can be spared from intensive human use.

Potato farms in central Wisconsin are unusual in their tendency to contain significant patches of marginal land without crops because these patches cannot be irrigated – a necessary factor in growing potatoes. The result is a complex mosaic of land in which remnant patches of disturbed natural habitat are isolated within an agricultural matrix. Zedler and his colleagues focused their research efforts on these patches of non-crop land.

Their research suggests that prescribed burns and control of invasive plant species can help restore disturbed non-crop land to the habitats that characterized central Wisconsin before European settlement: prairie, oak-pine savannah, and sedge meadow.

Thus far, the Healthy Grown program has restored more than 400 acres of privately owned farmland. According to Zedler and his colleagues, farmers’ strong ties to their land motivate their commitment to the conservation standard of the Healthy Grown eco-label.

Zedler, P. H., T. Anchor, D. Knuteson, C. Gratton, and J. Barzen. 2009. Using an ecolabel to promote on-farm conservation: the Wisconsin Healthy Grown experience. International Journal of Agricultural Sustainability 7(1): 61-74. DOI:10.3763/ijas.2009.0394

(Image courtesy of FotoosVanRobin at flickr under a Creative Commons license)

Thursday, October 29, 2009

Time management for grad students and researchers

As researchers, we all have incredible demands on our time. These demands can quickly snowball, leaving us feeling like things are out of control. This lack of control over your priorities and responsibilities can lead to anxiety and depression and perhaps to dropping out of graduate school. Getting control and developing good time management skills can go a long way towards preserving your sanity and making grad school and a career in academic research enjoyable. All it really takes is planning, and knowing the things to plan for. The critical priorities that every student and/or researcher must plan, includes:
  • Writing/outlining research questions
  • Taking courses
  • Teaching
  • Appointments with supervisor and committee
  • Design/set-up experiments/studies
  • Data collection
  • Analyzing data
  • Writing papers/chapters/articles
  • Rewriting papers/chapters/articles
  • Meetings/presentations
  • Finding a publisher/lay out/submitting manuscripts
  • Administrative duties
  • Holidays
  • The unexpected!
All these things tugging at you all at once can make it difficult to start any single thing -because you feel the anxiety about not starting other things. Here are seven strategies for controlling your time and priorities, and helping you to cope with time stress.

1 - Live by the calendar, die by the calendar. Basically, schedule everything. With freely available calendars like Google's or Sunbird there is no reason to not adopt a calendar. Web-based calendars, mean you can be anywhere, on any computer and still have access. Be sure to share the calendar with lab mates and professors, so they know when you are booked. Schedule everything from meetings, to large slots of time dedicated to time-intensive things like reviewing a manuscript or data analyses.

2- Gimme a break! Working for four straight hours without a break will cause you to be less productive, than four hours with a 5 minute break every 40-60 minutes. Don't be afraid to get up from your desk in between tasks to reset your brain. You could also call or chat with someone, make a coffee, watch a Daily Show clip, update your Facebook status, etc. Don't feel guilty about the 5 minute solitaire game (only about the 2 hour ones).

3- Leave. Have a secret work spot. It could the back corner of a library, a coffee shop, home, or some special place. The point is to have a productive site where you are not tempted to do nonproductive things when you need to be focusing on a task. Leave your e-mail behind if possible and do not let colleagues know where you are. Make it your time.

4- Delegate. You do not need to do everything yourself. If you are collaborating, don't be afraid to ask collaborators to do something. If you are at a big university, search for undergrad volunteers to help out. If you are really swamped, ask a friend to help out with an experiment.

5- Write it down or lose it. I write down everything, and I do it for two reasons. First, I will forget it if it is not written down in front of me (which saves me anxiety about forgetting things). Secondly, these notes become defacto to-do lists which saves me time from having to think about what to do next. If I have ten minutes before a meeting and my list has me e-mailing someone, then I get the reward of ticking something off the list.

6- Enough is enough. Remember, it will never be perfect. Likely, the 13th draft of paper is not appreciably better than the 12th. Plus, reviewers will ALWAYS recommend revisions and you will never win a literary award for it. So if you pour your soul into a manuscript and take 2 years to write it, likely you'll be devastated when you are asked for major revisions. The important thing is getting it submitted and learning when enough is enough can go a long way toward freeing up valuable time.

7- Have fun. Likely, you got into research because you love science. If your work is tedious and boring, find some fun research to offset it. If you have to choose between two projects, and one seems like it will be personally more enjoyable, go for that one. Don't be afraid to shelve a unrewarding project for one that is fun and exciting. Most importantly, reward your self! When you submit a paper, take the rest of the afternoon off. When you finish an intense summer of field work, go to the beach for four days. Tell your close colleagues when you get a paper accepted or an award -you are not bragging, and they will always say 'congrats' or 'awesome', which feels nice. Whatever works as a reward, use it.

Remember, at the end of the day what matters is getting papers out and being a good collaborator/student/mentor/human being. Control of priorities and successful time management will make it a lot easier to get those papers out and be a relaxed, good person to be around.

Monday, October 26, 2009

Conscientious conservation?

A colleague once said at a bar that she didn't believe in "conservation genetics". I'm not quite sure which aspect she was disputing, but one certain conflict is between gearing research toward conservation, while watching chemicals and consumables go into the waste stream. Most of the reactions in my lab are done using pipet tips and tubes made of virgin polypropylene. Nobody wants to recycle this stuff - even though 99% of the chemicals we use are fairly meek reagents like ethanol, water, nucleotides, and barnacle DNA, there's just no way to guarantee the waste stream coming from a building that does molecular research (e.g. you'd probably balk if that plastic got melted down and used for toys). Researchers have enough problems with reactions going wrong to also worry about whether their supplies are contaminated with the products of reactions past. Still, we have to constantly consider how we can minimize waste in the lab.

Lab Waste from Eva Amsen on Vimeo.

As a marine biologist, I'm also very conscious where all this plastic eventually ends up. I'm entertaining ideas for tip and tube recycling, though it is barely worth the effort for a single lab to do so: my lab probably consumes about 10kg of virgin polypropylene a year, into the trash. Super bummer. But that recycling effort could be balanced out if I just got my entire lab (including me) to stop drinking so much soda! Better would be to find institutional solutions, and we're a long way off on that.

Of course a lab is more than plastic. There are chemicals - which we've chosen to avoid some of the nastier ones, like ethidium bromide (using Ames-tested GelRed instead), isotopes (fluorescent-labeled primers), but still must use a little bit of polyacrylamide and a few other things in very small quantities that you wouldn't want to put in a smoothie. There are heating and cooling costs, which we can't do a lot about in our grumpy 1980's-era building at the University of Georgia (we'll assume that under budget constraints physical plant is doing what they can in that regard, though we did install some motion sensors on lights in the auxiliary rooms).

And then, there are all the gizmos. For the holidays I got a fun gift: a Kill-A-Watt. As procrastination during grant writing, I decided not only to check the energy consumption of things at home, but things in the lab. I don't know whether I believe paying to balance carbon emissions works (though at $3/month, I do it anyway), but it is interesting to know what the footprint of a lab like mine is. To make a long story short, it's mostly about the computers. Each computer in my lab used around 5kWh/day - up to $150 in annual energy bills, and actually the only things that compete with computers are my big chromatography fridge and my ultracold freezers (the -80° will use around 6000kWh/year!). Anyway, by unplugging some things that weren't being effectively used - one of the refrigerators, some water baths, an incubator, 2 of the computers - and ensuring that the rest were using the most appropriate power-saving settings - I cut the kWh consumption of my lab (only counting plug-in stuff) by over 10%.

The question is, how does this energy usage affect the science? One could argue that my research program hasn't expanded to fill the resources I had available, or that I can only cut back to the detriment of productivity. Only time will tell! We may have to devise a metric for productivity per kWh - but right now if I calculate my Hirsch index per kWh, it is not the thrilling kind of number I want to run to the administration with. I better get back to work.

Saturday, October 24, 2009

Fall colors redux

For those of us in temperate deciduous regions, now is the time of landscapes splashed in red, orange and gold. Here is a link to a post I wrote back in March about the evolutionary meaning of autumn colors. It seemed appropriate to dig it up.

Wednesday, October 21, 2009

Adaptation and dispersal = (mal)adapted

ResearchBlogging.orgEver since Darwin, we often think of organisms as being in a constant battle against other organisms and local environments. Thus natural selection and the resulting arms race results in organisms highly adapted to local conditions and against local antagonists. At the same time, and especially driven by theoretical advances in the 1990's, researchers began to ask how dispersal -that is, the flow of genetic material from elsewhere, can disrupt local adaptation. On the one hand it may provide genetic variation allowing for novel solutions to new difficulties. On the other hand, dispersal may reduce the prevalence of fitness-increasing genes within local populations.

In a simple but elegant experiment, Jill Anderson and Monica Geber performed a reciprocal transplant experiment, moving Elliott's Blueberry plants between two habitats. One population was from highland, dryer habitats and the other from moist lowlands. They further evaluated performance in greenhouse conditions. Their results, published in Evolution, show that these two populations have not specialized to local conditions. Rather, due to asymmetric gene transfer, lowland individuals actually performed better when planted in highlands than compared to their home habitat. Further, in the greenhouse trials, lowland species did not perform better under higher moisture conditions. While genetic or physiological constraints may also limit adaptation, Anderson and Geber present a fairly convincing case that gene flow is the culprit.

These results reveal that populations may actually be relatively mal-adapted to local conditions, which has numerous consequences. For example, we need to be cognizant of adaptations to particular conditions when selecting populations for use in habitat restoration and when trying to predict response to altered climatic or land-use conditions. Importantly what does this mean for multi-species coexistence? Dispersal seems to limit the ability to adapt, and thus, better use local resources or maximize fitness, making for a better competitor. At the same time, dispersal can offset high death rates, allowing for the persistence of a population that would otherwise go extinct. Understanding how these two consequences of dispersal shape populations and communities is an interesting question, and work like Anderson and Geber's provides a foundation for future studies.


Evolution DOI: 10.1111/j.1558-5646.2009.00825.x

Mycorrhizal Networks: Socialists, capitalists or superorganisms?

ResearchBlogging.orgMycorrhizal networks – fungal mycelium that colonize and connect roots of one or more plant species – are a very intriguing type of fungal-plant association. There is evidence of substantial facilitation between plant individuals via these fungal networks. This can have drastic implications for our understanding of nature, given that the common perception is that other mechanisms, like competition, herbivory or dispersal, are the main drivers of plant community associations. This may be far from reality if the existence of “socialist” networks is widespread (e.g. the ability to connect and profit from a network may be more important than competitive abilities). In the last issue of the Journal of Ecology ( that has a very interesting special feature on facilitation in plant communities), Marcel Van der Heijden and Tom Horton conducted a review of the topic. They found a general positive effect of mycorrhizal networks on seedlings and large plants (i.e. plants tend to grow better if they are associated with a network). However, the reviewers also found some networks can have a neutral or even a negative effect on plants. The plant responses were highly variable depending on other variables including fungal species, nutrients availability, and plant identity. The positive effect of some fungal networks on seedlings growing nearby adult trees of its same species is somehow opposite to the predictions of the Janzen-Connell hypothesis. We need further studies to understand the overall importance of mycorrhizal networks in relation to other better understood mechanisms.

van der Heijden, M., & Horton, T. (2009). Socialism in soil? The importance of mycorrhizal fungal networks for facilitation in natural ecosystems Journal of Ecology, 97 (6), 1139-1150 DOI: 10.1111/j.1365-2745.2009.01570.x

Saturday, October 17, 2009

The making of an open era

With the availability of open access (OA) journals, academics now have a choice to make when deciding where to send their manuscripts. The idealistic version of OA journals represents a 'win-win' for researchers. The researchers publishing their work ensure the widest possible audience and research has shown a citation advantage for OA papers. The other side of the 'win-win' scenario is that researchers, no matter where they are, or how rich their institution, get immediate access to high-caliber research papers.

However, not all researchers have completely embraced OA journals. There are two commonly articulated concerns. The first is that many OA journals are not indexed, in most notably Thomson Reuters Web of Knowledge, meaning that a paper will not show up in topic searches, nor will citations be tracked. I for one do not like the idea of a company determining which journals deserve inclusion, thus affecting our choice of journals to submit to.

The second concern is that some OA journals are expensive to publish in. This is especially true for the more prestigious OA journals. Even though such OA journals often provide cash-strapped authors the ability to request a cost deferment, the perception is that you generally need to allocate significant funds for publishing in OA journals. While this cost may be justifiable to an author for inclusion in a journal like PLoS Biology, because of the level of readership and visibility. However, there are other, new, profit-driven journals, which see the OA model as a good business model, with little overhead and the opportunity to charge $1000-2000 per article.

I think that, with the rise of Google Scholar, and tools to assess impact factors (e.g., Publish or Perish), assessing difference sources for articles is available. The second concern is a little more serious, and a broad-scale solution is not readily apparent.

Number of Open Access journals

Regardless, OA journals have proliferated in the past decade. Using the directory of biology OA journals, I show above that the majority of OA journals have appeared after 2000. Some of these have not been successful having faltered after a few volumes, such as the World Wide Web Journal of Biology which published nine volumes with the last in 2004. I am fairly confident that not all these journals could possibly be successful, but I hope that enough are. By having real OA options, especially higher-profile journals, research and academia benefit as a whole.

Which journals become higher profile and viewed as an attractive place to submit a paper is a complex process depending on a strong and dedicated editorial staff and emergent property of the articles submitted. I hope that researchers out there really consider OA journals as a venue for some of their papers and become part of the 'win-win' equation.

Wednesday, October 14, 2009

The Nobel prize and the grandeur view of life

As news of the latest Nobel prizes in physics and medicine were announced, science became a central story for many news outlets. Numerous stories and interviews were held about the discoveries that earned the laureates their just rewards. I’ve heard interviews with medicine winners, Elizabeth Blackburn and Carol Greider (2/3 of the prize, the other being Jack Szostak), about their discovery of telomeres and telomerase, and with Willard Boyle (for physics) on inventing an imaging semiconductor circuit (i.e., digital recording of light). The media play up the applications to humanity. Telomeres and telomerase offer a deeper understanding of cancer and potential treatments. The digital recording of light gave us digital cameras (among a plethora of other technologies).

However, in the interviews with these great scientists, there was a common thread in what they said. They reiterated the need to support basic science and that the pursuit of curiosity-driven science is a worthy and valuable enterprise. I found the fact that they found it necessary to reiterate this to be interesting and something that interviewers thought worthy of reiterating themselves. I know that news stories need to relate to a person’s everyday experience, but, I think, basic science offers something more. To quote Darwin “There is grandeur in this view of life”. That is, while the products of science have surely improved our quality of live, science has given us something deeper and more meaningful. Basic curiosity-driven research has changed our understanding of the world and our place in it. We now look up at the stars and have a pretty good idea of what they are. We know what causes thunder and lightening. We understand why our pet cat looks kinda of like a lion and gorillas like people. We no longer look to superstition and myth to explain these aspects of nature. To me, this is the fundamental contribution of science to humanity, and I wish this were as celebrated as technological advances. Though being able to take 2 gigabytes of photos and movies when my daughter is doing something cute is pretty cool too, I guess.

Friday, October 9, 2009

Blog your way to North Carolina!

(sorry for reiterating what you may have already seen)

Science in a web-base universe now has the potential to link vast numbers of researchers together and be communicated to the global citizenry. Exploring the power of the web in science is the fourth annual Science
Online 2010 conference, which will be held from Jan. 14-17 in the Research Triangle Park, NC. The conference is free, but of course you still must pay for travel and housing. Unless of course you've written an outstanding evolution blog post! NESCENT, the National Evolutionary Synthesis Center, is offering two $750 awards for the best evolution blog post about an evolutionary-oriented paper published in 2009.

For more details see the Deep-Sea News post. Be sure to tell your blogger friends!

Wednesday, October 7, 2009

Exotic plants integrate into plant-pollinator networks

ResearchBlogging.orgAt almost any spot on the globe, there are species present that are not native to that locale, having been transported by human activities. Whether and how exotic species impact communities is a multifaceted problem that requires understanding the multitude of direct and indirect species interactions that occur. In a paper published in the Proceedings of the Royal Society, B, Montserrat Vila and colleagues asked if exotic plants where integrated into plant-pollinator networks, and whether this integration had any observable impacts on these networks. This is an important question, as most ecological theory predicts that plant-pollinator networks are actually quite resilient to perturbations since most associations tend to be between generalists as opposed to the more susceptible specialists.

They studied invaded plant communities across Europe, observing pollinator visits to flowers in multiple 50 x 50 m plots. They calculated connectance as the number of interactions standardized by network size. They showed that exotics fully integrated into plant-pollinator networks. Exotic species accounted for 42% of all pollinator visits and 24% of all network connections -a testament to the overall abundance of exotics in many communities. However, these exotics did not affect overall changes in network connectedness, revealing that these networks are quite robust to invasions.

That said, researchers must now ask if this is true in networks that do contain high numbers of specialists (e.g., orchids) or if the relative few specialists in generalist-dominated systems are more susceptible to changes from exotics.

Vila, M., Bartomeus, I., Dietzsch, A., Petanidou, T., Steffan-Dewenter, I., Stout, J., & Tscheulin, T. (2009). Invasive plant integration into native plant-pollinator networks across Europe Proceedings of the Royal Society B: Biological Sciences, 276 (1674), 3887-3893 DOI: 10.1098/rspb.2009.1076

Friday, October 2, 2009

How to keep up on your favorite journals

Researchers live busy lives. Either you are spending your waking hours writing grant proposals, running experiments, analyzing data, writing papers, preparing lectures, supervising students, attending committee meetings, and not to mention taking care of your personal life. Often the activity that slips to the bottom of this list is keeping up on the current literature. How should one go about maximizing their ability to efficiently peruse recent publications. I think the best approach is to use journals RSS feeds (otherwise known as Really Simple Syndication). RSS is a web format that allows publishers to syndicate the abstracts of papers as they are published online.

The simplest way to do this is to make sure you have a Google account and use their Google reader. If you go to a journal's website you click on either of these symbols:

You'll be sent to their RSS feed page and at the top is a subscription option and you can select Google to subscribe using:

When you click on 'Subscribe Now', it prompts you to select the Google homepage or reader -I use reader, but that just depends on your preference. You can subscribe to as many Journals as you want, and I think that all the major ones have RSS set up. Then to keep up on recently published papers, you simply go to your Google reader and scroll through the journals you have RSS subscriptions. Or if you check it more often, the reader keeps a list of the most recent items from all your subscriptions. No more getting e-mail alerts and no more going to a bunch of different journal pages.

By the way, you can also subscribe to this blog in the same way (see 'subscribe to' links on side panel).

Friday, September 25, 2009

Global warming and shifts in food web strucutre

ResearchBlogging.orgPredicting the effects of global warming on biological systems is of critical importance for informing proactive policy decisions. Most research so far has been on trying to predict shifts in species distributions and changes in interactions within local habitats. But what many of these studies assume is that the basic biological processes and requirements of the individual species will not change -that is their biology is fixed and they simply need to find the place that best suits them. Not so, say Mary O'Connor and colleagues, in a just-released study in PLoS Biology.

O'Connor and colleagues experimentally warmed marine microcosms and tested two alternative hypotheses on food web structure: 1) that productivity increases with warming; and 2) warming increases metabolic rates, thus changing consumer-autotroph (i.e., primary producers) interactions. What they found was that warming indeed altered consumer-autotroph interactions. Warming increased base metabolic rates of consumers, as well as primary production, and the net effect was that food webs shifted towards increasing consumer control (i.e., top-down control).

What this research means is that global warming may alter food web interactions by increasing resource needs of organisms as their metabolic rates increase. This may increase the stress on communities and change diversity patterns as increased needs may shift competitive hierarchies or affect autotroph's ability to withstand consumer effects.

O'Connor, M., Piehler, M., Leech, D., Anton, A., & Bruno, J. (2009). Warming and Resource Availability Shift Food Web Structure and Metabolism PLoS Biology, 7 (8) DOI: 10.1371/journal.pbio.1000178

Monday, September 21, 2009

Everything but extinct: invasion impacts on native diversity

ResearchBlogging.orgThere has been a persistent debate in the plant invasions literature about whether exotic plant invasions are a major threat to native plant persistence. While there are clear examples of animal invasions resulting in large scale extinction -e.g., the brown tree snake or Nile perch, evidence has been ambiguous for plants. Most ecologists are not so sanguine as to actually conclude that plant invasions are not a threat, and I think most believe that plant invader effects are an issue of temporal and spatial scale and that the worst is yet to come.

In a forthcoming paper from Heinke Jäger and colleagues in the Journal of Ecology, Cinchona pubescens invasions on the Galápagos Islands were monitored in long-term plots for more than seven years. What they found was that there was a four-fold increase in Cinchona density as the invasion progressed and that this increase had measurable effects on native species abundance. While they did not observe any native extirpations in their plots, native densities decreased by at least 50%. Of the greatest concern was that Island endemics appear to the most susceptible to this invasion.

What these results show is that, while there were not any observed extinctions, there were serious deleterious changes to native diversity. Further, the native species, and especially the endemics, are now more susceptible to other invasions or disturbances due to their lower abundances. The impact of exotic invaders may not be readily apparent but may be a major contributor to increased extinction risk.

Jäger, H., Kowarik, I., & Tye, A. (2009). Destruction without extinction: long-term impacts of an invasive tree species on Galápagos highland vegetation Journal of Ecology DOI: 10.1111/j.1365-2745.2009.01578.x

Wednesday, September 9, 2009

BES day two...

It was a day full of talks, and I really enjoyed being able to spend the whole day just absorbing the presentations. Here are some highlights from today's events:

  • Ian Wright gave an interesting talk about the history of functional plant ecology. Basically, covering where trait ecology has been and where we are now. It is really amazing to see the truly large scale analysis and collaborations currently driving modern trait analysis.
  • In another overview type talk, Gerlinde De Deyn, talked about carbon sequestration in soils. I'm sure to many ecosystem ecologists this maybe well known, but I found it fascinating. Did you know that tundra ecosystem have as much soil carbon as tropical rain forests? The reason is that tundra has very slow process rates (cold) while rain forests have fast production rates. In fertilization experiments, soil carbon is reduced, so in order to manipulate soil carbon stores one must understand the interaction between plant traits and soil organisms.
  • Finally, Kyle Dexter, in a great field survey of Inga tree species in a region of Peru, showed that different functional diversity metrics show differing patterns of over- and under-dispersion. For example, phylogenetic diversity tends to be under-dispersed for Inga assemblages, while chemical and anti-herbivory traits are over dispersed and leaf size measures are under-dispersed.

Also, there was the annual general meeting, which was rather somber as three obituaries were read aloud. The three deceased, John Harper, Bob Jefferies and Simon Thirgood, were all superb ecologists who absences were obviously felt. Harper (my Master's advisor's advisor) and Jefferies (my colleague at Toronto) were both eminent ecologists with long and distinguished careers, while Thirgood (a fellow Senior Editor at the Journal of Applied Ecology) was in the prime of his very successful career.

Exploring ecology through GMOs

This year's Tansley Lecture at the BES meeting was a superb presentation given by Ian Baldwin from the Max Planck Institute for Chemical Ecology. He was enjoyable to watch as his folksy, mid-western American style disarmed the listener and leaving them unprepared for his ascorbic wit and, at times, controversial message. Prof. Baldwin* is a chemical ecologist who studies plant biochemical and physiological processes and their interaction with herbivores. Through his use of molecular tools and superb natural history, he has gained new insights into how and why plants respond to herbivory. He has discovered the pathways allowing wild tobacco, Nicotiana attenuata, to detect chemicals in tobacco hornworm spit and the resulting chemical defense response. More than this though, part of his talk was about the use of transformed plants to study this plant defense response. Using genetic tools, his group was able to knockout certain segments of these biochemical pathways in order to determine how various chemicals affected hornworms. He showed chemical responses involved signaling hornworm predators whereas other responses directly targeted wornworm's ability to digest plant material.

I think that ecologists are often wary of GMOs and his talk was a convincing case for their use in basic research, and he advocated for a more reasoned approach to their use.

*Note: He has run into trouble with German authorities over using the title 'Dr.' -see here.

Monday, September 7, 2009

An ecological meeting, British style.

I'm in Hatfield, outside of London, for the British Ecological Society (BES) meeting, and I'll be blogging thoughts, happenings, etc. I posted several observations from the American equivalent (ESA) last month, and one thing is readily apparent, even though talks do not start until tomorrow. While the ESA meeting is a great chance to meet a lot of people and see a lot of talks, at a few thousand conference goers, it can be a bit overwhelming. At any given time the ESA meeting had up to 26 concurrent sessions, which makes for a lot of running around if there are talks you want to see in different sessions. At the BES there is a maximum of 7 concurrent session. The BES is definitely smaller than ESA and the meeting and venue feel compact and intimate. I'm looking forward to experiencing the BES meeting this week.

Check back for more.

Wednesday, September 2, 2009

Ecology and evolution jobs 2009

After a horrendous year of canceled job searches and a barren landscape lacking many opportunities for academic-track job seekers, the jobs posted this season seem to be a stark contrast. In a previous post, I blogged about the best ecology job wiki, and when you look through last year's job postings you notice that the 'updates' column contains a multitude that had their searches canceled. Most people assumed that there wouldn't be very many tier-one academic jobs this year, but looking at the list of jobs announced so far this year, things look pretty good! I've also caught wind of a few other positions at good institutions that have not yet advertised. Job seekers keep your eyes open, and definitely check the job wiki regularly. This could be your year!

I for one have been (overly) optimistic and really didn't buy the hype that the job market would crash this year and for the foreseeable future. I think that many institutions over-reacted to the recession. Of course some states, like California, are in absolute dire straights. But my feeling is that over the next couple of years many institutions will try to recover from their self-imposed professor deficits, meaning that many similar-sounding job searches will be active at the same time. The net result is that schools will be competing against one another for good researchers.

Tuesday, August 25, 2009

March of the polyploids!

ResearchBlogging.orgSpeciation by polyploidy (see here for a general description of polyploidy) is one of the mechanisms of speciation and evolutionary diversification. We all learn about it in Bio 101, right after allopatry and sympatry. It is thought to be an especially important driver of speciation in plants, and anecdotal evidence, such as the origination of the invasive polyploid, Spartina anglica in the UK in the 1800's, reinforced that view. But how important has been unanswered until now.

In a new publication in PNAS by Wood et al. -from the Loren Rieseberg lab (one of the best lab homepages BTW) this questions has been answered. The authors go through all available chromosome counts on the Missouri Botanical Garden's Index to Plant Chromosome Numbers, and assess the proportion of polyploid species. They find that about 15% of all angiosperm speciation events coincided with an increase in chromosome number (and about 30% of fern species). Further, about 35% of all genera contain polyploids. Looking across the phylogeny of major plant groups, they find that all major lineages, except Gymnosperms, have significant proportions of polyploids (again with ferns have the greatest proportion). Polyploidy is a ubiquitous feature of plant diversity and a major driver of plant speciation. And now we can quantify just how important.

Wood, T., Takebayashi, N., Barker, M., Mayrose, I., Greenspoon, P., & Rieseberg, L. (2009). The frequency of polyploid speciation in vascular plants Proceedings of the National Academy of Sciences, 106 (33), 13875-13879 DOI: 10.1073/pnas.0811575106

Tuesday, August 18, 2009

Unifying invader success and impact

ResearchBlogging.orgSomething that has continuously bothered me about our collective narrative concerning invasions has been the conflicting processes determining invader success and impact. Numerous studies (including some of my own) show that invaders are successful often because they are different from residents. That is, they are thought to occupy some unique niche. However, occupying a unique niche means that competition is minimized and these successful invaders should have relatively low impact on residents. Conversely, species that have large impacts are thought to be superior competitors, but why are they able to be so successful?

In a new paper in the Journal of Ecology, Andrew MacDougall, Benjamin Gilbert and Jonathan Levin use Peter Chesson's framework where ability for two species to coexistence (or conversely the strength of competitive exclusion) is a process relative to two factors -the magnitude of fitness differences and the degree of resource use overlap. Here competitive exclusion is rapid if species have a large fitness difference and high resource overlap, and slow if fitness differences are low. Species that are successful because of reduced resource overlap likely have little impact unless there are large fitness inequalities.

If we then view the invasions process on a continuum (see figure), then by determining basic fitness and resource use, we can predict success and impact. This is an exciting development and I hope it inspires a new generation of experiments.

MacDougall, A., Gilbert, B., & Levine, J. (2009). Plant invasions and the niche Journal of Ecology, 97 (4), 609-615 DOI: 10.1111/j.1365-2745.2009.01514.x

Thursday, August 6, 2009

Macroecology is dead, long live macroecology!

I went to a session on a macroecology yesterday, which featured some wonderful speakers, and came away with an unsure feeling about this field. The Session started off with a fantastic talk by Rob Dunn on how macroecologists differ on what the main mechanisms are for explaining diversity patterns. He argued that perhaps the complexity of natural and human-altered systems make simple generalizations not very fulfilling. Next Lauren Buckley showed how species turnover had complex relationships with broad environmental changes and that species turnover patterns are better correlated with other species turnover then with the environmental variables we think drive the patterns. Next Brian McGill tried to make the case for a truly unified theory. He walked through several general models of random species packing, showing that some models fit observed data very well. I was impressed by the data/model fits but am skeptical of a general theory which lacks biological mechanisms. My view of a scientific theory is that it ought to contain basic mechanisms and that a unified theory should explain patterns and processes at multiple scales. That said, I also think McGill has done more to forward the field than almost any other younger ecologist. In Allen Hurlbert's talk, he nicely showed how independently accounting for energy and area can provide a better basis to constructing and understanding species-area relationships. The basic reason is that area and energy availability differentially affect the number of individuals.

Back to my real life tomorrow!

Wednesday, August 5, 2009

Pleasant invasions surprise

Normally I run around ESA looking for talks that have the best potential to inform or entertain me. This time around I decided to go to a session on invasions and communities and settle in for the long haul. Am I glad I did. I was afraid the session would be dominated by similar sounding talks, but instead each talk was wildly interesting and different. Talks included looking at the genetic variability of the dominant native resident as a proxy for niche preemption. Another good one looked at the role of propagule pressure for an understory invasion into tropical dry forests -I seldomly hear about invasions into these ecosystems. Next was a look at how invaders behave over long term successional trajectories and they by and large appear to follow native trends. Next was a great modeling talk where individual-based models and riverine networks were used to assess the role of distrubance and trait differences in invasion dynamics. The final one I saw was on how to potentially restore Californian serpetine plant communities using little more that gravel and a few chemicals, with the goal of reintroducing extirpated butterflies, which have not been able to cope with the shift to exotic-dominated grasslands.

I am looking forward to more great talks!