Shortening the R curve

I am a strong proponent of R for all data management, analysis and visualization. It is a truly egalitarian analysis package -open source and community-contributed analysis packages. The true power comes from complete control and automization of your analyzes as well as publicly accessible new functions created by members of the community. However, the drawback for a lot of people has been the rather steep learning curve, as with any programing language. But there are now a plethora of good books available that help shorten this curve. The Human Landscapes blog as reviewed and ranked introductory and reference R books, which should serve as an invaluable resource for those striving to become aRgonauts.

Don’t miss the mechanism when testing for biodiversity effects

Variation in the strength of diversity effects among experimental studies raise the question when and where consequences of diversity loss is strongest. As in grassland experiments, diversity effects on plant biomass production can be observed in systems with marine macroalgae. However, even among marine macroalgae experiments variation in the strength of the diversity effect cannot be explained because of largely differing experimental set-ups (i.e. long-termed vs. short-termed studies, mesocosms vs. field experiments, using inter- or subtidal habitats). From literature Stachowicz et al. assumed that short termed factors regulating diversity effects in such systems could be attributed to spatial complementarity in photosynthesis rates or different limiting nutrients. Long-term regulating factors could be attributed to habitat differentiation, temporal complementarity, fascilitation, recruitment and natural heterogeneity of substrate. In a very elegant way Stachowicz and his co-workers tested whether mechanisms responsible for diversity effects change with experimental procedure and/or study type within the same marine algae system. In a series of three experiments, that is a short-termed mesocosm with transplanted thalli, a short-termed (two month) field-experiment with naturally recruited thalli and heterogeneous substrate, and in a long-term (three years) field-experiment, the authors were able to show that strong diversity effects are positively correlated with experimental duration, environmental heterogeneity and population responses (recruitment). Whereas in the mesocosm species identity affected biomass production, in the field studies it was species richness but not identity. Fractional change of species biomass could be explained by species identity in the mesocosm, and by both identity and richness in the field. The authors are making an important point by showing that mechanisms for diversity effects are not exclusive but occur together and become stronger over time. They conclude that the absence or the detection of only weak diversity effects in short-termed experiments does not necessarily mean that there is no effect because such approaches detect only a limited number of potential mechanisms.


John J. Stachowicz, Rebecca J. Best, Matthew E. S. Bracken, Michael H. Graham (2008). Complementarity in marine biodiversity manipulations: Reconciling divergent evidence from field and mesocosm experiments. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0806425105

Local extinctions reveal metacommunity dynamics.

Metacommunity dynamics (i.e., that dispersal limitation among locales creates spatially-contingent community processes) have been in vogue over the past half-decade. Many of the advances in this field have come from theoretical models, computer simulations, artificial laboratory assemblages of micro-organisms (with yours truly being a major offender) and field experiments using small-bodied, short-lived organisms. An oft-repeated criticism has been that the necessary conditions for metacommunity processes are what are manipulated in simulations or lab tests and that simple extinction-colonization dynamics are rarely observed for larger, longer-lived organisms. In a recent paper by Kevin Burns and Christopher Neufeld, high levels of extinction and colonization are shown in patchy communities of woody plants. They sampled 18 islands off the west coast of Canada in 1997 then again in 2007 and found that substantial numbers of local extinctions were observed. These results reveal that what we often think of as relatively stable communities (woody plant species) are actually quite dynamic, creating the conditions were metacommunity processes are an important mechanisms driving patterns of diversity. They further show that communities with greater exposure to ocean storms had higher extinction risk and species with hardier leaves were less prone to local extinctions.

Kevin C. Burns, Christopher J. Neufeld (2009). Plant extinction dynamics in an insular metacommunity Oikos, 118 (2), 191-198 DOI: 10.1111/j.1600-0706.2008.16816.x

I have one of the worst jobs in science!

According to Popular Science's annual ranking of the worst jobs in science, I (no really me!) have one of the worst jobs. They list scientists doing triage -that is having to evaluate which species to save given that we can't save all, as being particularly crummy. They specifically cite my study of phylogenetic uniqueness and ecosystem function as an example. Well I guess it is a little depressing to try to evaluate which species should be saved over others, but I don't think it is as bad as a medical waste burner...

Small experimental plots predict entire ecosystem responses! (if you work in peatlands…)

The possibility of extrapolating results from experimental plots to larger (or “real”) scales is a major issue in ecology. For several reasons ecologists conduct manipulative experiments in relatively small experimental units. This that has been suggested to be a big problem since the effect of the studied factor could change with spatial scale. An example of this can be found in biological invasions where there is some evidence that the more species you have at a small scale (e.g. a plot), the less likely an exotic can invade; but, at the regional level, the more species there are, the more likely that exotics can invade, so invasion has a scale-dependent response to species richness. However, if you work on peatlands you are very lucky! A recent paper by Magdalena Wiedermann and collaborators found that in peatlands, experiments in 2 x 2 meter plots represented really well what was happening at the entire ecosystem level. They compared a manipulative experiment where they added nitrogen at different concentrations, with an observational study in a region with gradient of nitrogen concentrations similar to the ones used in the experiment. They found that cover of Sphagnum and vascular plants could be explained by the levels of nitrogen equally well at plot and regional scales

Magdalena M. Wiedermann, Urban Gunnarsson, Mats B. Nilsson, Annika Nordin, Lars Ericson (2009). Can small-scale experiments predict ecosystem responses? An example from peatlands Oikos DOI: 10.1111/j.1600-0706.2008.17129.x

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.