Friday, February 27, 2009

Peace and conservation biology


A recent study published in Conservation Biology found that conservation hotspots are also hotspots for wars. Most of the wars (90%!) from 1950 to 2000 have been on countries that have these key areas for conservation, and 80% of these conflicts took place directly within the conservation hotspots. The authors mention many problems, such as the destruction of vegetation (i.e. the application of Agent Orange to detect enemies), poaching by soldiers, or that the cost of war could come at the expense of other government projects, such as conservation programs. But, there is not all bad news regarding biodiversity conservation (of course is Always bad news for humans), since these wars have created spaces with very low human impact (such as buffer areas with no human activity), or reduces economic activity that can make wartime a recovery period for some exploited species, and other unique situations. They conclude that since most of our biodiversity is in unstable regions, plans to conserve biodiversity should be also active in these regions, which are not the most appealing to work in, but may the most important. Also, that we need to integrate conservation biology into military and humanitarian programs that operate in these conflict zones.

These news are really sad, and I hope that we can live in peace for the benefits of all the species living in here (including, of course, Homo sapiens).

THOR HANSON, THOMAS M. BROOKS, GUSTAVO A. B. DA FONSECA, MICHAEL HOFFMANN, JOHN F. LAMOREUX, GARY MACHLIS, CRISTINA G. MITTERMEIER, RUSSELL A. MITTERMEIER, JOHN D. PILGRIM (2009). Warfare in Biodiversity Hotspots Conservation Biology DOI: 10.1111/j.1523-1739.2009.01166.x

Sunday, February 22, 2009

The incredible spreadable weeds

ResearchBlogging.orgResearch into the spread of non-native species usually assumes a long time lag between introduction and rapid spread, and many studies cite 50 years as the lag time. The reason for believing this is that it is thought that there needs to be sufficient time for adaptations to fine tune the fit between the exotic and its new environment, or that densities are so low to start with, finding mates and buffering populations from stochasticity (i.e., Allee effects) takes time. However, Curtis Daehler at the University of Hawaii, collected information on purposeful plant introductions into Hawaii in the 1920s. 23 of those planted have become serious invaders and the herbacious species showed a lag time of 5 years and 14 years for woody species. Knowing that lag times can be much shorter then we previously thought means that monitoring and management activities need to much more aggressive. It seems we can no longer assume a period of relative safety after a new species in introduced, new records of non-natives needs to be followed active assessment and perhaps intervention.

Curtis C. Daehler (2009). Short Lag Times for Invasive Tropical Plants: Evidence from Experimental Plantings in Hawai'i PLoS ONE, 4 (2) DOI: 10.1371/Journal.pone.0004462

Friday, February 20, 2009

Increased access to science, but who gets to publish?

ResearchBlogging.orgWhat role will open access (OA) journals play as science publishing increasingly moves to the internet and involves a more diverse array of participants? In a recent short article in Science, Evans and Reimer tried to answer this using citation rates from 8253 journals and examine trends in citation rate shifts. They found that researchers from wealthier countries were not likely to shift to citing OA journals while researchers from poorer countries did. The authors conclude that the overall shift to citing OA journals has been rather modest, but these journals have increased inclusion for researchers at institutions in poorer countries that cannot afford commercial subscriptions. However, there is an unfortunate flip side to the OA model -paying to publish. Most OA journals recoup the lack of subscription earnings by placing the financial onus on to the publishing scientists. This means that while researchers from poorer countries can now read and cite current articles in OA journals, they still are limited from publishing in them. True, most OA journals allow for deferring costs for researchers lacking funds, there is usually a cap to the frequency in which this can be done.

J. A. Evans, J. Reimer (2009). Open Access and Global Participation in Science Science, 323 (5917), 1025-1025 DOI: 10.1126/science.1154562

Wednesday, February 18, 2009

Functional traits and trade-offs explain phytoplankton community structure


After attending the presentation by Elena Litchman at the ASLO Aquatic Science Meeting in Nice three weeks ago I came across this paper. Although it was published already two years ago, this works need to be highlighted! Marine phytoplankton is important. It contributes approximately 50% to world primary productivity. Among other factors phytoplankton communities are structured by competition for limiting nutrients (mainly for nitrate and ammonia) in the ocean. Litchman et al. base their paper on the presumption that phytoplankton organisms can achieve higher competitive ability (Tilman’s R*) by different strategies. That is, the organisms can either increase their maximum nutrient uptake and/or growth rate or they decrease the minimum cell quota, the half saturation constant for nutrient uptake and/or their mortality. Litchman et al. tested if they can find constraints and trade-offs on the evolution of better competitive abilities (lower R*) in major phytoplankton groups. Specifically they asked if there is a positive relationship between maximum growth rate and R* which would show a gleaner-opportunist trade-off.
The authors show positive relationships between measurements for growth and nitrate uptake which can constrain the evolution on competitive ability. Indeed major groups of phytoplankton group along these trade-off curves. Whereas coccolithophores e.g. show low nitrate uptake rates and low half-saturation constants, diatoms and dinoflagelates show the opposite nitrate uptake strategy with high uptake rates and high half-saturation constants. A gleaner-opportunist trade-off, i.e. a positive correlation between maximum growth rates and R*which would result in a super species, could not be found across major groups but within the diatoms. The paper gives more results about trait differences among taxonomic groups and allometric scaling relationships. Trade-offs and different strategies in nutrient uptake are discussed in a very concise way either from a mechanistic physiological view as well as from the evolutionary history perspective.


Elena Litchman, Christopher A. Klausmeier, Oscar M. Schofield and Paul G. Falkowski (2009) The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level. Ecology Letters. DOI: 10.1111/j.1461-0248.2007.01117.x

Sunday, February 15, 2009

The next generation of invasive plants

The study of plant invasions has usually focused on plants adapted to colonizing areas immediately after a disturbance (early successional species or “weeds” by some definitions). An example of this, is the seminal work of Herbert Baker, with his list of traits to explain why some species become weeds and others do not (e.g. fast growth, production of lots of seeds, good dispersal.). So why do late-successional species (for example, forest understory species) not invade? The answer is: we did not look close enough - they indeed invade!! This is the point of a paper by Patrick Martin and collaborators, who study forests – which are usually known as “invasion resistant systems” – and the colonization of exotic shade-tolerant species in them. Their central point is that there have been larger numbers of introductions of early successional species compared to late successional species (or shade tolerant), and that forest dynamics are much slower than other systems (e.g. a forest gap must be created for a species that need disturbances to colonize). And it is for these reasons that we associate invasive plants solely with early successional species, and we see forests as invasion-resistant systems. We are now observing many highly invasive plants that are not disturbance dependent. These may be a lot harder to control and could have important detrimental effects on native communities.

Patrick H. Martin, Charles D. Canham, Peter L. Marks (2009). Why forests appear resistant to exotic plant invasions: intentional introductions, stand dynamics, and the role of shade tolerance Frontiers in Ecology and the Environment DOI: 10.1890/070096

Friday, February 13, 2009

40% believe in evolution, but only 25% do not!

Gallup released a poll, that coincides with Darwin's birthday, which examines American's belief in biological evolution. It is a great poll, breaking down belief patterns across education attainment, age , religiousness, etc.

However, several reports and blogs about this poll disparage Americans for their lack of scientific sophistication, but I think that the results are far more positive then I would have guessed. Only 25% outright deny evolution! I would have thought a clear majority would take this stance as was shown in 2005. A further 36% do not have an opinion, and as scientists and educators, these folks are the reason why we educate and hold events like Darwin Day. Thank you to all those who work so tirelessly promoting science education and literacy, like those at NCSE.

Wednesday, February 11, 2009

Charles Darwin, founder of evolution AND ecology

Perhaps a good alternative title should be: “Why we need a second modern synthesis”

Darwin is rightfully seen (or vilified in some quarters) as the founder of modern evolutionary biology. He gave the naturalists of that era an observable and testable mechanism explaining species change and for understanding the similarities and differences among species. As we celebrate Darwin’s 200th birthday and the 150th anniversary of the publication of the Origin of the Species, it seemed right to think about Darwin’s contributions beyond just evolutionary change, namely ecological patterns and processes.

I’ve read Origin probably half a dozen times now and as an ecologist, I am always amazed by the depth and breadth of Darwin’s insights. Every time I read it, there are passages that directly relate to what I happen to be thinking about or working on at the time, which leads me to the conclusion that he thought a lot about what scientists would come to call ecology. Though the word “ecology” wouldn’t be invented for another seven years (by Ernst Haeckel in 1866) and the first ecology text book didn’t appear until 1895 (by Eugenius Warming, and which includes interesting Lamarckian invocations in the last chapter), Darwin thought and wrote about ecology extensively.

In the Origin (1st edition), Darwin makes predictions about ecological patterns. On page 109, he states, “a … larger number of the very common and much diffused or dominant species will be found on the side of larger genera”. That is community dominance likely relays on inherited traits linked to species success. This certainly sounds like the result of some recent, interesting papers (e.g., Strauss et al.*).

Almost the whole discussion in the Struggle for Existence chapter is about ecological interactions and the severity of negative interactions, which stems from the fact that populations, if unchecked, will increase exponentially (i.e., page 116). We all know from work by ecologists such as Connell and Huston that those negative, deterministic interactions can be overridden by non-equilibrium processes, especially disturbances. Here again Darwin’s observations lead him to this conclusion; “If turf which has long been mown …be let to grow, the more vigorous plants gradually kill the less vigorous” and he observes that diversity in a plot goes from 20 species to 11 when the disturbance is removed.

Further, we often think of Darwin’s view of the environment as a selective pressure (e.g., fur thickness), but he also saw the environment as a determinant of species interactions. Lush places support a lot of species and the control of populations is due to competitive interactions, whereas in harsh places, populations are controlled by “injurious action” of the environment (e.g., page 121). Thus there is a shift from biotic to abiotic controls on ecological processes.

I think that we have collectively forgotten that evolution directly informs our expectations and predictions of ecological patterns and processes. While ecological geneticists drove much of the modern synthesis in the mid 1900’s by incorporating ecology (namely selection) into evolutionary processes, the reverse, bringing evolution into ecology is only now really starting to happen. Lets hope this second modern synthesis completes Darwin’s vision.

Monday, February 9, 2009

Stability begets diversity

ResearchBlogging.orgA classic hypothesis to explain the high diversity found in tropical rain forests is that areas within the tropics served as climatic refuges during Pleistocene global climate fluctuations (e.g., ice ages). These refuges beget diversity because they face much lower extinction rates then non-refuges and they are older, allowing speciation events to accrue. This hypothesis has proven controversial as evidence has been circumstantial and circular (i.e., high diversity areas are taken as evidence of a refuge and the outcome of a refuge is high diversity.).

This conundrum has been solved by Ana Carnaval, a postdoctoral researcher in Craig Moritz's lab at UC Berkeley, and colleagues. They use patterns of diversity to identify probable refuges and then support several independent hypotheses about refuge effects on patterns of frog diversity. They show 1) that there is higher genetic diversity within and among refuge populations relative to non-refuges. 2) They show a multi-species pattern of recent population expansion in non-refuges from adjacent refuges. 3) The absence of isolating divergence in non-refuges because of a lack of time. Finally, 4) strong phylogenetic patterns of between refuge structure, indicating periods of isolation and divergence.

This paper reveals that hypotheses about the origin of species diversity in hotspots can be tested by using genetic divergence below the species level. Not only does this strongly support the spatial refuge hypothesis for tropical diversity patterns but it also elegantly intertwines microevolutionary processes with macroevolutionary patterns. There couldn't have been a more appropriate study published in the week before Darwin's birthday.

A. C. Carnaval, M. J. Hickerson, C. F. B. Haddad, M. T. Rodrigues, C. Moritz (2009). Stability Predicts Genetic Diversity in the Brazilian Atlantic Forest Hotspot Science, 323 (5915), 785-789 DOI: 10.1126/science.1166955

Sunday, February 8, 2009

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.

Friday, February 6, 2009

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

Tuesday, February 3, 2009

Local extinctions reveal metacommunity dynamics.

ResearchBlogging.orgMetacommunity 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

Monday, February 2, 2009

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...