Monday, December 26, 2011

Rumors of community ecology’s death were greatly exaggerated: reflections on Lawton 1999

In 1999, John Lawton, eminent British ecologist, published a lament for the state of community ecology entitled “Are there general laws in ecology?” Cited more than 600 times, Lawton’s paper forced a re-evaluation of community ecology’s value, success, and even future existence. Other scientists at the time seemed to agree, with papers starting with phrases like “Although community ecology is a struggling science…” and “Given the lack of general laws in ecology…”. Lawton appeared to be suggesting that community ecology be abandoned for the generality of macroecology or the structure of population ecology.

An important point to be made is that Lawton was simply making a particularly public expression of ecology’s growing pains. In 1999, ecology was at a crossroads between the traditional approach of in-depth system-based study, and a fairly single-minded focus on competition as an explanation for patterns (e.g., Cooper 1993 ‘The Competition Controversy in Community Ecology’ Biology and Philosophy 8: 359-384), while at the same time there were emergent approaches and explanations like neutrality, macroecology, spatial ecology, ecophylogenetics, and improved computer and molecular methods. There was also growing dissent about ecology’s philosophical approach to ecology (e.g., Peters 1991 ‘A Critique for Ecology’; Haila and Heininen 1995 ‘Ecology: A New Discipline for Disciplining’ Social Text 42: 153-171): ecologists tended to ignore the Popperian approach, which required falsification of existing hypothesis, instead tending to look for support for an existing hypothesis, or at least advocated looking for patterns without considering alternative mechanisms. Not only this, but the applications for ecology were more clear than ever – the Intergovernmental Panel for Climate Change was meeting , and the ecological consequences of human actions were perhaps more obvious they had ever been. But ecologists were failing at providing solutions –Lawton argued-correctly-that in 1999 ecologists could provide little insight into how a community might change in structure and function in response to changing climate.

Although everyone should read Lawton’s paper, a simple synthesis of his concerns would be this – that community ecology is too contingent, communities are too complex, and therefore community ecology cannot formulate any laws, cannot make predictions, cannot be generalized from one system to another. This makes community ecology suspect as a science (physics being the most common example of an “ideal” science), and certainly not very useful. Lawton suggests that population ecology, where only a few models of growth could explain the majority of species’ dynamics, or macroecology, which focuses on the most general, large-scale patterns, were a better example of how ecology should be practiced.

Community ecology, rather than dying, has experienced an incredible surge in popularity, with a large contingent represented at meetings and in journal publications. Ecology itself is also thriving, as one of the fastest growing departments in universities. So what, if anything, has changed? Has ecology addressed Lawton’s criticisms?

Two major things happened in the late 1990’s and early 2000’s, which helped ecologists see beyond this general malaise. The first was that a number of well-thought out alternative ecological mechanisms explaining community membership were published. Before the late 90’s community ecologists looked for evidence of competition in patterns of community composition, either among locales or through time following disturbance. When local competition was insufficient to explain patterns, researchers likely cited, but did not test other mechanisms. Or if they did test other mechanisms, say predation, it was as an alternative, mutually exclusive mechanism. The new publications, drawing on previous ideas and concepts formalized assembly mechanisms like neutral processes or metacommunity dynamics where uneven fitnesses in a heterogeneous landscape can affect local coexistence. More than these as solely alternative mechanisms, these allowed for a synthesis where multiple mechanisms operate simultaneously to affect coexistence. Probably the most emblematic paper of this renewed excitement is Peter Chesson’s 2000 ‘Mechanisms of maintenance of species diversity’ published in Annual Reviews of Ecology and Systematics. This paper, cited over a thousand times, offers a way forward with a framework that includes competitive and niche differences but can also account for neutral dynamics.

A second major development that rejuvenated ecology was the formation of technological and statistical tools engendering broad-scale synthetic research. Suddenly the search for general explanations – Lawton’s most piercing criticism - became more common and more successful. With the advent of on-line databases, meta-analytic procedures and centers (e.g., the National Center for Ecological Analysis and Synthesis) that foster synthetic research, ecologists routinely test hypotheses that transcend local idiosyncrasies. Often, the capstone publication on a particular hypothesis is no longer a seminal experiment, but rather a meta-analysis that is combines all the available information to assess how strongly and how often a particular mechanism affects patterns.

While these theoretical and technological developments have been essential ingredients in this ecological rejuvenation, there has also been a subtle shift the philosophical approach to what it is ecological theory can and should do. Criticism in the 1990’s (e.g., Peters 1991 ‘A Critique for Ecology’) centered on the inability of ecological theory to make accurate predictions. The concept of science common in ecology in the 1990’s was that a rigorous, precise science (i.e., with laws) results in the ability to accurately predict species composition and species abundances given a set of mechanisms. This view of ecological science has been criticized as simplistic ‘physics-envy’ (e.g., see Massimo Pigliucci’s PhD dissertation ‘Dangerous habits: examining the philosophical baggage of biological research’published by the University of Tennessee in 2003). The subtle philosophical change has been a move from law=prediction to law=understanding. This is as true for physics as it is for ecology. We don’t expect a physicist to predict precisely where a falling feather will land, but we do expect to totally understand why it landed where it did based on fundamental processes. (for more on the contrast of prediction and understanding, see Wilhelm Windelband’s nomothetic and idiographic knowledge)

While the feather example above is simplistic, it is telling. In reality a physicist can produce probability contours of where the feather is likely to land, which could be very focused on a calm day or broad on a windy one. This is exactly what ecologists do. Once they understand how differing mechanisms come together to shape diversity, they make probabilistic predictions about the outcome of a set of known mechanisms.

Ecology today is as vibrant as ever. This is not a result of finding new laws that proved Lawton incorrect. Rather, ecologists now have a more sophisticated understanding of how various mechanisms operate in concert to shape diversity. Moreover, conceptual, technological and philosophical revolutions have fundamentally changed what ecologists do and what they are trying to explain. It is a great time to be an ecologist.

Lawton, J. H. (1999). Are there general laws in ecology? Oikos, 84(2), 177-192.

By Marc Cadotte and Caroline Tucker

Sunday, December 18, 2011

holiday caRd

I wasn't planning on making any more "caRds", but since I received a number of requests, find below a holiday card from the EEB & flow. For optimal viewing, perhaps throw some Jingle Bells on in the background.

This code relies heavily on the rgl package in R. Be sure to run the first line of code to install this package if you don't already have it. 

###holiday caRd

#install "rgl" package if necessary:

#load library


##Plot card
text3d(matrix(c(0.54,-100,300),ncol=3),text="Happy Holidays",font=5,cex=1.9,color="darkred",adj=c(0.5,1))
text3d(matrix(c(0.54,75,-780),ncol=3),text="a Happy New Year",font=5,cex=1.9,color="darkred",adj=c(0.5,1))

##Play card
for(i in 1:10){
plot3d(X,Y,Z,col=c("yellow","red"),type="s",radius=4,add=TRUE) } }
text3d(matrix(c(0,140,-900),ncol=3),text="From the EEB & Flow",font=1,cex=1.0,color="darkgreen",adj=c(0.5,1))

##The rgl device window allows you to use your mouse to manipulate the plot in 3-dimensions, so feel free to do so before closing it.

You can also access the script here.

Thursday, December 1, 2011

What should be the basic unit of community ecology, 2011.

Why intraspecific variation matters in community ecology Bolnick et al. 2011, Trends in Ecology and Evolution.

Intraspecific variation in gastropod
shell morphology (Goodrich 1934).
 There has been a long debate in community ecology on the fundamental unit, a debate on what Tansley described as the “necessity of first determining empirically our natural units”. In early years, it involved tension between Clements' and Gleason’s view of the plant community, either as a “superorganism” or simply as a conglomeration of co-occurring species. This latter, Gleasonian view won out, signaling a move towards the species-oriented approach that dominates community ecology today. In later years, there was a push to view the individual—not the species—as the fundamental unit, championed by people like Dan Simberloff. However, though this view has had some influence, it has never been mainstream.

 The basis of these debates about the basic unit is simple: do similarities matter more than differences? Recently, the argument that intraspecific differences are important and that community ecology should consider individuals has become much stronger. In “Why intraspecific variation matters in community ecology”, Bolnick et al. suggest that a species-level view of community ecology is an incomplete one, and that we should be aware of making simplifying assumptions about intraspecific variation (e.g. that it is minimal and species-level means are appropriate). Bolnick et al. state their hypothesis clearly:
  “… many models of species’ interactions implicitly assume that all conspecific individuals are effectively interchangeable. In this paper we argue that this assumption is misleading and that intraspecific trait variation can substantially alter ecological dynamics.” 
 To that end, the paper does an excellent job of identifying the key mechanisms by which intraspecific variation might be expected to alter ecological dynamics (especially as summarized in the paper's Table 1). Some of these mechanisms might be fairly ubiquitous. For example, when there are nonlinear relationships between trait values and interaction strengths, Jansen’s Inequality means that the amount of intraspecific variation around the species mean will alter the strength of that interaction. The mechanisms discussed make a convincing argument that intraspecific variation can alter ecological interactions and evolutionary dynamics.

However, a move to individual level ecology has many practical implications*: for example, it would require that we move beyond using average species-level demographic rates, dispersal abilities, and interaction strengths, since these miss important intraspecific variation; that phylogenetic trees be built to the level of the individual, requiring additional genetic information; and that perhaps fundamental changes be made to current coexistence theory. Possibly this would mean many more hours of fieldwork, more complex theory, and much more explanatory power is required. On the other hand, it could mean breakthroughs in how we understand longstanding ecological problems like ecosystem functioning, species diversity and coexistence, or trophic web structure.

For that reason, the fact that Bolnick et al. doesn’t demonstrate very clearly the gains or breakthroughs that could result from including intraspecific differences is a bit of a disappointment. Will we find that increasingly smaller amounts of variation are explained as we divide our units increasingly smaller? Or is the key to explaining community-level interactions found at the individual scale? Most of the examples in this paper are too simplistic to be useful, and for understandable reasons of space, there is little review of the literature (though they cite a number of important papers). That’s really too bad, since there are some subfields that have focused on intraspecific differences (for example, the ecosystem functioning literature), and their findings would contribute to the question of what makes intraspecific differences so promising for community ecologists. Despite that, when the mechanisms presented in Bolnick et al. are considered in combination with papers such as Crutsinger et al. 2006, Clark et al 2010, Albert et al. 2011, and Schindler et al. 2010 (just as a few examples), there is some tantalizing evidence suggesting that intraspecific variation can and does matter.

 *Although no doubt similar concerns about workload have accompanied any shift in approach throughout ecology's history. And certainly most shifts in ecological approach (spatial, phylogenetic, etc) only occur once the necessary methodological infrastructure was in place.