Wednesday, June 21, 2017

What do we mean when we talk about the niche?

The niche concept is a good example of an idea in ecology that is continually changing. It is probably the most important idea in ecology that no one has yet nailed down. As most histories of the niche mention, the niche has developed from its first mention by Grinnell (in 1917) to Hutchinson’s multi-dimensional niche space, to mechanistic descriptions of resource usage and R*s (from MacArthur’s warblers to Tilman’s algae). Its most recent incarnation can be found in what has been called modern coexistence theory, as first proposed by Peter Chesson in his seminal 2000 paper.

Chesson’s mathematical framework has come to dominate a lot of discussion amongst community ecologists, with good reason. It provides a clear way to understand stable coexistence amongst local populations in terms of their ability to recover from low densities, and further by noting that those low density growth rates are the outcome of two types of processes: those driven by fitness differences and those driven by stabilizing effects that reduce interspecific competition relative to intraspecific competition. Many of the different specific mechanisms of coexistence can be classified in terms of this framework of equalizing and stabilizing effects. “Niche” differences between species in this framework can be defined as those differences that increase negative intraspecific density dependence compared to interspecific effects. If, as a simplistic example, two plant species have different rooting depths and so access different depths of the water table, then this increases competition for water between similar root-depth conspecifics relative to interspecific competition. Thus, this is a niche difference. Extensions on modern niche theory have offered insights into everything from invasion success, restoration, and eco-phylogenetic analyses.

But it seems as though the rise of 'modern coexistence theory' is changing the language that ecologists use to discuss the niche concept. When Thomas Kuhn talks about paradigm shifts, he notes that it is not only theory that changes but also the worldview organized around a given idea. At least amongst community ecologists, it seems as though this had focused the discussion of the niche to an increasingly local scale, particularly in terms of stabilizing and equalizing terms measured as fixed quantities made under homogenous, local conditions. A recognition of the role of spatial and temporal conditions in altering these variables seems less common, compared to the direction of earlier, Hutchinsonian-type discussions of the niche.

Note that this was not Chesson's original definition, since he is explicit that: “The theoretical literature supports the concept that stable coexistence necessarily requires important ecological differences between species that we may think of as distinguishing their niches and that often involve tradeoffs, as discussed above. For the purpose of this review, niche space is conceived as having four axes: resources, predators (and other natural enemies), time, and space.”

On a recent manuscript, an editor commented that the term 'niche processes' shouldn't be used to refer to environmental filtering since (paraphrased) “when ecologists refer to niche processes, they are usually thinking of processes that constrain species’ abundances locally, confer an advantage on rare species...” But is it fair to say that this is the only thing we mean (or should mean) when we discuss niches? I’ve had discussions with other people who’ve had this kind of response – e.g., reviewers asking for simulations to be reframed from niches defined in terms of environmental tolerances to things that fit more clearly into equalizing and stabilizing terms. That is a good description of a stabilizing process, which is termed a 'niche difference' in the modern coexistence literature. But there is still a lot of grey space we have yet to address in terms of how to integrate (e.g.) the effects of the environment (including over larger scales) into local 'niche processes' or stabilizing effects. It's a subtle argument - that we can use the framework established by Chesson, but we should try to do so without dismissing too-quickly the concepts that don't fit easily within it. In addition, elsewhere the niche is still conceptualized in varying ways from comparative evolutionary biologists who talk about niche conservatism and mean the maintenance of ancestral trait values or environmental tolerances; to functional ecologists who may refer to multidimensional differences in trait space; to species distribution modellers who thinks of large-scale environmental correlates or physiological determinants of species’ distributions. 

The niche is probably the most fundamental, yet vaguely–defined and poorly understood idea in ecology. So, formalizing the definition and constraining it is a necessary idea. And modern coexistence theory has provided great deal of insight into local coexistence and thus has allowed for a better understanding of the niche concept. But there is also a need to be careful in how quickly and how much we restrict our discussion of the niche. It's possible to gain both the strengths of modern coexistence theory as well as appreciate its current limitations. Modern coexistence theory isn’t yet complete or sufficient. It’s currently easier to estimate stabilizing and equalizing terms from experimental data in which conditions are controlled and homogenous, and this can inadvertently focus future research and discussion on those types of conditions. Models which consider larger scale processes and the impacts of changing abiotic conditions through space in time exist, but across different literatures, and these need continued synthesis. There is still a need to understand how to most realistically incorporating and understand the complex interactions between multiple species (e.g. Levine et al. 2017). The application of modern coexistence theory to observational data in particular is still limited, and such data is essential when species are slow lived or experimentally unwieldy. Further, when quantities of interest (particularly traits or phylogenetic differences) contribute to both equalizing and stabilizing effects, its still not clear how to partition their contributions meaningfully.

Friday, June 2, 2017

Image in academia

Not many seminar speakers are introduced with a discussion of their pipetting skills. When we talk about other scientists we discuss their intelligence, their rigour, their personality, above and beyond their learned skills. Most people have an image of what a scientist should be, and judge themselves against this idealized vision. There are a lot of unspoken messages that are exchanged in science and academia. It’s easy to think that the successful scientists around one interacts with are just innately intelligent, confident, passionate, and hard-working. No doubt imposter syndrome owes a lot to this one-sided internalization of the world. After all, you don’t feel like you fulfill these characteristics because you have evidence of your own personal struggles but not those of everyone else. 

"Maybe no one will notice".
The most enlightening conversation I had this year (really! Or at least a close tie with discovering that PD originally was discussed as a measure of homologous characters…) was with a couple of smart, accomplished female scientists, in which we all acknowledged that we—not infrequently—suffered from feeling totally out of our depths. It is hard to admit our failings or perceived inadequacies, for fear we’ll be branded with them. But it’s really helpful for others to see that reality is different than the image we’ve projected. If everyone is an imposter, no one is. There is something to be said for confidence when scientists are presenting consensus positions to the public, but on the other hand, I think that being open about the human side of science is actually really important. 

For those who already feel like outsiders in academia, perhaps because they (from the perspective of race, gender, orientation, social and economic background, etc) differ from the dominant stereotype of a ‘scientist’, it probably doesn’t take much to feel alienated and ultimately leave. Students have said things to me along the lines of “I love ecology but I don’t think I will try to continue in academic because academia is too negative/aggressive/competitive”. Those are legitimate reasons to avoid the field, but I always try to acknowledge that I feel the same way too sometimes. It’s helpful to acknowledge that others feel the same way, and that having this kind of feeling (e.g. that you aren’t smart enough, or you don’t have a thick enough skin) isn’t a sign that you don’t actually belong. Similarly, it’s easy to see finished academic papers and believe that they are produced in a single perfect draft and that writing a paper should be easy. But for 99% of people, that is not true, and a paper is the outcome of maybe 10 extreme edits, several rounds of peer review, and perhaps even a copy-editor. Science is inherently a work-in-progress and that’s true of scientists as well.

The importance of personal relationships and mentorship to help provide realistic images of science should be emphasized. Mentorship by people who are particularly sympathetic (by personal experience or otherwise) to the difficulties individuals face is successful precisely for this reason. This might be why blog posts on the human side of academia are so comparatively popular – we’re all looking for evidence that we are not alone in our experiences. (Meg Duffy writes nice posts along these lines, e.g. 1, 2). And though the height of the blogosphere might be over, the ability of blog posts to provide insight into humanity of academia might be its most important value.