Monday, December 19, 2016

2016 holiday caRd

Once more, tis the season! Hope you had an excellent year of science and R coding. This card requires the igraph library - it (loosely) relies on an infection (S-I model) moving through a network :-)

To view season's greetings from 2016:
Go to the gist and download the file directly ("download gist") or hit "raw" and copy/paste. Or, copy and paste the code below.

Users of Rstudio will not be able to see the animation, so base R is highly recommended.

For those not able or willing to run the card, you can view it and the past years' cards here!

Tuesday, December 13, 2016

150 years of 'ecology'

The word ‘ecology’ was coined 150 years ago by Ernst Haeckel in his book Generelle Morphologie der Organismen published in 1866. Mike Begon gave a fascinating talk at the British Ecological Society meeting in Liverpool on what ecology as meant over these past 150 years and what it should mean in the future. The description of ecology that follows, is largely taken from Begon’s remarks.

Ernst Haeckel, 1860
Haeckel defined ecology as ‘the science of the relations of organism to its surrounding outside world (environment)’, which is in obvious contrast to the then burgeoning science of physiology, which was concerned with the world inside of an organism. Interestingly, the first 50 years of this new field of ecology was dominated by the study of plants. In America, Clements, while in the UK, Tansley, both saw ecology as the description of patterns of plant in relation to the outside world. In many ways, this conception of ecology was what Haeckel had envisioned.

Frederic Clements

However, by the 1960s, the domain of ecology began to grow rapidly. Ecologists like Odum used ‘ecology’ to mean the structure and function of ecosystems, while others focussed on the abundance and distribution of species. By this time ecology had grown to encapsulate all aspects of organismal patterns and functions in nature.

The post-60s period saw another expansion -namely the value of ecology. While Begon points out that text books, including his, focussed on the science of ecology in its pure form, many were ignoring the fact that ecology had/has important repercussions for how humanity will need to deal with the massive environmental impacts we’ve had on Earth’s natural systems. That is, the science of ecology can provide the foundation by which applied management solutions can be built. I personally believe that applied ecology has only just begun its ascension to being the most important element of ecological science (but I’m biassed -being the Executive Editor of the Journal of Applied Ecology). Just like how human physiology has become problem oriented, often focussed on human disease, ecology will too become more problem oriented and focus on our sick patients.


Begon went on to say what ecology should be in the near future. He juxtaposed the fact and truth based necessity of science to the post-truth Brexit/Trump era we now find ourselves in. If ecologists and scientists are to engage the public, and alter self-destructive behaviours, it cannot be with logic and evidence alone. He argued that we need to message like those post-truthers. Use metaphors, simple messages that are repeated, repeated, and repeated.

Friday, November 25, 2016

Can coexistence theories coexist?

These days, the term ‘niche’ manages to cover both incredibly vague and incredibly specific ideas. All the many ways of thinking about an organism’s niche fill the literature, with various degrees of inter-connection and non-independence. The two dominant descriptions in modern ecology (last 30 years or so) are from ‘contemporary niche theory’ and ‘modern coexistence theory’. Contemporary niche theory is developed from consumer-resource theory, where organisms' interactions occur via usage of shared resources. (Though it has expanded to incorporate predators, mutualists, etc), Analytical tools such as ZNGIs and R* values can be used to predict the likelihood of coexistence (e.g. Tilman 1981, Chase & Leibold 2003). Modern coexistence theory is rooted in Peter Chesson’s 2000 ARES review (and earlier work), and describes coexistence in terms of fitness and niche components that allow positive population growth.

On the surface these two theories share many conceptual similarities, particularly the focus on measuring niche overlap for coexistence. [Chesson’s original work explicitly connects the R* values from Tilman’s work to species’ fitnesses in his framework as well]. But as a new article in Ecological Monographs points out, the two theories are separated in the literature and in practice. The divergence started with their theoretical foundations: niche theory relied on consumer-resource models and explicit, mechanistic understanding of organisms’ resource usage, while coexistence theory was presented in terms of Lotka-Volterra competition models and so phenomenological (e.g. the mechanisms determining competition coefficients values are not directly measured). The authors note, “This trade-off between mechanistic precision (e.g. which resources are regulating coexistence?) and phenomenological accuracy (e.g. can they coexist?) has been inherited by the two frameworks….”

There are strengths and weaknesses to both approaches, and both have been used in important ecological studies. So it's surprising that they are rarely mentioned in the same breathe. Letten et al. answer an important question: when directly compared, can we translate the concepts and terms from contemporary niche theory into modern coexistence theory and vice versa?

Background - when is coexistence expected? 
Contemporary niche theory (CNT) (for the simplest case of two limiting resources): for each species, you must know the consumption or impact they have on each resource; the ratio at which the two resources are supplied, and the ZNGIs (zero net growth isoclines, which delimit the resource conditions a species can grow in). Coexistence occurs when the species are better competitors for different resources, when each species has a greater impact on their more limiting resource, and when the supply ratio of the two resources doesn’t favour one species over the other. (simple!)

For modern coexistence theory (MCT), stable coexistence occurs when the combination of fitness differences and niche differences between species allow both species to maintain positive per capita growth rates. As niche overlap decreases, increasingly small fitness differences are necessary for coexistence.

Fig 1, from Letten et al. The criteria for coexistence under modern coexistence theory (a) and contemporary niche theory (b).  In (a), f1 and f2 reflect species' fitnesses. In (b) "coexistence of two species competing for two substitutable resources depends on three criteria: intersecting ZNGIs (solid red and blue lines connecting the x- and y-axes); each species having a greater impact on the resource from which it most benefits (impact vectors denoted by the red and blue arrows); and a resource supply ratio that is intermediate to the inverse of the impact vectors (dashed red and blue lines)."

So how do these two descriptions of coexistence relate to each other? Letten et al. demonstrate that:
1) Changing the supply rates of resources (for CNT) impacts the fitness ratio (equalizing term in MCT). This is a nice illustration of how the environment affects the fitness ratios of species in MCT.

2) Increasing overlap of the impact niche between two species under CNT is consistent with increasing overlap of modern coexistence theory's niche too. When two species have similar impacts on their resources, there should be very high niche overlap (weak stabilizing term) under MCT too.

3) When two species' ZNGI area converge (i.e. the conditions necessary for positive growth rates), it affects both the stabilizing and equalizing terms in MCT. However, this has little meaningful effect on coexistence (since niche overlap increases, but fitness differences decrease as well).

This is a helpful advance because Letten et al. make these two frameworks speak the same (mathematical) language. Further, this connects a phenomological framework with a (more) mechanistic one. The stabilizing-equalizing concept framework (MCT) has been incredibly useful as a way of understanding why we see coexistence, but it is not meant to predict coexistence in new environments/with new combinations of species. On the other hand, contemporary niche theory can be predictive, but is unwieldy and information intensive. One way forward may be this: reconciling the similarities in how both frameworks think about coexistence.

Letten, Andrew D., Ke, Po-Ju, Fukami, Tadashi. 2016. Linking modern coexistence theory and contemporary niche theory. Ecological Monographs: 557-7015. http://dx.doi.org/10.1002/ecm.1242
(This is a monograph for a reason, so I am just covering the major points Letten et al provide in the paper. It's definitely worth a careful read as well!).

Wednesday, November 16, 2016

The value of ecology through metaphor

The romanticized view of an untouched, pristine ecosystem is unrealistic; we now live in a world where every major ecosystem has been impacted by human activities. From pollution and deforestation, to the introduction of non-native species, our activity has influenced natural systems around the globe. At the same time, ecologists have largely focused on ‘intact’ or ‘natural’ systems in order to uncover the fundamental operations of nature. Ecological theory abounds with explanations for ecological patterns and processes. However, given that the world is increasingly human dominated and urbanized, we need a better understanding of how biodiversity and ecosystem function can be sustained in the presence of human domination. If our ecological theories provide powerful insights into ecological systems, then human dominated landscapes are where they are desperately needed to solve problems.
From the Spectator

This demand to solve problems is not unique to ecology, other scientific disciplines measure their value in terms of direct contributions to human well-being. The most obvious is human biology. Human biology has transitioned from gross morphology, to physiology, to molecular mechanisms controlling cellular function, and all of these tools provide powerful insights into how humans are put together and how our bodies function. Yet, as much as these tools are used to understand how healthy people function, human biologists often stay focussed on how to cure sick people. That is, the proximate value ascribed to human biology research is in its ability to cure disease and improve peoples’ lives. 


In Ecology, our sick patients are heavily impacted and urbanized landscapes. By understanding how natural systems function can provide insights into strategies to improve degraded ecosystems. This value of ecological science manifests itself in shifts in funding and publishing. We now have synthesis centres that focus on the human-environment interaction (e.g., SESYNC). The journals that publish papers that provide applied solutions to ecological and environmental problems (e.g., Journal of Applied Ecology, Frontiers in Ecology and the Environment, etc.) have gained in prominence over the past decade. But more can be done.


We should keep the ‘sick patient’ metaphor in the back of our minds at all times and ask how our scientific endeavours can help improve the health of ecosystems. I was once a graduate student that pursued purely theoretical tests of how ecosystems are put together, and now I am the executive editor of an applied journal. I think that ecologists should feel like they can develop solutions to environmental problems, and that their underlying science gives them a unique perspective to improving the quality of life for our sick patients.