Wednesday, December 2, 2015

Paper of the lustrum*

(*lustrum = five years)

I’m co-teaching (with Kendi Davies and Julian Resasco) a graduate seminar focused on current trends and advances in community ecology. It’s been great, and having a small group with varied backgrounds (disease ecology, microbial ecology, restoration, community ecology theory, etc) allows for flexible and interesting discussions. Somehow the topic last week drifted to favourite papers, and we ended up with a plan to choose and defend the paper that was—in our opinion—the best one published in ecology in the last 5 years.

Today we described and defended our choices and tried to decide what the ‘best’ actually means, anyways. I don’t think anyone quite realised just how difficult this exercise would be. First, 5 years isn’t actually a very long time when measured in academic publishing years. That’s only the time of the average PhD, or less than the entire tenure-track period. I immediately thought of several papers I love, only to realize that sadly, they were from before 2010 (e.g. papers like these). 

Nearly everyone started their search the same way: with a Google Scholar search, looking at the most cited papers between 2010-2015. Some people looked at the most popular papers from high impact journals (Ecology Letters, Science, Nature, PNAS, etc); others looked at the output of eminent ecologists during that time period. At least one used his committee members for advice, and for the new grad students this was a nice crash course in the recent literature. Citations, quality journals, or eminent names might have been starting points for finding these papers, but it was interesting how little these actually seemed to matter. When defending their choice of paper, absolutely no one mentioned citations or journal as deciding factors. 

The papers we chose, and why: 
Conceptual synthesis in community ecology. (The Quarterly Review of Biology) Vellend 2010  
This was my choice, although I went back and forth between a short list of papers. For me, the ‘best’ paper had to either change how we do ecology, or how we think about ecology. I think Vellend 2010 has a lot of value as a pedagogical tool, and a device for organizing ecological knowledge. It has the potential to aggregate the varied, context dependent data that ecologists have been collecting for generations. Further, rather than the disjointed approach my undergraduate texts took for community ecology (productivity here, lynx-hare plot there), a single framework should help students understand community ecology as a cohesive set of ideas. And I admire papers that have big ideas.

 This was a cool choice, because it turns out to be a massively important development that many of the less molecularly-inclined knew little about. This paper introduced the use of CRISPR/Cas for gene editing. The CRISPR system is been found in archaea and bacteria, and provides a form of adaptive immunity against viruses. Importantly, it has been developed for use in incredibly precise genome editing that is heritable. It has massive implications for the study of evolution, microbial ecology, disease, population genetics, and everything in between. It is also the source of ethical concerns because it can (and has) be used to modify human embryos. 

Biodiversity loss and its impact on humanity. (Nature) Cardinale et al. 2012 
This was the choice of two students, so it may have been the de facto winner. It is a massively cited paper (>1000), and both students chose it in part because it makes a clear contribution to human welfare and society. It represents a massive undertaking (they analysed more than 1000 papers) reviewing research on how biodiversity relates to a large number of relevant ecosystem services. In particular, Table 1 (below) can be used for applied and basic research, and shows where research and data agree, disagree, or are lacking. This is certainly a must read for ecologists.

This paper helped to concentrate and inspire research on intraspecific variation and to highlight the areas of research that are still poorly studied (and it actually made my short list too). There is obvious variation within species (long acknowledged as important to evolution, starting with Darwin) but this is often ignored in community ecology. Bolnick et al. point out the many possible and important implications that arise from such variation. The writing is clear and highlights extremely well the general mechanisms that might interact with intraspecific variation. For the student who chose it, it was inspiring enough when it first came out, that they changed their research direction. 
Table 1: Bolnick et al. 
This paper was chosen in an opposite fashion: it is brand new, and rather than having inspired current research, the student thought it would inspire future approaches. The paper integrates community ecology and disease ecology in a novel and sophisticated way, advancing an area of research currently receiving a lot of attention. In this paper, mice are ‘mesocosms’ in which the importance of bottom-up versus top-down control of infection (by malaria and a nematode) could be tested. (Quote: "It's a real page-turner"). 

This was another paper chosen because it inspired the student's current studies. Ladau et al. brought together a massive data set for marine bacterial biodiversity, allowing them to map it on a global scale and develop predictive distribution models. Interestingly, they found that diversity patterns were lower at the equator, contrary to typical findings in other organisms. The student cited the careful methodology, extensive data, and comparison of results to those in macro-scale systems as the paper’s strengths. 
From Ladau et al. "Maps of predicted global marine bacterial diversity. Color scale shows relative richness of marine surface waters as predicted by SDM. Samples were rarefied to 4266 rDNA sequences to enable accurate estimation of relative richness patterns on a global scale from data sets with different sequencing depths. True richness is expected to exceed estimated values. (a) In December, OTU richness peaks in temperate and higher latitudes in the Northern Hemisphere. (b) In June, OTU richness peaks in temperate latitudes in the Southern Hemisphere..."

The final paper was Kendi’s choice. Community ecology has struggled with weak connections between pattern and process. The experimental and quantitative work coming from this research group has provided multiple examples for how to connect theory, statistics, and experimental results in a very rigourous fashion. In this paper, the focus is particularly on functional/trait approaches to community assembly and coexistence, and the authors manage to connect careful experimental data with Chessonian coexistence theory, using trait data to estimate species’ fitness and niche differences, and then using these to predict species coexistence.

After the fact, of course, lots of other great papers came to mind. It isn't really possible to choose one best paper, either. But the characteristics people looked for in a great paper were pretty similar - inspiring, providing novel approaches to particular questions, focused on big questions or ideas, and making contributions that go beyond academic ecology.

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