A little late off the mark this time around, we asked people in the lab to nominate a paper they had enjoyed in 2016. This year, we based one of our fortnightly reading groups on this topic and everyone gave a short summary of their paper. We had an interesting mix of papers closely related to people’s research, papers on how better to do that research, and papers inspired by other aspects of life that engaged our attention in 2016 (*cough* the US election *cough*). We hope you enjoy them as much as we did!
Bliss-Ketchum, L. L., de Rivera, C. E., Turner, B. C., & Weisbaum, D. M. (2016) The effect of artificial light on wildlife use of a passage structure. Biological Conservation, 199, 25-28.
I chose this paper because it is relevant to my Master’s degree project and also because to my knowledge it is the first paper that presents an experimental study about the impacts of artificial lights on mammals’ use of crossing structures. Lights with different intensities were set up at different sections of an existing crossing structure. Their results showed that artificial lights reduced the use of the crossing structures for some species such as black-tailed deer and opossums but not for others, such as raccoons, as they’re probably more adapted to urban landscapes. I would have liked a more thorough and clear description of the study site (e.g. presence of wildlife fences?) and a more clear discussion about the results connected to their second hypothesis presented at the end of the introduction.
Kohler, F. and Brondizio, E. S. (2016) Considering the needs of indigenous and local populations in conservation programs. Conservation Biology doi:10.1111/cobi.12843
This paper describes conflicts and frustrations that can be created when Indigenous or local people are expected (by NGOs or governments etc.) to act as idealized conservationists, rather than act as people who are faced with economic and cultural realities in their everyday lives. These conflicts can be especially pronounced in conservation programs taking place in areas undergoing rapid development, or when certain traditional practices produce a collateral (rather than intended) environmental improvement. The paper is a reminder that local populations need to be included as stakeholders or partners in conservation initiatives to best incorporate both environmental and socioeconomic factors.
Côté,, I.M, Darling, E.S., Brown, C.J. (2016) Interactions among ecosystem stressors and their importance in conservation. Proc. R. Soc. B 283: 20152592
‘Synergy’ is one of those ecological buzzwords, increasingly used to describe alarming interactions between environmental stressors. This insightful review by Côté and colleagues shows that synergistic interactions are likely over-reported in the ecological literature, and illustrates the expected outcomes of different types of stressor interactions (additive, antagonistic, synergistic, ‘super-synergistic’ etc.) It also provides useful recommendations for experimental approaches that could be used to explore stressor interactions with direct relevance for management.
Williams, P. J. and Hooten, M. B. (2016) Combining statistical inference and decisions in ecology. Ecological Applications, 26: 1930–1942. doi:10.1890/15-1593.1
When we fit statistical models, we tend to focus on the mean of any parameters we’re estimating; at a stretch we might consider the 95% CI as an indicator of uncertainty. Yet over- or under-estimating our uncertain parameters can have different consequences depending on our management context. Williams and Hooten provide a nice framework for bringing together our entire distribution of parameter uncertainty and management context using loss functions.
Port, J. A., O’Donnell, J. L., Romero‐Maraccini, O. C., Leary, P. R., Litvin, S. Y., Nickols, K. J., … & Kelly, R. P. (2016) Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Molecular Ecology, 25(2), 527-541.
When starting my masters this year, I was really interested in different applications of environmental DNA (eDNA) sampling. This paper was a real eye opener for me in that it demonstrated the potential for community wide surveys in a dynamic marine environment. While you might assume the detection probability of eDNA in coastal environments (such as kelp forests) would be low compared to traditional survey methods, there was a low false negative rate and 18 more species detected using eDNA compared to visual dive surveys.
Stephens, P. A., Mason, L. R., Green, R. E., Gregory, R. D., Sauer, J. R., Alison, J., … & Chodkiewicz, T. (2016) Consistent response of bird populations to climate change on two continents. Science, 352(6281), 84-87.
This paper compiles local trends in bird populations to track the divergent fates of species favoured or disadvantaged by climate change at a continental level. The indices the authors present are a really neat way to communicate the collective responses of multiple species, across multiple locations, while allowing for spatial variation in species responses. It was also a nice link between predictions of climate suitability made from species distribution models and realised species trends.
McAlpine, C., C. P. Catterall, R. Mac Nally, D. Lindenmayer, J. L. Reid, K. D. Holl, A. F. Bennett, R. K. Runting, K. Wilson, R. J. Hobbs, L. Seabrook, S. Cunningham, A. Moilanen, M. Maron, L. Shoo, I. Lunt, P. Vesk, L. Rumpff, T. G. Martin, J. Thomson, and H. Possingham (2016) Integrating plant- and animal- based perspectives for more effective restoration of biodiversity. Frontiers in Ecology and the Environment 14:37–45.
McAlpine et al. (2016) is a review paper written by a group of CEED researchers and associates that draws attention to the divide between plant- and animal- based perspectives on restoration. This article draws attention to an often over-looked and possibly detrimental consequence of the way we go about research (what research we read, who we do it with, what techniques we consider). Completely unintentionally, plant and animal restoration research has been drifting apart even though there would be valuable insights gained from working together. When people are researching or implementing restoration they are almost always just considering the plants, with the idea that, for animals, ‘if you build it they will come’. A small subset of papers focus on animal only restoration- this usually involved re-introductions into seemingly viable habitat. Interestingly and unfortunately, it seems that there isn’t much cross pollination (mind the pun) between plant- and animal- based perspectives on restoration. It would have been interesting to see the review (or perhaps a follow-up one) examine similar divides in ecological literature and practice that also have implications for restoration success. For example, there is often little communication with soil scientists and between terrestrial and aquatic ecologists.
Holmes, T. Q., Head, B. W., Possingham, H. P., & Garnett, S. T. (2016) Strengths and vulnerabilities of Australian networks for conservation of threatened birds. Oryx, 1-11. Early view: https://doi.org/10.1017/S0030605316000454
It’s my opinion that one of the largest drivers of successful conservation is the driven individuals behind the scenes who are pushing to protect and save species, and that as conservation is historically a biological discipline this is generally under-appreciated and under-studied. In this Oryx paper, Holmes and mob give us a great look at how human social networks organized to conserve bird species in Australia affect what actually happens on the ground. Fascinating stuff.
Stawski, C., Kortner, G., Nowack, J. and Geiser, F. (2016) Phenotypic plasticity of post-fire activity and thermal biology of a free-ranging small mammal. Physiology and Behavior, 159, pp. 104-111.
This research group is making great progress in determining the mechanisms that allow small mammals to survive and persist in landscapes affected by fire. By tracking brown antechinus (Antechinus stuartii), in both densely vegetated and very recently burned habitats using temperature-sensitive VHF transmitters, they were able to show that these small mammals increase their use of torpor in post-fire environments and that this was more pronounced in females than in males. This allows them to conserve energy when resources become less available due to fire and (speculatively) better avoid predators due to reduced activity in open, burned environments.
Monnahan, C. C., Thorson, J. T. & Branch, T. A. (2016) Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo. Methods in Ecology and Evolution.
General-purpose MCMC modelling software (like the QAEco favourite JAGS) has enabled major advances in quantitative ecology over the past decade, and there are now plenty of resources available to help ecologists understand how they work and what to do when they don’t. Stan is the new kid on the block and promises even faster MCMC by using a sampling method called Hamiltonian Monte Carlo. Monnahan & co. do a great job of filling the void in the literature by spelling what HMC does out in words, pictures, and code, and when to pick pick Stan over JAGs.
Zuur, A. F., & Ieno, E. N. (2016) A protocol for conducting and presenting results of regression‐type analyses. Methods in Ecology and Evolution, 7(6), 636-645.
In this paper Zuur and Ieno offer a 10-step protocol for conducting and presenting regression analyses. The protocol guides an author through the process with steps including how to visualise their study design, identify the structure of their data, and write a clear definition of the model to be used. I have found the protocol to be very helpful in presenting clear and logical analysis to a reader.
Kennedy, R., Wojcik, S., & Lazer, D. (2017) Improving election prediction internationally. Science, 355(6324), 515-520.
The paper reports results of a study to predict executive elections at a global scale, using election data from over 500 elections in 86 countries and polling data from 146 elections. The results show strong evidence of the effects of democratic consolidation, international aid and incumbent advantage on election outcomes. Particularly interesting is that economic predictors are weak, despite literature suggesting otherwise.
Van Ha, P., Kompas, T., Nguyen, H. T. M., & Long, C. H. (2016) Building a better trade model to determine local effects: A regional and intertemporal GTAP model. Economic Modelling.
This paper is one I must have read at least 10 times last year. It’s the basis for a project I’ve been working on, but being an economic paper, it’s very much outside my normal field, and has taken that many reads to get my head around (just don’t ask me about the equations, still, please). The paper predicts the potential impacts of a free trade policy (the now-likely-defunct TPP) on different sectors of the Vietnamese economy, through an intertemporal computable general equilibrium model. I find it fascinating that such a complex, multi-national agreement can be broken down into its effects on, say, the agriculture sector of Vietnam, and the opportunities that presents to properly plan for the future of both people and the environment under these policies.