Qaeco’s favourite papers of 2017

We asked our lab members to nominate a paper published in 2017 that they had enjoyed. Recommendations ranged from the skill-based (scientific writing, reproducible coding, camera-trapping) to global reviews (plant traits, climate change, size-based models) and some great case studies (questionable psychologists, waterbirds at Lake Eyre, Finnish foxes).  We hope you find them as interesting as we did!

– Kate & Bron, hosts of QAECO Reading Group

Natasha Cadenhead

Doubleday, Z.A. & Connell, S.D. (2017) Publishing with objective charisma: breaking science’s paradoxTrends in Ecology & Evolution32, 803-805.

At the risk of sounding a little too Eat, Pray, Love, 2017 was a year in which I decided to try and actively improve my scientific writing. Not only is there an inherent joy to reading a well-written paper, but it makes the scientific message within that much clearer. Doubleday & Connell’s (thankfully, eloquent) paper recognises the problem with much of scientific writing – we spend a lot of our time doing it, but we’re never taught how to do it in an engaging way. They run through some steps for bringing out that charismatic “Ingredient X” in your writing, without falling prey to sensationalism. On this topic (although less science-focused) I would also recommend anything by the excellent Helen Sword.

Dave Duncan

Watson, D.M., Doerr, V.A.J., Banks, S.C., Driscoll, D.A., van der Ree, R., Doerr, E.D. & Sunnucks, P. (2017) Monitoring ecological consequences of efforts to restore landscape-scale connectivity. Biological Conservation, 206, 201–209.

My favourite paper from this year is the culmination of a monitoring framework I saw presented by one of the authors back in about 2015.  The article sets out a framework for thinking about the design of monitoring activities for projects whose intention is to restore connectivity at landscape scales.

Now, you might be saying to yourself: does the world really need another monitoring framework? Sadly, apparently yes. Well that and some kind of institutional revolution on the other side of which we actually implement some of these great ideas.

Monitoring or learning about the effectiveness of interventions is done infrequently, and generally very poorly, for reasons that have been set out innumerable times in the literature.  This paper, after recapping all that, sets out the ecological processes that are intended to be affected by projects about connectivity, and provides thoughtful and well-argued pointers that should be of practical help in designing more effective monitoring.

As a side-note, the collection of authors on this paper lends it great authority, combining mid-career researchers who have done a lot of primary research and synthesis across most of the relevant fields, from individual movement studies to genes and landscapes.

Nick Golding

A Guide to Reproducibile Code in Ecology and Evolution, (2017) Cooper, N. & Hsing, P.-Y. (Ed.), British Ecological Society

I’m cheating a bit. This isn’t a scientific paper, it’s a free guide published by the British Ecological Society on how to make your research code easier for you or anyone else to reuse and extend. Written by a team of computational ecologists and research software engineers, I think this is the clearest and most accessible introduction to the range techniques you can use to improve your code, including reproducible workflows, version control, literate programming and archiving. Essential reading for anyone who uses code in their research!

Hannah Fraser

Agnoli, F., Wicherts, J.M., Veldkamp, C.L.S., Albiero, P. & Cubelli, R. (2017) Questionable research practices among Italian research psychologists. PLoS ONE 12, 1–17.

This paper particularly tickled me because we’ve been working on something very similar in ecology (naturally). Also, the study is replication of previous work and I’m becoming obsessed with the importance of replicating studies. Agnoli et al. investigated the prevalence of questionable research practices (p-hacking, cherry-picking, harking etc.) in Italian psychologists, providing support to a previous study with an American focus. Both studies found that questionable research practices were common. For example, one of the most prevalent questionable research practice was “in a paper, failing to report all of a study’s dependent measures” which 63% of American and 48% of Italian psychologists admitted to doing. A lot of the research practices they discuss are directly relevant to ecology and we’re currently writing up a paper about how similar/different the prevalence of these practices is in ecology.

Kate Giljohann

Moles, A.T. (2018) Being John Harper: Using evolutionary ideas to improve understanding of global patterns in plant traits. Journal of Ecology, 106, 1-18.

This review paper by Moles presents a comprehensive overview of the current state of plant trait ecology and outlines promising avenues for future research. As a novice in trait research, I appreciated Moles’ explanation of five key plant traits [seed mass, plant height, wood density, leaf mass per unit area, leaf size], their evolutionary context and ecological importance, and how they vary between species and along gradients. Using the same five traits, Moles demonstrates how integrating traits can provide unexpected insights into species lifetime fitness; that understanding trait selection and variation is likely to require consideration of response to both good times and bad times; and finally, the potential benefit of accounting for phylogeny and history when predicting species and community response to global change. A great read for anyone interested in the field of plant traits.

Anwar Hossain

Trull, N., Böhm, M. & Car, J. (2018) Patterns and biases of climate change threats in the IUCN Red List. Conservation Biology 32, 135-147.

I selected this paper because this is relevant to my MPhil project. Studies suggest that IUCN criteria are not suitable in predicting species’ vulnerability due to climate change and this paper discussed the biases in selecting threats potentially correlated to climate change impacts. Their results showed that certain ecosystems (i.e., grassland, shrubland) and subject to particular threats (i.e., invasive species) were more likely to have climate change as a listed threat. Also, broad tolerance to temperature was found to be related to an increased likelihood of climate change threat, indicating a counterintuitive relationship to IUCN assessments. This paper concluded with the recommendation that ‘IUCN should adopt a more cohesive approach that integrate specific traits particularly relevant to climate change impacts’.

Bronwyn Hradsky

Fedriani, J.M., Wiegand T., Ayllón, D., Palomares, F., Suárez-Esteban, A., Grimm, V. (2017) Assisting seed dispersers to restore oldfields: An individual-based model of the interactions among badgers, foxes and Iberian pear trees. Journal of Applied Ecology (early view).

A really nice example of how individual-based modelling can be used to address applied management problems – in this case, the restoration of abandoned farmlands in Spain.  One of the strengths of the paper is the variety of approaches Fedriani et. al. used to parameterise their model, depending on the quality of data available – including direct extraction from published studies, global sensitivity analyses, and calibration across a biological plausible range to reproduce observed patterns (i.e. pattern oriented modelling).  Inspiring!

Luke Kelly

Schoennagel, T., Balch, J.K., Brenkert-Smith, H., Dennison, P.E., Harvey, B.J., Krawchuk, M.A., Mietkiewicz, N., Morgan, P., Moritz, M.A., Rasker, R. & Turner, M.G. (2017) Adapt to more wildfire in western North American forests as climate changes. Proceedings of the National Academy of Sciences, 114, 4582-4590.

This paper is more relevant than ever given the recent and ongoing wildfires in western USA. The authors give a neat overview of the growing problem of larger and more frequent fires occurring close to where people live. To pick out one idea from the new ‘adaptive resilience’ approach the authors encourage, they make a good case for actively and opportunistically managing wildfires. This is an idea we’re now exploring with a team from QAECO and collaborators from fire management agencies in southern Australia.

Mick McCarthy

Zurell, D. (2017) Integrating demography, dispersal and interspecific interactions into bird distribution models. Journal of Avian Biology, 48, 1505-1516.

An interesting and useful review paper looking at the state of the art in species distribution modelling. While focused on birds and published in a distinctly avian journal, it is relevant to all taxa.

Joslin Moore (friend of qaeco)

Tomkins, A., Zhang, M. & Heavlin, W.D. (2017) Reviewer bias in single- versus double-blind peer review. Proceedings of the National Academy of Sciences, 114, 12708-12713.

Bias towards famous authors and prestigious institutions in single-blind review

I really enjoyed this paper on bias in single-blind vs double-blind review because it was a rare experiment where the same material was reviewed single and double blind (by different reviewers though). The field is computer science. The study found a large bias towards ‘famous’ authors and prestigious institutions so plenty of scope for indirect effects.  It’s not clear how unconscious this bias is but it does suggest that bind reviewing (and probably assessment too) is needed if one wants to avoid this bias. The study couldn’t detect a direct bias against women but they were not prepared to rule one out since there was a non-zero (but insignificant) effect size (and there was a small proportion of women). Other diversity dimensions weren’t considered.  Personally, the next time I review a paper, I’ll be trying not to notice the names of the authors or their institutions…

Matt Rees

Pasanen‐Mortensen, M., Elmhagen, B., Lindén, H., Bergström, R., Wallgren, M., Velde, Y., & Cousins, S.A. (2017). The changing contribution of top‐down and bottom‐up limitation of mesopredators during 220 years of land use and climate changeJournal of Animal Ecology86, 566-576.

Think that you’re finally starting to understand your predators and their associated trophic interactions? Well, think again, because they’re 100 times more complex and context specific, and you shouldn’t bother because there’s too many things to consider. This is a really inconvenient paper. Do not read it, continue living in your blissful ignorance.

Gerry Ryan

Scotson, L., et al. (2017) Best practices and software for the management and sharing of camera trap data for small and large scales studiesRemote Sensing in Ecology and Conservation, 3, 158-172.

Starting a camera trap study and want to make the most of your hard field yards? Ignoring soooo many photos of ‘bycatch’ species? Not sure how to manage your data? Doing anything camera trap related? Have a read. Now.

Freya Thomas

Wenk, E.H., Abramowicz, K., Westoby, M. & Falster D. (2017) Coordinated shifts in allocation among reproductive tissues across 14 coexisting plant species. Biorxiv.

This paper discusses reproductive effort in plants – how plants allocate energy and how this effects reproductive outcomes. This paper provides a succinct discussion of what reproductive effort is and provides empirical data of detailed measurements of reproductive effort across 14 different plant species. Reproductive effort is difficult and time consuming to measure but these authors provide convincing arguments and data to suggest a viable and relatively quick field based measure. This paper extends our understanding and measurement of reproductive effort in the field and outline a spectrum of reproductive traits with ‘parental optimists’ at one end, and ‘parental pessimists’ at the other.

Inka Veltheim

Kingsford, R. T., Bino, G., & Porter, J. L. (2017) Continental impacts of water development on waterbirds, contrasting two Australian river basins: global implications for sustainable water use. Global Change Biology, 23, 4958–4969.

This 32-year study investigated waterbird community trends in the developed Murray-Darling Basin and the undeveloped Lake Eyre Basin, which have vastly contrasting levels of water extraction. The study examined waterbird abundance at three different spatial scales – major wetlands, river catchment and river basin scales. Waterbird abundance was highly variable in both basins, but waterbirds in the Murray-Darling Basin experienced a 72% decline over the 32-year period. Waterbirds in the Lake Eyre Basin showed no such declines, except for brolgas within the Georgina-Diamantina rivers’ catchment. Further modelling showed flow restoration to Murray-Darling Basin of 2750 GL per year would result in 18% recovery of waterbird abundance in the basin.

Pete Vesk

Trouvé, R., Nitschke, C.R., Robinson, A.P. & Baker, P.J. (2017) Estimating the self-thinning line from mortality data, Forest Ecology and Management, 402, 122-134.

I really liked this paper by Raphael Trouve and colleagues. They take a tree mortality model and use it to predict self-thinning lines. Self thinning is a phenomenon central to the link between population dynamics and ecosystem function. The paper does a nice job of making the link explicit through statistical modelling of empirical data on mortality. It opens the way to modelling how self-thinning might vary from place to place by virtue of environment and species.

David Wilkinson

Courchamp, F. & Bradshaw, C.J.A. (2018) 100 articles every ecologist should read. Nature Ecology & Evolution 2, 395–401.

In today’s publish or perish environment there is a lot of published literature every year. We need to stay on top of new developments in our field but we can’t read everything, and it becomes too easy to forget that we are dwarfs standing on the shoulders of giants. This paper aimed to collate a list of seminal ecological papers that all ecologists should read regardless of their particular research focus. They achieve this using expert elicitation of “ecology experts” (read: journal editors) and random sample voting. Most people aren’t going to read them all, but you should try!

…Or maybe this wasn’t the best paper of 2017 and I just wanted an excuse to nominate 101 papers. Read it and find out.

Chung-Huey Wu

Toomey, A.H., Knight, A.T. & Barlow, J. (2017) Navigating the space between research and implementation in conservationConservation Letters, 10.5, 619-625.

‘Research-implementation gap’, the challenge of translating and implementing evidence-based scientific methods in real-world management, is widely recognized.  Interestingly, viewing this challenge as a ‘gap’ may actually make things worse, as it may attract researchers to produce more expert-based science, without the inputs from managers and stakeholders, to ‘fill the gap’ (“Let us ‘expert scientists’ to develop the best, practically-usable tools and teach you ‘non-experts’ how to use them”).  In their article, Toomey et al. argue that we should re-conceptualize the implementation issue as overlapping and interacting ‘spaces’ of science, decision-making, local knowledge, value, and human behaviour instead of a ‘gap’.  They explain how such mindset may help engage scientist and public together in developing research outputs that are both ‘for the people in need’ and ‘by the people in need’ (“Let us understand each other’s knowledge, values, and concerns, and do research together to create ‘our’ solutions”), fundamentally resolving the barriers between science and management implementation.

Jian Yen

Blanchard, J.L., Heneghan, R.F., Everett, J.D., Trebilco, R., & Richardson, A.J. (2017) From Bacteria to Whales: Using Functional Size Spectra to Model Marine Ecosystems. Trends in Ecology and Evolution 32, 174-186.

Size is often viewed as a “master variable” in ecology, acting as a proxy for many morphological and physiological traits. In this paper, Julia Blanchard and colleagues give an overview of existing size-based models, with an emphasis on aquatic ecosystems. They look towards a future where size-based models can be applied to all size classes (“From Bacteria to Whales”) in all ecosystems. They outline one key advance that will support this: the inclusion of functional traits in size-based models. In this context, functional traits can soak up variation that isn’t captured by size alone. This paper is an easy read, succinctly reviews a huge literature, and outlines a clear vision for the next steps in size-based ecological modelling.

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