The best ecology and conservation papers of 2012

We asked everyone at QAECO to name their favourite ecology and conservation science paper of 2012. Here’s what they chose and why.

Geoff Heard

Hudgens, B.R. et al. (2012). How complex do models need to be to predict dispersal of threatened species through matrix habitats? Ecological Applications 22: 1701-1710.

This paper covers several areas of interest for me, and neatly wraps them into one. It’s about testing the value of more complex models of dispersal for an endangered butterfly to simpler ones. Hudgens and co assessed the relationship between a model’s predictive capacity and the financial cost of developing it. The answer: simple models performed poorly when applied to novel situations, and more complex (and better) models weren’t drastically more expensive to develop. So, in this case, they concluded that spending the bucks on a more complex model was worth it.


Martin et al. (2012) argue that failure to act quickly led to the extinction of the the Christmas Island Pipistrelle (Pipistrellus murrayi). Photo:

Els Van Burm

Martin, T.G. et al. (2012) Acting fast helps avoid extinction. Conservation Letters 5: 274-280.

I choose this one because I am really interested in the question “how long should we wait and gather more information before making an environmental management decision?”.

Freya Thomas

Ruger N, et al. (in press) Functional traits explain light and size response of growth rates in tropical tree species. Ecology.

This paper explores relationships between functional traits (wood density, adult stature, seed mass and leaf traits) and demographic rates with the aim of providing insight into the functional constraints of life history strategies in tropical tree species. Awesomely, Ruger et al. use a hierarchical bayesian model where individual tree growth is a function of light and size and then functional traits are used as linear species predictors. Relating growth characteristics to functional traits in a hierarchical model allows a mechanistic understanding of trait-rate relationships, while at the same time allowing for the inclusion of several sources of uncertainty such as intraspecific variability of traits and measurement error! This was an interesting paper in terms of functional trait and growth analysis but also a very useful example of using hierarchical bayesian models.

Luke Kelly


Didham et al. argue that landscape ecologists should focus on the ‘interdependent’ effects of habitat loss and fragmentation. Photo: © Marek and Ewa Wojciechowscy

Didham, R, et al. (2012) Rethinking the conceptual foundations of habitat fragmentation research. Oikos 121:161-170.

The authors do just what the title promises: they challenge ecologists to rethink how they study landscape change and argue for a greater focus on the interacting drivers of habitat fragmentation.

Mick McCarthy

McCarthy, D.P. et al. (2012) Financial costs of meeting global biodiversity conservation targets: current spending and unmet needs. Science 338: 946-949.

This is an important paper because it is the first to examine, at a global level, how much money is needed to conserve biodiversity. I’ve tackled this at a national level for one group of species (Australian birds; McCarthy, M.A., Thompson, C.J., and Garnett, S.T. (2008). Optimal investment in conservation of species. Journal of Applied Ecology 45: 1428-1435.). And plenty of studies have asked how should money be spent most efficiently to conserve global biodiversity. But the question of what is a sufficient level of global funding for conservation is important. While the methods used in the paper are limited by the available data, this paper helps us answer this key question.
(Note: the primary author is not related to me!)

Edit: I’m also adding one more. I thought “What’s the most important paper from QAECO?” That is hard to answer, but this should be massive:

Pollock, L. J. et al. (2012) The role of functional traits in species distributions revealed through a hierarchical model. Ecography 35: 716-725.

Why? It shows how functional traits can explain the response of species to the environment. It does it by building hierarchical models in which the regression coefficients of species distribution models are a function of the traits. This integrates two major areas of ecology: functional traits and species distribution models. Researchers in both these large fields need to be aware of this paper.

Michael Bode

M’Gonigle, L.K. et al. (2012) Sexual selection enables long-term coexistence despite ecological equivalence. Nature 484: 506-509.

Understanding how multiple biotic units – genes, species, communities – can stably coexist is one of the most important questions in ecology. This paper used an individual-based spatial simulation model to demonstrate that sexual selection can allow two ecologically identical species to coexist indefinitely, as long as the environmental is heterogeneous and there are costs involved in searching for a suitable mate. I liked the fact that data-free reductionist ecological theory is alive and well, trying to understand what might be internally consistent and possible. I wish the paper had better explained why these three disparate factors were necessary for coexistence.


The Great Barrier Reef. Photo: Copyright (c) 2004 Richard Ling

Skip Woolley

Harnik, P. et al. (2012) Extinctions in ancient and modern seas. Trends in Ecology & Evolution 27: 608-617.

This paper is one of the first reviews to synthesize information on extinctions in the marine environment. Unlike terrestrial environments, information on extinctions and extinction risks are largely unknown. This paper is novel as it aims to collate information on causes of extinction, which species will adapt and which species are at most at risk of extinction under current and future climate regimes. Although there are issues with sparse fossil records, limited taxonomy and data poor sampling in many marine environments, this paper is a good first attempt to gather relevant information on patterns and processes of extinction in the marine environment.

Gurutzeta Guillera-Arroita

Wenger, S., & Olden, J. (2012). Assessing transferability of ecological models: an underappreciated aspect of statistical validation. Methods in Ecology and Evolution 3: 260-267.

A reminder on the importance of considering model transferability and the risk that very flexible models such as those based on machine-learning methods may be less transferable and provide less interpretable relationship curves. More on the paper at MEE’s blog (

Stefano Canessa

Christie, M.R. et al. (2012) Genetic adaptation to captivity can occur in a single generation. PNAS 1090: 238-242.

We know adaptation to captivity is a serious issue in captive breeding programs, but this paper shows, using fisheries data, just how detrimental it can be. One generation is almost no time when breeding from very few founders, and yet the fitness of released individuals can already decrease quite dramatically. So this paper is my pick for 2012 because it’s a powerful reminder, with empirical evidence, that ex-situ conservation requires us to think clearly in advance.

Gerry Ryan (so keen he’s even picked two)

Phillis, et al. (in press) Multiple pathways to conservation success. Conservation Letters


A Forest Elephant (Loxodonta cyclotis) Photo:

Thought this was an inventive test of the science-policy-public nexus and a good reminder of how scientific soundness is not the determinant of how change is affected. As if we needed one.

Nicholson et al. (2012) Making Robust Policy Decisions Using Global Biodiversity Indicators. PLOS ONE.

This one struck me a s a well thought out examination of some high profile global indicators and realistic potential policy decisions, with important caveats in their use as the outcome.

Pia Lentini

Noss, R. F., A. P. Dobson, R. Baldwin, P. Beier, C. R. Davis, D. A. Dellasala, J. Francis, H. Locke, K. Nowak, R. Lopez, C. Reining, S. C. Trombulak, and G. Tabor. 2012. Bolder thinking for conservation. Conservation Biology 26:1-4.


An invasive exotic species, Sagittaria platyphylla, dominating a wetland in Cobrawonga, Victoria. Photo: Jane Catford

Jane Catford

Dawson, W., M. Fischer, and M. van Kleunen. 2012. Common and rare plant species respond differently to fertilisation and competition, whether they are alien or native. Ecology Letters 15:873-880.

Looking at more than just species origin – thankfully!

Jose J Lahoz-Monfort

Yackulic, C. et al. (in press) Presence-only modelling using MAXENT: when can we trust the inferences? Methods in Ecology and Evolution

I think it’s a perfectly valid and clear warning message for the abuse of presence-only methods like Maxent in constructing species distribution models.

Chris Jones

Zenner E.K, Olszewski S.L, Palik B.J, Kastendick D.N, Peck J.E, and Blinn C.R (2012) Riparian vegetation response to gradients in residual basal area with harvesting treatment and distance to stream. Forest Ecology and Management 283: 66-76

It just happens to relate to both of my primary research areas in one fowl swoop. Gold.

Diego Correa


Colombian montane forests (Santuario de Fauna y Flora Otún-Quimbaya, Risaralda). Photo: Diego Correa

Lavorel, S & Grigulis, K (2012). How fundamental plant functional trait relationships scale-up to trade-offs and synergies in ecosystem services. Journal of Ecology 100: 128-140.

Interesting paper that proposes a framework that would help to support the management of ecosystem services, based on functional traits of plants.

Carly Cook

Martin, T et al. (2012) Eliciting Expert Knowledge in Conservation Science. Conservation Biology 26: 29-38.

Inka Veltheim

Jonsen et al. (in press). State-space models for bio-loggers: a methodological road map. Deep-Sea Research Part II. Topical Studies in Oceanography.

The paper provides a good review of methods for analysing animal movement data and for building mechanistic models of animal movement.


Kearney et al. 2010 explored mechanistic and correlative models of Greater Glider distribution. Photo: Brendan Wintle

Dormann et al. (2012) Correlation and process in species distribution models: bridging a dichotomy. Journal of Biogeography. 12: 2119-2131.

Ecologists love to argue about semantics. Dormann et al. set the record straight when it comes to ‘mechanistic’ vs. ‘correlative’ models of species distributions.

So, what do you think? Let us know what your selection is in the comments section.

Merry Christmas and Happy New Year!

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4 Responses to The best ecology and conservation papers of 2012

  1. Pingback: Recent Qaecologist blog posts | Quantitative & Applied Ecology Group

  2. Sadly the proportion of female first authors seems to reflect publishing rates in scientific journals. 5/18 of the papers nominated is similar to the ~30% female first authorship across science, according to this article
    Women tend also to be under-represented as authors, in other words, we publish less, exacerbating the existing bias in numbers of women in research.

  3. George Evans says:

    No shortage of white males. Merry Christmas.

    • Hi George.

      Thanks for the brief yet perceptive comment. Of the 18 papers chosen, only 45 (Tara Martin has two papers listed) had a woman as lead author (edit: with Laura Pollock’s paper added, there are now 6/19 with female first authors). Unconscious gender bias exists, and we might have succumbed to it. These papers were selected by individuals within the lab who chose to nominate one. We didn’t set detailed criteria, or ask people to be aware of unconscious gender bias. Those two actions might have helped limit any bias.

      Of the people making selections, 10 were male and 7 were female. This is a slight under-representation of women in our group, where women are in the majority. It is possible that self-selection of contributors was biased against women – there can be a tendency for women to be less active online than men.

      We have been discussing gender issues within our lab group and encouraging other research groups to do the same. You might be interested in some of our thoughts on the subject.

      Similarly, there might also be unconscious racial bias in our selections. If racial bias does exist in our selections, we suspect it might reflect authorship in the ecology and conservation journals that we tend to read.

      Feel free to nominate your own best paper!

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