QAECO’s favourite ecology and conservation papers of 2014

We asked everyone at QAECO to name their favourite ecology, conservation and decision science papers of 2014. The list shows our diverse interests including models and monitoring, fire and frogs, botany and biodiversity and invasions and indices. Here’s what we chose and why. Enjoy!

Happy Christmas and New Year from everyone at QAECO!

Freya Thomas

Muir, A.M, Vesk, P.A, Hepworh, G (2014) Reproductive trajectories over decadal time-spans after fire for eight obligate-seeder shrub species in south-eastern Australia. Australian Journal of Botany, 62: 369-378.

Information about trajectories of reproductive performance for many plant species is limited and often qualitative.  This neat paper estimates flowering and fruiting quantitatively for 8 obligate shrub species in south-eastern Australia and infers reproductive maturity times by generating reproductive response curves over time-since fire sites.  A nice example of incorporating quantitative estimates of plant life history trajectories into ecological fire management.


Natasha Cadenhead

Farnsworth, L. M., Nimmo, D. G., Kelly, L. T., Bennett, A. F., & Clarke, M. F (2014) Does pyrodiversity beget alpha, beta or gamma diversity? A case study using reptiles from semi‐arid Australia. Diversity and Distributions, 20: 663-673.

Another interesting paper from the Mallee Fire and Biodiversity Project, and another nail in the coffin for the “pyrodiversity begets biodiversity” hypothesis, despite the catchy maxim. This paper investigates whether the number of fire-age classes in a landscape is correlated with the mean number of species at a site (alpha diversity), the compositional similarity between landscapes (beta diversity), or the total number of species in a landscape (gamma diversity). I haven’t read a lot about measuring different types of biodiversity, so this was a great way to understand the concept, and to see how the different measures can interact with each other. Plus: fire, reptiles, spinifex, semi-arid landscapes – the case study is right up my alley!

Reid Tingley

Y.E. Stuart, T.S. Campbell, P.A. Hohenlohe, R.G. Reynolds, L.J. Revell, and J.B. Losos (2014) Rapid evolution of a native species following invasion by a congener. Science 346: 463-466.

This is a neat example of just how quickly strong selective forces can result in evolutionary change. I particularly liked how the authors were able to sift through alternative hypotheses using a variety of experiments and approaches.

David Duncan

Michael, D.R., Wood, J.T., Crane, M., Montague-Drake, R., Lindenmayer, D.B. (2014) How effective are agri-environment schemes for protecting and improving herpetofaunal diversity in Australian endangered woodland ecosystems? Journal of Applied Ecology, 51: 494–504.

My choice is one I haven’t picked over every detail of, but liked immediately.  It is the latest work emerging from Damien Michael and others’ study of herpetofauna in the agricultural landscapes of southern NSW. As far as the researchers go, I think this work shows how the combination of strong ecological expertise, research questions, and analytical framework can result in a very authoritative and constructive piece of research. I reckon it successfully links the detail a local manager or program investor can use, with the research findings of international interest.

As far as the funding and opportunity is concerned, the work was apparently done on a bunch of sites funded by the Murray CMA via Caring For our Country.  I think this is the calibre of work that all of our major investment schemes should routinely be supporting, and that learning of this kind should be an explicit performance criteria for those who design and commission investment programs.


Guillera-Arroita, G., Lahoz-Monfort, J.J., MacKenzie, D.I., Wintle, B.A., McCarthy, M.A. (2014) Ignoring imperfect detection in biological surveys is dangerous: a response to “fitting and interpreting occupancy models”. PLoS One 9, e99571.

My second choice is very local, in fact the lead author is about 3 m to my left at this moment. Gurutzeta Guillera Arroita and co-authors’ recently published a rejoinder to Welsh et al (2013, PLoS ONE 8:e52015)’s suggestion that accounting for imperfect detection is possibly unhelpful.  This kind of piece is a cleansing breeze for the whiff of gentle conspiracy that can settle within a discipline. As long as an idea is consistent with one’s own beliefs it will probably not be challenged in the various forums that we inhabit, e.g., conference presentation, journal article.  When a disagreement emerges, you often see science being performed at its best.  I particularly like that Guru presented the argument in person at a conference, and also made a (relatively) accessible blog post about it.

Luke Kelly

Giljohann, K.M., McCarthy, M.A., Kelly, L.T. and Regan, T.J (in press) Choice of biodiversity index drives optimal fire management decisions. Ecological Applications.

Fire management requires clear, measurable objectives. Yet objectives can be set in many different ways – even when the overall goal is to promote biodiversity. Giljohann et al. (in press) show that fire management actions aimed at maximizing biodiversity are dependent on the species of concern and the biodiversity indices used. A key take home message was that land managers should carefully consider how they specify objectives when managing fire. I’m a bit biased because I co-authored this one! It builds on some of the other work we published this year on optimal fire histories for biodiversity conservation.

Lucie Bland

Harfoot, M et al. (2014) Emergent Global Patterns of Ecosystem Structure and Function from a Mechanistic General Ecosystem Model. PLoS Biology: e1001841.

Microsoft Research and UNEP-WCMC have aimed high and published the first General Ecosystem Model that applies to both terrestrial and marine environments. Based on fundamental ecological principles and mechanistic modelling, it accurately describes emergent properties of global ecosystems. I look forward to seeing the developments of the Madingley model in different fields: conservation applications, testing of alternative stable state theory, and more complete capture of physical processes. Also, it’s open source!OLYMPUS DIGITAL CAMERA

Laura Pollock

Graham, CH, Carnaval, AC, Cadena CD et al. (2014) The origin and maintenance of montane diversity: integrating evolutionary and ecological processes. Ecography,  37: 711-719.

I like this paper because it skates the middle ground between ecological and evolutionary explanations for diversity patterns- and offers a concrete pathway for further studies. And it’s about mountains, and mountains are really important reservoirs of diversity.. and they are pretty.

Gerry Ryan

Hunter, ML, Redford, KH, & Lindenmayer, DB (2014) The Complementary Niches of Anthropocentric and Biocentric Conservationists. Conservation Biology 28: 641–645.

From the sidelines the ‘new conservation’ vs. ‘old conservation’ debacle made great tit-for-tat entertainment. If you didn’t catch the show, prominent conservationists threw mud around over whether people had any place in conservation priorities; there are stacks of links in that article. Hunter, Redford, and Lindenmayer provided a sound “Surely we should be united against the common enemy” moment in a debate was just as important for exploring our underlying philosophies, and just as silly, as Python.

Jane Catford

Miller AL, Diez JM, Sullivan JJ, Wangen SR, Wiser SK, Meffin R, Duncan RP (2014) Quantifying invasion resistance: the use of recruitment functions to control for propagule pressure. Ecology 95: 920–929.


This paper tackles a very important topic in invasion ecology: how to assess and quantify ecosystem invasibility. Ecosystem invasibility has been widely discussed but it has proved difficult to assess because of the number of factors that are involved in the invasion process. Miller and colleagues disentangle propagule pressure from invasibility by using a (really innovative) seed addition experiment, the findings of which are complemented by results of a field survey. They remove the need to investigate the influence of species invasiveness by focusing on a single invasive species. The authors build on a conceptual/methodological paper that they wrote in 2009 by showing how an “index of safe sites” can be applied and used to interpret the invasibility of six different ecosystems in New Zealand. In short, I think this paper is an absolute ripper: it gets my vote for best paper of 2014.

Chris Baker

I have two. A maths maths one and a maths one.

Leander, Rachel, Suzanne Lenhart, and Vladimir Protopopescu (2014) Optimal Control of Continuous Systems with Impulse Controls. Optimal Control Applications and Methods doi:10.1002/oca.2128.

Biological systems change continuously over long time-scales, while human intervention often occurs at a much shorter time-scales. For example in projects where invasive populations are baited, there are often large gaps between successive baiting events. We can call this type of invasive species control ‘pulse control’. As with any invasive species problem, we are interested in optimising baiting schedules, and this paper sets up the mathematical machinery to better analyse these control problems.

Lampert, Adam, Alan Hastings, Edwin D. Grosholz, Sunny L. Jardine, and James N. Sanchirico (2014) Optimal Approaches for Balancing Invasive Species Eradication and Endangered Species Management. Science 344: 1028–31.

Completely removing an invasive species can have negative consequences for endemic species. This paper solves for the optimal way to eradicate and invasive plant, while ensuring that a threatened bird species, which uses the invasive plant, doesn’t go extinct.

Saras Mei Windecker

Is biodiversity offset effective? This paper concludes that current restoration efforts result in a net loss of biodiversity and have a high rate of failure. The authors suggest we need to reconsider how we allocate precious conservation resources.

Curran, M., Hellweg, S., & Beck, I (2014) Is there any empirical support for biodiversity offset policy? Ecological Applications, 24: 617–632.


Chris Jones

Yes, this is my own paper but it is my first one after 7 years of postgrad research so I don’t care. To be honest though, I do really like this paper, for it’s contribution to a growing field of research, and the way we were able to bring the study together. Dense woody regrowth is increasing in extent worldwide and is a problem for vegetation structure and function. Thinning is a commonly cited solution but its influence on understorey vegetation is largely unknown. We explore all of this in this paper.

Jones CS, Duncan DH, Rumpff L, Thomas FM, Morris WK, and Vesk PA. [in press] Empirically validating a dense woody regrowth ‘problem’ and thinning ‘solution’ for understorey vegetation. Forest Ecology and Management, DOI:10.1016/j.foreco.2014.12.006

Cindy Hauser

Springborn, M.R. (2014) Risk aversion and adaptive management: insights from a multi-armed bandit model of invasive species risk. Journal of Environmental Economics and Management, 68, 226-242.

Those of us who geek out over adaptive management algorithms are frequently disappointed to discover that the elegance of active adaptive management rarely translates to major improvements in outcomes. Springborn points out that this might be because we’re all hung up on the mean outcome. If we instead look at the entire distribution of plausible outcomes then these approaches have more to offer, such as guarding against disaster.

Hannah Pearson

Favaro, B. (2014). A carbon code of conduct for science. Science, 344: 1461

The article that has excited me the most and had the most impact on me was Brett Favaro’s Carbon Code of Conduct for Science.

And there is another one which has influenced me equally.

Herrando-Perez, S., Brook, B.W. & Bradshaw, C.J.A. (2014). Ecology needs a convention of nomenclature. Bioscience, 64, 311–321.


Stefano Canessa

I have chosen four papers this year, part of the ongoing debate on the role of zoos in species conservation. Within this debate, people agree that zoos can be important for conservation, and that their potential is still to be realised. People agree that threatened species are currently under-represented in zoos. However, people also agree that the potential impact of zoos is multi-faceted, and can go beyond the establishment of captive populations. Apparently, people do not yet agree on how to achieve that maximum potential. Lesson: conservation decisions can be hard!

Martin, T. E., Lurbiecki, H., Joy, J. B. and Mooers, A. O (2014) Mammal and bird species held in zoos are less endemic and less threatened than their close relatives not held in zoos. Animal Conservation, 17: 89–96.

Bowkett, A. E (2014) Ex situ conservation planning is more complicated than prioritizing the keeping of threatened species in zoos. Animal Conservation, 17: 101–103.

Fa, J. E., Gusset, M., Flesness, N. and Conde, D. A (2014) Zoos have yet to unveil their full conservation potential. Animal Conservation, 17: 97–100.

Martin, T. E., Lurbiecki, H. and Mooers, A. O (2014) The economic geography of ex situ conservation. Animal Conservation, 17: 104–105.

Alejandra Moran-Ordonez 

Merow, C., Smith, M. J., Edwards, T. C., Guisan, A., McMahon, S. M., Normand, S., Elith, J (2014) What do we gain from simplicity versus complexity in species distribution models? Ecography 37: 1267-1281.

How many predictors should I use to fit my model? What are the problems/advantages of using more or less predictors? Should I use proximal or distal predictors? Is it advisable to fit a complex model with the data set I have? This paper explores some of these questions but the main take home message is that there is not a simple answer!: the complexity of model must depend on the study objective, the attributes of the data and the understanding of the ecology of the species or the biological process under study.


Gurutzeta Guillera-Arroita 

Fithian, W., Elith, J., Hastie, T., Keith, D. A (2014) Bias correction in species distribution models: pooling survey and collection data for multiple species. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12242

An exciting development in species distribution modelling! This paper presents methods for the joint analysis of presence-only and presence-absence data to exploit their complementary strengths. Presence-absence data is of higher quality but usually quite restricted in amount; on the other hand presence-only datasets tend to be larger but these data are susceptible to sampling bias. The method presented in this paper combines both types of data and, by pooling data from many species, it attempts to correct for sampling bias that may be present in the presence-only data.

Brendan Wintle

Pollock, L.J., Tingley, R., Morris, W.K., Golding, N., O’Hara, R.B., Parris, K.M., Vesk, P.A., and McCarthy, M.A. 2014. Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM). Methods in Ecology and Evolution, 5:397

This paper breaks new ground in distribution modelling; elegantly dealing with species interactions when modelling a species distribution. Should be a citation classic!

Estibaliz Palma

Laughlin, D.C (2014) Applying trait-based models to achieve functional targets for theory-driven ecological restoration. Ecology Letters 17: 771–784. 

Great paper that brings theory and practice together. First, it reviews the role of plant traits in community assembly and ecosystem functioning using ecological theory. Then, it explains how restoration goals can be defined in terms of traits and the benefits of this approach to achieve a more rigorous, quantitative management framework. Finally, it applies the trait-based framework to particular restoration problems.

Alina Pung

Robinson, N.M., Leonard, S.W.J., Bennett, A.F. and Clarke, M.F (2014) Refuges for birds in fire-prone landscapes: The influence of fire severity and fire history on the distribution of forest birds. Forest Ecology and Management 318: 110-121.


This paper explores the impact of time since fire and fire severity on bird species richness and composition. The authors highlight he importance of unburnt patches of long time since fire as refuges for birds. Additionally, they discuss the potential application of prescribed burning in reducing the severity of future wildfires.

Mick McCarthy

Bland, L.M., Collen, B., Orme, C.D.L. and Bielby, J (in press) Predicting the conservation status of data-deficient species. Conservation Biology.

When assessing species’ extinction risk using IUCN criteria, many species will be listed as being data deficient – we just don’t have the data to assess them against the criteria. However, many of those species might be at risk. Lucie Bland shows that we can predict conservation status based on what we do know. The result is that many of these data deficient species are likely to be threatened, so they will warrant conservation actions.

Heini Kujala

Kelly, L.T., Bennett, A.F., Clarke, M.F. & McCarthy, M.A (in press) Optimal fire histories
for biodiversity conservation. Conservation Biology.

Linking species distribution models, biodiversity indices and decision tools to solve problems in fire ecology. What’s not to like!

Amy Whitehead

Garrard, G.E., S.A. Bekessy, M.A. McCarthy and B.A. Wintle (2014) Incorporating Detectability of Threatened Species into Environmental Impact Assessment. Conservation Biology. doi:10.1111/cobi.12351


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2 Responses to QAECO’s favourite ecology and conservation papers of 2014

  1. Pingback: Dbytes #180 (20 January 2015) | Dbytes

  2. Pingback: Recommended Reading | December 2014 | Cindy E Hauser

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