QAEco’s favourite papers of 2015

compiled by Natalie Briscoe

For our final post of the year, we asked everyone at QAEco to name their favourite ecology, conservation and decision science papers of 2015. The list shows our diverse interests including modelling methods (metapopulation, mechanistic, and many more), traits and terminology, extreme weather events and ecosystem services, indices and interactions, detection and diversity. Here’s what we chose and why. Enjoy!

Gerry Ryan

McClintock, B. T., Onorato, D. P., Martin, J. (2015), Endangered Florida panther population size determined from public reports of motor vehicle collision mortalities. Journal of Applied Ecology, 52: 893–901.

It’s no secret that I love counting animals and new methods to do it get me a little bit excited. Single model approaches are always better than tacking together disparate information in ad hoc fashion. Here Brett McClintock and colleagues show how to tie telemetry mark-resight data with public reports of animals killed by cars to get a handle on panther numbers in Florida. Woohoo for abundance estimation!


Florida Panther Crossing. Source: Jay Iwasaki

Kate Giljohann

Costelloe, B.T., Collen, B., Milner-Gulland, E.J., Craigie, I.D., McRae, L., Rondinini, C. & Nicholson, E. (in press) Global biodiversity indicators reflect the modeled impacts of protected area policy change. Conservation Letters

This paper is a nice example of how biodiversity indicators can be used to investigate the impact of alternate policy and management actions on biodiversity status. It makes a great point, that rather than just using indices to show how we are failing to conserve biodiversity, they can be used to tell us how we can best conserve biodiversity. Their case study also highlights the importance of measuring management effectiveness and not just protected area coverage to indicate conservation success – cool.

Jane Elith

MUG Kraemer, SI Hay, DM Pigott, DL Smith, GRW Wint, N Golding (in press) Progress and Challenges in Infectious Disease CartographyTrends in parasitology.

The models I work with are also used in epidemiology, and this review is an interesting summary of the state of play in infectious diseases modelling and mapping. Nick Golding, the last author, will be furthering his research based at QAEco next year, and I’m looking forward to collaborating with him and strengthening our links with the epidemiological modellers here at Melbourne Uni.

Hannah Fraser

Fraser, H., Garrard, G. E., Rumpff, L., Hauser, C. E., & McCarthy, M. A. (2015). Consequences of inconsistently classifying woodland birds. Frontiers in Ecology and Evolution, 3(83).

This article provides the first quantitative evidence to resolve debate about whether consistent terminology is required in ecology. By investigating the use of the term ‘woodland bird’ the authors (all QAEco members) demonstrate that i) the term is being used inconsistently, ii) this is due to difference in study aims and linguistic uncertainty about ‘woodlands’ and ‘woodland birds’, and iii) results are strongly dependent on how the term is used.

Charbonneau, B. R. (2015). A Review of Dunes in Today’s Society. Coastal Management, 43(5), 465–470.

This article is written to address hysteria and miscommunication in the wake of Superstorm Sandy. Sand dunes in New Jersey were very effective at protecting coastal settlements during the storm and there is now a strong emphasis on dune health but a lack of terminological consistency impeding this process. The author clarifies the appropriate use of terms ‘blowout’, ‘washout’, and bowling.

Lucie Bland

Philosophical Transactions Series B Special Issue – Marine regime shifts around the globe

My favourite paper of 2015 was an entire special issue of the Philosophical Transactions Series B on “Marine regime shifts around the globe”. Sudden and long-lasting shifts in ecosystem structure and function are increasingly documented in marine ecosystems. This is important for the study of complex systems, but also for management as these regime shifts affect commercial fisheries and mega-diverse coral reefs. The 16 papers in this special issue are very special to me as they constitute half of my sample size for a systematic review on the collapse of marine ecosystems!


Kelp Forest. Source: NOAA’s National Ocean Service.


Luke Kelly

Hanski (2015) Habitat fragmentation and species richness. Journal of Biogeography 42, 989–994.

Fahrig (2015) Just a hypothesis: a reply to Hanski. Journal of Biogeography 42, 989–994.

I’m nominating one of the most interesting correspondences in the ecology literature in 2015. Two leaders in spatial ecology – Lenore Fahrig and Ilkka Hanski – debate how to measure the influence of habitat fragmentation on species richness. While it’s an insightful debate about study design and models in spatial ecology it is also a bit frustrating to see continued divisions between landscape ecology and metapopulation ecology. On that note, watch this space for publications by QAEco student Dini Fardila in 2016!

Inka Veltheim

Fitzpatrick, M.J., Mathewson, P.D., & Porter, W.P. (2015) Validation of a mechanistic model for non-invasive study of ecological energetic in an endangered wading bird with counter-current heat exchange in its legs. PLoS ONE, 10, e0136677.

Mechanistic models can be used to understand energy expenditure of animals, as well as physiological and behavioural responses to their environment. This study incorporates counter-current heat exchange in legs and wading behavior to provide estimates of energy expenditure, and a mechanistic understanding of heat loss and environmental tolerance of Whooping Cranes (Grus americana). The mechanistic model, Niche Mapper, incorporating these additional features, can be applied to a wide range of long-legged wading birds and used to advise threatened species conservation. A paper about a crane, a non-invasive method, and a threatened species, with results that can be applied to conservation management. What’s there not to like!

Pia Lentini

Butt, N., Seabrook, L., Maron, M., Law, B. S., Dawson, T. P., Syktus, J., & McAlpine, C. A. (2015). Cascading effects of climate extremes on vertebrate fauna through changes to low‐latitude tree flowering and fruiting phenology. Global Change Biology 21, 3267–3277.

This paper provides a nice framework for thinking about how climate changes and associated extreme weather events are likely to impact on key phonological patterns of fruiting and flowering. These changes affect animal species dependent on these resources, and in turn the associated ecosystem services they provide such as pollination and seed dispersal. Although the authors focus on vertebrate fauna in subtropical and tropical regions, I think it’s equally useful for guiding thinking about invertebrates or higher-latitudinal areas.

José Lahoz-Monfort

Chambert T, Miller DAW, Nichols JD (2015) Modeling false positive detections in species occurrence data under different study designs. Ecology, 96, 332-339.

A nice round paper that gives a clear structured overview of a specific area of statistical modelling: accounting for false positives in occupancy-detection models. It describes the different modelling approaches available and provides R code to run simulations and analysis for both maximum-likelihood and Bayesian inference. The definitive starting point if you want to get into this topic!

Finley Roberts

McGregor, H. W., S. Legge, J. Potts, M. E. Jones, and C. N. Johnson. 2015. Density and home range of feral cats in north-western Australia. Wildlife Research 42:223.

Hugh McGregor has come up with some cool ways to hack’ existing technologies to monitor feral cats: last year at ESA he showed us the world from a cat’s point of view, playing footage from Go-Pro cameras strapped to feral cats to investigate what influences their hunting success (you can watch the footage – with Hugh’s Attenborough-like commentary – here). At AMS this year he presented the research published in the paper above, estimating feral cat densities in WA’s Kimerberly region. Using photos of cats, captured by camera traps, Hugh painstakingly identified which snaps were of which individual cats (using their markings), using mark recapture analysis he derived an estimate of numbers and home ranges. Cats are estimated to be present in very low densities, meaning that it’s incredibly difficult to catch/kill enough of them to put a long-term dent in their numbers, potentially making the Government’s cat killing plan challenging to implement in much of Northern Australia.

Geoff Heard

Thomas, C. D. and G. Palmer. 2015. Non-native plants add to the British flora without negative consequences for native diversity. Proceedings of the National Academy of Sciences 112:4387-4392.

Over the last two years I had the privilege of working with Chris Thomas at the University of York as part of a Victorian Postdoctoral Research Fellowship. I watched Chris and post doc Georgina Palmer bash this paper into shape, and learnt much from my fly-on-the-wall vantage point. What I really like about this paper is that it makes me squirm a little. It challenges my Antipodean view of evil invaders and heroic natives. And it tells me that the human-hand in ecosystem evolution is not to be repudiated, but rather accepted and managed in a sensible, objective and evidence-driven approach.

Freya Thomas

Wenk, EH, and Falster, DS (2015) Quantifying and understanding reproductive allocation schedules in plantsEcology and Evolution, 5, 5521 – 5538.

Reproductive maturity in plants fascinates me.  This was a neat paper to read because it reviews the literature on how perennial plants allocate energy to reproduction, describes theoretical models of reproductive allocation in plants and highlights the wide range of reproductive schedules across species.  The authors conclude that surprisingly little data actually exists about reproductive allocation in perennial plants, despite this being one of the most fundamental components of life history strategies.  A motivating paper to read.

Lupinus variicolor

Lupinous variicolor. Source: D In Orbit

Pete Vesk

Winfree, R., Fox, JW., Williams, NM., Reilly, JR., and Cariveau, DP., (2015) Abundance of common species, not species richness, drives delivery of a real-world ecosystem service. Ecology Letters 18: 626–635.

I quite liked this paper from Rachel Winfree and colleagues who addressed a continuing question in ecosystem function research: what components of biodiversity are most important to change in the supply of ecosystem services. Here they used the Price equation, which comes from evolutionary genetics where it is used to attribute the contributions to evolutionary change of natural selection and other processes.  In Winfree et al’s case, they used the Price equation to partition the changes in pollination success in 4 field experiments into effects of components of the pollinator biodiversity: species richness changes, species compositional changes and species abundance changes. They key result was that abundance changes (in common species) were most influential. This is an important finding from this analysis of field experiments, because most Biodiversity Ecosystem Function experiments standardise abundance and so are insensitive to assessing abundance effects.

Lai, HR, . Mayfield, MM., Gay-des-combes, JM., Spiegelberger, T. & Dwyer, JM. Distinct invasion strategies operating within a natural annual plant system, Ecology Letters (2015) 18: 336–346

I also quite liked this one from Hao Ran Lai and colleagues where they analyse how exotic plants invade an annual plant system in Western Australia. They demonstrated that species have distinct strategies for invading. Two nice things for me were the demonstration that trait hierarchies matter: some traits characterise competitive ranking and so higher positions are meaningful in understanding competitive outcomes.  Secondly that invasion is not homogeneous, there are different dimensions to invasion success and if there are different ways of being an invader, we should expect different traits to be associated with those ways of invading.

Michaela Plein 

Fründ, J. , McCann KS., Williams, NM. (in press) Sampling bias is a challenge for quantifying specialization and network structure: lessons from a quantitative niche model, Oikos

There are a multitude of reasons why your data is imperfect: maybe the vegetation is too dense to detect the lemur in it, maybe it’s too cold for your insects to be active or maybe you’re just too tired to see the birds early in the morning. Interaction network data is not exempt from this common problem. In their study, Fruend et al. (2015) neatly show how network data suffers from imperfect sampling and how this affects networks metrics, especially specialisation, that describe the network properties. While the content of the paper is already interesting, I really liked the description and illustration of the methods.

Bee on flower

Bee on flower. Source:


Saras Windecker

Moreno-Mateos, D., Meli, P., Vara-Rodriguez, M. I., & Aronson, J. (2015) Ecosystem response to interventions: lessons from restored and created wetland ecosystems. Journal of Applied Ecology, 52: 1528-1537.

Ecosystem restoration is a costly endeavour. Assessing the success of different techniques is equally challenging. In an analysis of the recovery trajectories of restored and created wetlands, this paper concludes there is not strong evidence in support of more costly revegetation restoration techniques compared to other methods.

Mick McCarthy

Ovaskainen O, Roy DB, Fox R and Anderson BJ (in press) Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models. Methods in Ecology and Evolution.

I learnt a thing or two from reading this.

Nicholson, E. (2015) Accounting for career breaks. Science, 348, 830.

I like how The Conversation decided not to publish it (or something similar by Em), yet this was one of the most-read articles in Science.

Esti Palma

González-Moreno, J.M. Diez, D.M. Richardson & M. Vilà (2015) Beyond climate: disturbance niche shifts in invasive speciesGlobal Ecology and Biogeography 24, 360–370

This is a very nice paper that investigates niche shifts of Oxalis pes-caprae between the native and the introduced ranges. It is a great example of how using a combination of climatic and disturbance-related variables, we can quantify the potential of introduced plants to keep expanding their range.

Cindy Hauser

Canessa, S., Guillera-Arroita, G., Lahoz-Monfort, J.J., Southwell, D.M., Armstrong, D.P., Chadès, I., Lacy, R.C. and Converse, S.J. (2015). When do we need more data? A primer on calculating the value of information for applied ecologists. Methods in Ecology and Evolution 6(10): 1219-1228.

Value-of-information analysis is nothing new, dating back to the 1960s and scoring mentions in the adaptive management literature since the early 1980s. Yet it’s still underused, and is really something that most of us should embark upon to justify management-centred research. Canessa and co-authors provide the most accessible treatment yet for applied ecologists, including two case studies and thoughtful discussion. They don’t, however, address a case of iterative updating and state-dependent decision-making. Here’s hoping for a sequel!

Natalie Briscoe

Ma, G., Rudolf. V., Ma, C. (2015). Extreme temperature events alter demographic rates, relative fitness, and community structure. Global Change Biology 21(5): 1794-1808.

Ma and colleagues use a range of different approaches to look at how changes in the frequency and amplitude of extreme temperatures affect the relative fitness of three co-occurring aphid species. It’s great to see studies looking past shifts in long-term averages and trying to understand the likely impacts of other dimensions of climate change. For me this study was a nice reminder of how important species-specific responses to changes in climate are likely to be in shaping communities in the future, and the benefits of integrating lab, field and modelling studies.

Heard, G. W., Thomas, C.D., Hodgson, J.A., Scroggie, M. P., Ramsey, D.S. and Clemann, N. (2015) Refugia and connectivity sustain amphibian metapopulations afflicted by disease. Ecology Letters: 18 (8) 853-863.

As someone who thinks a lot about how species respond to spatial and temporal variation in the environment, I am increasingly struck by the value of comprehensive long-term data sets. This study makes great use of an 11-year monitoring dataset on growling grass frogs, microclimates, water chemistry and chytrid infection to show that relatively barren, man-made habitats can actually help frogs persist by providing refuges from disease caused by chytrid fungus. Very nice!


Growling Grass Frog. Source: Geoff Heard.

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