Monthly Archives: March 2018

On Detecting Rare Species with Camera Trapping

If you are a conservation biologist and you wish to save all or as many species as possible, your first problem is detectability. Does the species of concern live in this habitat? If it is present how many are there, and is their abundance changing from year to year? These are fundamental questions in conservation science and there is accordingly a very large literature on how to answer these simple questions for animals in different taxonomic groups. I want to deal briefly here with rare species in which the issue of detectability is most critical.

There is a large array of papers on detection methods in the conservation literature (e.g. Brodie et al. 2018; Crates et al. 2017; Steenweg et al. 2016; Clement et al. 2016, Trolliet et al. 2014). Detection methods vary from live trapping marked individuals, visual sighting of unmarked individuals, camera photos of marked or unmarked individuals, sign data such as tracks or scats in snow, mud or sand, DNA fingerprinting, and many clever natural-history- derived methods to measure detection. These methods are well developed for common animals (Williams et al. 2002).

Rare species are the first problem faced by all these detection methods. Rare species range from those virtually impossible to detect with current technology to those that turn up infrequently in the designated detection device. The conservation challenge of rare species is difficult if they are hard to detect and difficult to study so that we have few natural history parameters to guide conservation actions. For these we can only set aside what we think are suitable areas and conserve them.

The technology of monitoring rare species that can be detected at some reasonable level has greatly improved with the advent of passive-infrared-cameras that can be deployed 24-7 to capture images of whomever walks or swims by. But this technology raises a whole set of methodological issues that must be addressed. The first and most obvious one is the skill of the observer both in setting up the cameras and in looking at the photos to identify correctly the species present. The second and more difficult question is what to count as a detection or ‘hit’. If your question is simply ‘occupancy’ seeing one photograph in the time period of the study provides a + for occupancy. But many ecologists wish to connect the dots from occupancy scores to abundance so that some index of population numbers can arise from these camera data. To make this leap of faith relies heavily on the experimental design of the camera placements, the number of cameras, the make of the cameras (Meek et al. 2014), and the exact placement of cameras on trees or stakes to cover a specific area of habitat. Clearly if cameras are placed too close to one another, the photos from the different cameras are not independent, as most of the models of occupancy assume (Brodie et al. 2018). If bait is used with the cameras the situation becomes even more complex because some species may be attracted while others are repelled by the bait. In general camera detections or ‘hits’ for a particular species are a measure of activity rather than a direct measure of abundance, and so often the assumption is made that activity = abundance, which must be justified. In the extreme case in which a density estimate is needed from camera data, the problem of ‘edge effects’ of the sampled area must be considered just as it does with grid trapping (e.g Thornton and Pekins 2015). New approaches for estimating density from camera data appear almost daily and must be evaluated for accuracy (Nakashima et al. 2018).

We are now in the exponential phase of camera trapping with cameras put up in all sorts of spatial designs for different lengths of time with the hope that someone will have time to look at the photos and some clever statistician can factor out all the potential biases and non-independence of the resulting data. So in a nutshell my simple advice is to use cameras to gather wildlife information but think carefully about what exactly you wish to achieve: occupancy?, an index of abundance?, actual numerical abundance? population density? Or simply beautiful photos of interesting animals? And in the end you may be envious of plant ecologists whose plants do not walk away when you census them.


Brodie, J.F., et al. (2018). Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment. Biotropica 50, 5-15. doi: 10.1111/btp.12500.

Clement, M. J., J. E. Hines, J. D. Nichols, K. L. Pardieck, and D. J. Ziolkowski. 2016. Estimating indices of range shifts in birds using dynamic models when detection is imperfect. Global Change Biology 22:3273-3285. doi: 10.1111/gcb.13283

Crates, R., L. Rayner, D. Stojanovic, M. Webb, and R. Heinsohn. 2017. Undetected Allee effects in Australia’s threatened birds: implications for conservation. Emu 117:207-221. doi: 10.1080/01584197.2017.1333392

Meek, P.D., et al. (2014). Camera traps can be heard and seen by animals. PLoS ONE 9, e110832. doi: 10.1371/journal.pone.0110832.

Nakashima, Y., Fukasawa, K., and Samejima, H. (2018). Estimating animal density without individual recognition using information derivable exclusively from camera traps. Journal of Applied Ecology 55, 735-744. doi: 10.1111/1365-2664.13059.

Smith, D.H.V. and Weston, K.A. (2017). Capturing the cryptic: a comparison of detection methods for stoats (Mustela erminea) in alpine habitats. Wildlife Research 44, 418-426. doi: 10.1071/WR16159.

Steenweg, R., et al. (2016). Camera-based occupancy monitoring at large scales: Power to detect trends in grizzly bears across the Canadian Rockies. Biological Conservation 201:192-200. doi: 10.1016/j.biocon.2016.06.020

Thornton, D.H. and Pekins, C.E. (2015). Spatially explicit capture-recapture analysis of bobcat (Lynx rufus) density: implications for mesocarnivore monitoring Wildlife Research 42, 394-404. doi: 10.1071/WR15092.

Trolliet, F., et al. (2014). Use of camera traps for wildlife studies. A review. Biotechnology, Agronomy, Society and Environment (BASE) 18, 446-454.

Williams, B.K., Nichols, J.D., and Conroy, M.J. (2002) ‘Analysis and Management of Animal Populations.’ (Academic Press: New York.). 817 pp.


Seven Prescriptive Principles for Ecologists

After three of us put together a paper to list the principles of applied ecology (Hone, Drake, and Krebs 2015), I thought that perhaps we might have an additional set of general behavioural principles for ecologists. We might think of using these seven principles as a broad template for the work we do in science.

  1. Do good science and avoid opinions that are not based on facts and reliable studies. Do not cite bad science even if it is published in Science.
  2. Appreciate and support your colleagues.
  3. Because you disagree with another scientist it is not acceptable to be rude, and it is preferable to decide what experiment can solve the disagreement.
  4. Adulterating your data to remove values that do not fit your hypothesis is not acceptable.
  5. Alternative facts have no place in science. A Professor should not profess nonsense. Nonsense should be the sole prerogative of politicians.
  6. Help your fellow scientists whenever possible, and do not envy those whose papers get published in Science or Nature. Your contribution to science cannot be measured by your h-index.
  7. We have only one Earth. We should give up dreaming about moving to Mars and take care of our home here.

Many of these principles can be grouped under the umbrella of ‘scientific integrity’, and there is an extensive discussion in the literature about integrity (Edwards and Roy 2017, Horbach and Halffman 2017). Edwards and Roy (2017, pg. 53) in a (dis-) service to aspiring young academics quote a method for increasing an individual’s h-index without committing outright fraud. Horbach and Halffman (2017) point out that scientists and policymakers adopt different approaches to research integrity. Scientists discuss ‘integrity’ with a positive view of ‘good scientific practice’ that has an ethical focus, while policy people discuss ‘integrity’ with a negative view of ‘misconduct’ that has a legal focus.

The immediate problem with scientific integrity in the USA involves the current President and his preoccupation with defining ‘alternative facts’ (Goldman et al. 2017). But the problem is also a more general one, as illustrated by the long discussion carried out by conservation biologists who asked whether or not a scientist can also be an advocate for a particular policy (Garrard et al. 2016, Carroll et al. 2017).

The bottom line for ecologists and environmental scientists is important, and a serious discussion of scientific integrity should be part of every graduate seminar class. Scientific journals should become more open to challenges to papers that use faulty data, and maintaining high standards must remain number one on the list for all of us.

Carroll, C., Hartl, B., Goldman, G.T., Rohlf, D.J., and Treves, A. 2017. Defending the scientific integrity of conservation-policy processes. Conservation Biology 31(5): 967-975. doi: 10.1111/cobi.12958.

Edwards, M.A., and Roy, S. 2017. Academic research in the 21st century: Maintaining scientific integrity in a climate of perverse incentives and hypercompetition. Environmental Engineering Science 34(1): 51-61. doi: 10.1089/ees.2016.0223.correx.

Garrard, G.E., Fidler, F., Wintle, B.C., Chee, Y.E., and Bekessy, S.A. 2016. Beyond advocacy: Making space for conservation scientists in public debate. Conservation Letters 9(3): 208-212. doi: 10.1111/conl.12193.

Goldman, G.T., Berman, E., Halpern, M., Johnson, C. & Kothari, Y. (2017) Ensuring scientific integrity in the Age of Trump. Science, 355, 696-698. doi: 10.1126/science.aam5733

Hone, J., A. Drake, and C. J. Krebs. 2015. Prescriptive and empirical principles of applied ecology. Environmental Reviews 23:170-176. doi: 10.1139/er-2014-0076

Horbach, S.P.J.M., and Halffman, W. 2017. Promoting virtue or punishing fraud: Mapping contrasts in the language of ‘scientific integrity’. Science and Engineering Ethics 23(6): 1461-1485. doi: 10.1007/s11948-016-9858-y.


A Need for Champions

The World has many champions for the Olympics, economists have champions for free trade, physicists have champions for the Hadron Collider, astronomists for space telescopes, but who are the champions for the environment?  We have many environmental scientists who try to focus the public’s attention on endangered species, the state of agriculture, pollution of air and water, and the sustainability of marine fisheries, but they are too much ignored. Why do we have this puzzle that the health of the world we all live in is too often ignored when governments release their budgets?

There are several answers to this simple question. First of all, the ‘jobs and growth’ paradigm rules, and exponential growth is the ordained natural order. The complaint we then get is that environmental scientists too often suggest that studies are needed, and the results of these studies produce recommendations that will impede jobs and growth. Environmental science not only does not produce more dollar bills but in fact diverts dollars from other more preferred activities that increase the GDP.

Another important reason is that environmental problems are slow-moving and long-term, and our human evolutionary history shows that we are poor at dealing with such problems. We can recognize and adapt quickly to short-term problems like floods, epidemics, and famines but we cannot see the inexorable rise in sea levels of 3 mm per year. We need therefore champions of the environment with the charisma to attract the world’s attention to slow-moving, long-term problems. We have some of these champions already – James Hansen, David Suzuki, Tim Flannery, Paul Ehrlich, Naomi Klein – and they are doing an excellent job of producing scientific discussions on our major environmental problems, information that is unfortunately still largely ignored on budget day. There is progress, but it is slow, and in particular young people are more aware of environmental issues than are those of the older generation.

What can we do to change the existing dominant paradigm into a sustainable ecological paradigm? Begon (2017) argues that ecology is both a science and a crisis discipline, and his concern is that at the present time ecological ideas about our current crises are not taken seriously by the general public and policy leaders. One way to change this, Begon argues, is to reduce our reliance on specific and often complicated evidence and convert to sound bites, slogans that capture the emotions of the public rather than their intellect. So, I suggest a challenge can be issued to ecology classes across the world to spend some time brainstorming on suitable slogans, short appealing phrases that encapsulate what ecologists understand about our current problems. Here are three suggestions: “We cannot eat coal and oil – support agriculture”, “Think long-term, become a mental eco-geologist”, and “The ocean is not a garbage can”. Such capsules are not for all occasions, and we must maintain our commitment to evidence-based-ecology of course (as Saul et al. 2017 noted). That this kind of communication to the general public is not simple is well illustrated in the paper by Casado-Aranda et al. (2017) who used an MRI to study brain waves in people exposed to ecological information. They found that people’s attitudes to ecological messages were much more positive when the information was conveyed in future-framed messages delivered by a person with a younger voice. So perhaps the bottom line is to stop older ecologists from talking so much, avoid talking about the past, and look in the future for slogans to encourage an ecological world view.

Begon, M. 2017. Winning public arguments as ecologists: Time for a New Doctrine? Trends in Ecology & Evolution 32:394-396. doi: 10.1016/j.tree.2017.03.009

Casado-Aranda, L.-A., M. Martínez-Fiestas, and J. Sánchez-Fernández. 2018. Neural effects of environmental advertising: An fMRI analysis of voice age and temporal framing. Journal of Environmental Management 206:664-675. doi: 10.1016/j.jenvman.2017.10.006

Saul, W.-C., R.T. Shackleton, and F.A. Yannelli. 2017. Ecologists winning arguments: Ends don’t justify the means. A response to Begon. Trends in Ecology & Evolution 32:722-723. doi: 10.1016/j.tree.2017.08.005