Monthly Archives: February 2015

On Broad Issues in Ecology

Any young ecologist wishing to get a grasp on the most important ecological questions of the century could find no better place to start than the thoughtful compilations of Bill Sutherland and his colleagues in the U.K. (Sutherland et al. 2006; Sutherland et al. 2010; Sutherland et al. 2013). In general none of these questions by itself could be the focus of a thesis which by definition must deal with something concrete in a 2-3 year time frame, but they can serve as an overarching goal for a life in science. In all of these exercises an attempt was made to canvass dozens to hundreds of ecologists mainly from Britain but including many from other parts of the world to suggest and then cull down questions into a feasible framework.

This whole approach is most useful, but the authors recognize there are some limitations on exercises of this type. A particularly crucial limitation is:

“…there was a tendency to pose broad questions rather than the more focussed question we were aiming for. There is a tension between posing broad unanswerable questions and those so narrow that they cease to be perceived as fundamental.” (Sutherland et al. 2013, p 60).

I want to focus here on the problems of decomposing broad unanswerable questions in ecology to guide our ecological research in the future. I will discuss here only two of the population ecology questions.

Begin with question 13 on page 61 of Sutherland et al. (2013):

13. How do species and population traits and landscape configuration interact to determine realized dispersal distances?

To translate this into a project we have first to decide on a species to study and specific populations of that species. This opens Pandora’s Box because there are many thousands of species and we have to pick. We do not pick the species at random, yet we wish to develop a general answer to this question, so right away we are lost in how to translate detailed species and area specific data on movements into a general conclusion. So just for illustration suppose we pick a convenient mammal like the red squirrel of North America. It is territorial and diurnal and can be fitted with GPS collars so that movements can be readily measured, so in a sense it would be considered an ideal species to study to answer question 13, even though it is not a random choice. It ranges from Alaska to Labrador down to Arizona and North Carolina. There are a variety of landscapes throughout this geographic range, some highly altered by humans, some not. I do not know how many intensive studies of red squirrels are being or have been carried out. I would wager that the entire NSF (or NSERC, or ARC) budget could be spent to set up a series of studies of duration 5-20 years to gather these data throughout the range of this species. Clearly this will never be done, and we can only hope that the results of a few specific studies in non-randomly chosen areas over shorter time periods will answer question 13 for this one species.

Landscape configuration alone boggles my mind. It is in many areas an historical artifact of fire or human occupation and land use, and yet we need principles to generalize about it. We can model it and pretend that our models mimic reality without the availability of an experimental test. Is this the ecology of the future?

Another way to answer question 13 is to use tiny organisms like insects that we can replicate readily in small areas at minimal cost. Such studies are useful but again I am not sure they will provide a general answer to question 13. These studies can provide insights about specific insects in specific communities and with a good number of such studies on a variety of systems perhaps we would be in a position to achieve some generality. Otherwise we could be accused of “stamp collecting”.

Question 14 (Sutherland et al. 2013 page 61) has similar problems to question 13 but is more tractable I think.

14 What is the heritability/genetic basis of dispersal and movement behaviour?

This is a simpler question, given modern genetics, and can be answered for a particular species in a particular ecosystem. It is restrictive, if it is a field study, in allowing only those species that do not disperse beyond the detection range of the equipment used, and in requiring long-term genetic paternity data to estimate heritability. The methods are available but have so far been used on few species in very specific areas (e.g. superb fairy wrens in a Botanical Garden, Double et al. 2005). It is an important question to ask and answer but again the generality of the results at the present time have to be assumed rather than measured by replicated studies.

The bottom line is that questions like these two have been with ecologists for some years now and have been answered in some detail only in a few vertebrate species in very specific locations. How we generalize these results is an open question even with modern technology.

Double, M.C., Peakall, R., Beck, N.R., and Cockburn, A. 2005. Dispersal, philopatry, and infidelity: dissecting local genetic structure in superb fairy-wrens (Malurus cyaneus). Evolution 59(3): 625-635.

Sutherland, W.J. et al. 2006. The identification of 100 ecological questions of high policy relevance in the UK. Journal of Applied Ecology 43(4): 617-627. doi:10.1111/j.1365-2664.2006.01188.x.

Sutherland, al. 2010. A horizon scan of global conservation issues for 2010. Trends in Ecology & Evolution 25(1): 1-7.

Sutherland, W.J. 2013. Identification of 100 fundamental ecological questions. Journal of Ecology 101(1): 58-67. doi:10.1111/1365-2745.12025.

On Graphics in Ecological Presentations

In the greater scheme of things, how you plot your data in a paper or in a PowerPoint presentation may not be the most important thing to worry about. But if you believe that small things matter, perhaps you should read on. The standard of presentation of data in graphs in ecological presentations is often less good than is desirable. Many authors have tried to help and for more instructions please read Cleveland (1993, 1994).

Begin with a few elementary rules that I should not have to state but are often ignored:

  1. Label the axes and give the units of measure
  2. Do not use a font size that requires a microscope to read.
  3. Do not present point data without some measure of possible error.

Beyond these general rules there are many that become more specific. I want to call attention here to two rules that are often violated even in our best ecological journals. The first and simplest is never to plot in logs. It is bad enough to plot an axis in log-10 units (most people can work out that 2 in log-10 means 100 in real units), but I have never met anyone who can decipher log-e units (what does 4.38 in log-e units mean in real units?). The solution is simple. Label the scales in real units so that for example the scale may read 1-10-100-1000 with equal spacing so the axis is scaled in logs but the units are given in real measurements. In this way the reader has some idea of the scale of changes shown on the graph.

The second and perhaps more controversial problem I find with ecological graphics is the use of histograms for data that should be illustrated as point estimates (with confidence limits). If we take the advice of Cleveland (1993, page 8) histograms would be rare in scientific publications:

“The histogram is a widely used graphical method that is at least a century old. But maturity and ubiquity do not guarantee the efficacy of a tool……The venerable histogram, an old favourite, but a weak competitor, will not be encountered again [in this book].” (Cleveland 1993, p. 8)

He goes on to evaluate a whole array of graphical methods most of which are rarely seen in ecological papers. The box plot is perhaps the most common example he recommends and is available in many graphing packages. But note that EXCEL is not a very good standard for graphics, and while some if its graphics might be useful, caution is recommended. Many graphics options are available in R ( ) and some in SIGMAPLOT. Discussions about graphics packages on the web are extensive and everyone has their favourite package along with complaints about other packages. The general point is to think carefully about the graphics you use to convey your message to make it as clear as possible.

What exactly is wrong with histograms? They are misleading if the scale of the axis does not start at zero. The width of the bars is misleading if the scales are categories or precise values. The information in each histogram bar is entirely concentrated in the top of the bar and the included error bars. The amount of replication is difficult to evaluate, and distributions of data that are skewed are not presented. Finally, outliers are not identified. Perhaps the message is that if you have data that you think should be presented as a histogram, check Cleveland (1994) to see if there is not a better way to present it to your audience.

A final observation on graphics. I realize that at the present time in movies and games 3-D images and animations are quite incredible. But remember these are for entertainment not for communication. If you think your PowerPoint requires 3-D graphs with animations, be sure to check whether you are aiming more for entertainment than clear communication.

Cleveland, W.S. 1993. Visualizing Data. Hobart Press, Summit, New Jersey.

Cleveland, W.S. 1994. The Elements of Graphing Data. AT&T Bell Laboratories, Murray Hill, New Jersey.


Why We Cannot Forget about Weeds

Weeds are one of world’s most significant ecological problems. As such it is surprising that the word “weeds” does not appear at all in Sutherland et al. (2013), and only once in Sutherland et al. (2006). (Perhaps there are no weeds in the UK.) Weeds affect plant and animal communities in national parks and nature reserves as well as in agricultural landscapes and cities. We have taken a benign neglect attitude toward weeds, perhaps because they are everywhere, but ecologists may also wish to avoid the word ‘weed’ because it is not a useful aggregate term about which we can draw some ecological generalizations. How should we respond to weeds?

I consider ‘weeds’ as a collective term for what might be the worst global example of serious ecological problems (Strayer 2012). But is this collective term a very useful one? At the first step when we deal only with plants, we get confused with native plants and exotic plants. A utilitarian perspective looks at all plants to see if they are useful or harmful for humans. So some conservation biologists want to get rid of all exotic plants outside of gardens and crops, and others wish to limit all harmful plants, whether native or exotic, and call them ‘weeds’. So the rose in your front yard is indeed an exotic species but a good one. Farmers want to get rid of at least some weeds to maximize production but at the same time to tolerate other exotic species that increase production. Weeds might be thought of as a convenient grouping to simplify ecological generalizations. But alas it has not been so.

The War against Weeds is in general not going well for conservation biologists (Downey et al. 2010). While biological control is very useful for some weeds, it does not at present seem to work for most weeds of national concern. So it does not seem to be a universal solution. Herbicides work for a time and then natural selection intervenes. The problem is that weed problems are very much a local problem in being species-specific and environment-specific, so that there is no overall weed strategy that works everywhere (Vilà et al. 2011). If one is interested in community productivity, weeds may increase plant biomass which might be considered a good result for the ecosystem. Graziers may encourage weeds that plant ecologists would consider destructive to natural communities. Ecosystem ecologists might welcome weeds that increase plant cover if they reduce soil erosion and nutrient leakage into water bodies.

This conflict of interest comes home to us in quarantine restrictions on weeds. In Australia government research scientists work to increase the tolerance of exotic pasture grassess to cold and drought, even though the species in question is a weed of national significance, and improving it genetically will make it more invasive in natural communities (Driscoll et al. 2014). The problem comes back to who wants what kind of an ecological world. Generalist grazing mammals may care little about the exact species composition of the grasslands they inhabit, or alternately they may be poisoned by specific weeds that are toxic to farm animals. The devil rests in the details, so the general message is that we cannot forget species names and attributes in the War on Weeds.

As a minimum, we ought to encourage our governments to place quarantine restrictions on all plant species listed as global weeds of significance. For the present time the best predictor of whether or not an introduced plant will become a destructive weed is: what happened to that plant in other countries to which it was introduced? That you can still buy at your local plant store the seeds of an array of weeds of national significance shouts to ecologists that quarantine systems needs to be strengthened. The War on Weeds is greatly under-financed like many long term problems in ecology, and we should put more effort into developing tactics to deal with destructive weeds rather than ignoring them.

Downey, P.O. et al. 2010. Managing alien plants for biodiversity outcomes—the need for triage. Invasive Plant Science and Management 3(1): 1-11. doi:10.1614/ipsm-09-042.1.

Driscoll, D.A. et al. 2014. New pasture plants intensify invasive species risk. Proceedings of the National Academy of Sciences USA 111(46): 16622-16627. doi:10.1073/pnas.1409347111.

Strayer, D.L. 2012. Eight questions about invasions and ecosystem functioning. Ecology Letters 15(10): 1199-1210. doi:10.1111/j.1461-0248.2012.01817.x.

Sutherland, W.J. et al. 2006. The identification of 100 ecological questions of high policy relevance in the UK. Journal of Applied Ecology 43(4): 617-627. doi:10.1111/j.1365-2664.2006.01188.x.

Sutherland, W.J. et al. 2013. Identification of 100 fundamental ecological questions. Journal of Ecology 101(1): 58-67. doi:10.1111/1365-2745.12025.

Vilà, M., et al. 2011. Ecological impacts of invasive alien plants: a meta-analysis of their effects on species, communities and ecosystems. Ecology Letters 14(7): 702-708. doi:10.1111/j.1461-0248.2011.01628.x.

Ecosystem Science to the Rescue

What can ecologists do to become useful in the mess that is currently the 21st Century? In Australia we have a set of guidelines now available as “Foundations for the Future: A Long Term Plan for Australian Ecosystem Science” ( ) It is a useful overall plan in many respects and the only question I wish to discuss here is how we ecologists come to such plans and whether or not they are realistic.

We should begin by treating this plan as an excellent example of political ecology – a well presented, glossy brochure, with punch lines carved out and highlighted so that newspaper reporters and sympathetic politicians can present sound bites on air or in Parliament. One example: “Healthy ecosystems are the cornerstone of our social and economic wellbeing”. No arguments there.

Six key directions are indicated:

  1. Delivering maximum impact for Australia: Enhancing relationships between scientists and end-users
  2. Supporting long-term research
  3. Enabling ecosystem surveillance
  4. Making the most of data resources
  5. Inspiring a generation: Empowering the public with knowledge and opportunities
  6. Facilitating coordination, collaboration and leadership

Most ecologists would agree with all 6 key directions, but perhaps only 2 and 3 are scientific goals that are key to research planning. Everyone supports 2, but how do we achieve this without adequate funding? Similarly 3 is an admirable direction but how is it to be accomplished? Could we argue that most ecologists have been trying to achieve these 6 goals for 75 years, and particularly goals 2 and 3 for at least 35 years?

As a snapshot of the importance of ecosystem science, the example of the Great Barrier Reef is presented, and in particular understanding reef condition and its changes over time.

“Australia’s Great Barrier Reef is one of the seven wonders of the natural world, an Australian icon that makes an economic contribution of over $5 billion annually. Ongoing monitoring of the reef and its condition by ecosystem scientists plays a vital role in understanding pressures and informing the development of management strategies. Annual surveys to measure coral cover across the Great Barrier Reef since 1985 have built the world’s most extensive time series data on reef condition across 214 reefs. Researchers have used this long-term data to assess patterns of change and to determine the causes of change.”

The paper they cite (De’ath et al. 2012) shows a coral cover decline on the Great Barrier Reef of 50% over 27 years, with three main causes: cyclones (48% of total), crown-of-thorns starfish (43%) and coral bleaching (10%). From a management perspective, controlling the starfish would help recovery but only on the assumption that the climate is held stable lest cyclones and bleaching increase in future. It is not clear at all to me how ecosystem science can assist reef recovery, and we have in this case another good example of excellent ecological understanding with near-zero ability to rectify the main causes of reef degradation – climate change and water pollution.

The long-term plan presented in this report suggests many useful activities by which ecosystem studies could be more integrated. Exactly which ecosystem studies should be considered high priority are left for future considerations, as is the critical question of who will do these studies. Given that many of the originators of this ecosystem plan are from universities, one worries whether universities have the resources or the time frame or the mandate to accomplish all these goals which are essentially government services. With many governments backing out of serious ecosystem research because of budget cuts, the immediate future does not look good. Nearly 10 years ago Sutherland et al. (2006) gathered together a list of 100 ecological questions of high policy relevance for the United Kingdom. We should now go back to see if these became a blueprint for success or not.

De’ath, G., Fabricius, K.E., Sweatman, H., and Puotinen, M. (2012). The 27–year decline of coral cover on the Great Barrier Reef and its causes. Proceedings of the National Academy of Sciences 109(44): 17995-17999. doi:10.1073/pnas.1208909109.

Sutherland, W.J., et al. (2006). The identification of 100 ecological questions of high policy relevance in the UK. Journal of Applied Ecology 43(4): 617-627. doi: 10.1111/j.1365-2664.2006.01188.x


The Naïve Ecologist

I confess to being a member of the Naïve Ecologist Society. I began research when Zoology and Botany Departments typically consisted of a great mix of scientists working at different levels of biological organization from cells and molecules to ecosystems. As far as I can remember no one thought that it was our job to save the Earth or even a part of it. Our job was to do good science to help understand the processes we see in front of us. Physiologists studied ion transfer in the gills of fish, and muscle energetics, geneticists tried to unravel the genetics of protozoa, and developmental biologists tried to understand the embryology and endocrinology of sex determination. We thought that it was the universities’ job to do excellent teaching and research, and the government’s job to take care of the society and to protect and enhance our natural environment.

Now time warp about 40-50 years later. As far as I can see the molecular and cellular physiologists and geneticists are doing the same thing now as they did then. The tools of course are much improved, their knowledge base has vastly expanded, and modern genetic technology has provided insights into how things work that no one could have imagined long ago. But still (in my experience) if you talk to these sub-organismal biologists in general they will still not tell you they are trying to save the Earth by doing science. They will certainly twist and turn to convince the granting agencies that their work is critical to solving all the problems of humanity, but everyone knows that this is fluff and will be immediately tossed off when the money is delivered. But somehow at the present time it has become the job of the ecologist to save the Earth from human destruction. There is no time left to do pure ecological research to try to find out how ecosystems work and how species interact. We must have answers now to all the pressing questions of conservation biology, and if you wish to get funding for your research you had best try to bend your goals to the solution of climate change, ecosystem services, adaptation, and evolution in the days ahead. There is no time to think and study and observe, we must know now what to do. So we build models of unknown validity and speculate with little data about plans to save the Earth based on untested theory. No other postgraduate student or scientist in a university will operate under this imperative.

This would not be a serious problem if we had a better division between more basic ecologists in universities and more applied ecologists in government labs. Some of this division still exists in some countries, but in many cases governments have cut applied ecology research programs to save money and have turned their applied ecologists into paper pushers assigned to stamp approval on environmental impact statements they have no time or resources to evaluate. So a partial solution to this problem would be to fund more applied ecology positions in government with the resources and regulatory authority to protect as much ecological integrity as possible. State of the Environment glossy brochures are not a substitute for ecological information on environmental impacts, and when you read them carefully you can begin to appreciate how little is truly known about the state of our planet.

I enjoy listening to science programs on the radio as it provides a tiny window into what the radio stations think we need to know about science in action. Science broadcasters usually concentrate on the physical sciences because since they have the big money, they must be very important, then on the space sciences, since no one wants to think about how things are on earth, and finally on behavioural ecology, nice stories that warm our hearts about how bees and birds and orchids make a living. The overall mantra is relatively simple: avoid population ecology lest you have to think about the problems of eternal growth and the human population, and avoid community and ecosystem ecology lest you have to provide more bad news about collapsing coral reefs and the impacts of climate change. Keep the Pablum flowing and hope that the Hadron Collider will save us all.

There is a certain irony is the vast expenditures now being used in medicine to make sure humans live a few more years versus the tiny expenditures being given to environmental science to check on the state of natural world. If the human population collapses in the near future, it will not be because they have not made enough progress in medicine to make us all live to be 95 instead of 85. It will be more likely be due to the inability to appreciate the twin juggernauts of overpopulation and pollution that will render the globe a less nice place for us. By that time the gated communities of Los Angeles will be passé and we will be looking for someone to blame.