Category Archives: General Ecology

On the Bonn Challenge: Tree Restoration and the Climate Emergency

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“Plant a tree and save the world” is the short version of the Bonn Challenge of 2011 and the UN Decade of Ecosystem Restoration 2021-2030 (Stanturf and Mansourian 2020), and so here we are with a major ecological challenge for the decade we have just started. Planting trees around the world to restore 350 million hectares of degraded land is the goal, and it is a challenge that ecologists must think clearly about to avoid failure of another grand scheme.

Restoring ecosystems is not easy as we have already learned to our dismay. What began as a relatively simple restoration of old fields used in agriculture, a few hectares of ploughed ground surrounded by forest or grassland, has now morphed into very large areas devastated by forest fires, insect outbreaks, or drought. The largest forest fires in Arizona prior to the year 2000 were 20,000 ha, but after prolonged drought by 2020 they have reached nearly 300,000 ha (Falk 2017). The larger and more severe the fire, the greater the distance seed must disperse to recolonize burnt areas, and hence the recovery from large fires differs dramatically from the recovery from small or patchy fires.

I concentrate here on forest restoration, but always with the caveat in mind that the trees are not the forest – there are a plethora of other species involved in the forest ecosystem (Temperton et al. 2019). The restoration of forest landscapes is driven by the estimate that forest originally covered about 5.9 billion ha of the Earth but at the present time there is about 4 billion ha of forest remaining. Restoration of degraded ecosystems has always been a good idea, and this program can now be tied in with the climate emergency. New trees will remove CO2 from the air as they grow so we can score 2 points with every tree we plant (Bernal and Pearson 2018).  

The scale of plans for the UN Decade of Ecosystem Restoration 2021-2030 are challenging and Stanturf and Mansourian (2020) provide current details country by country. For example, Brazil a country of 836 million ha has pledged to restore 12 million ha (1.44%), with some countries like Spain and Russia so far not pledging any Bonn Challenge restoration. The take-up of actual restoration is uneven globally. The USA has committed to restore 12 million ha to the Bonn Challenge, but Canada has made no formal commitment, although the federal government has proposed to plant 2 billion trees during this decade to counteract climate change.  

Many problems arise with every ecological restoration. Not the least is the time frame of the recovery of damaged ecosystems. Forests recover slowly even when carefully tended, and 100 years might be a partial target for temperate forests. For North American west-coast forests a 400+-year time frame might be a target. Most private companies and governments can not even conceive of this scale of time. For those who think everything should work faster than this, Moreno-Mateos et al. (2020) report a large sample of >600 restored wetlands that recovered to only 74% of the target value in 50-100 years. Schmid et al. (2020) found that the microbial community of a lignite mine in Germany had not recovered to the control level even after 52 years. Ecological time does not always conform readily to industrial time.

Other constraints blur the grand global picture. Restoration with trees should not be done on tropical grasslands because of their inherent biodiversity values (c.f. Silveira et al. 2020 for excellent examples), nor can we restore trees on rangeland that is used for agricultural production lest we engage in robbing agricultural Peter to pay forester Paul (Vetter 2020). These important ecological critiques must be incorporated into country-wide plans for reforestation whose primary aim might be CO2 capture. Again the devil is in the details, as Vetter (2020) clearly articulates.  

The Bonn Challenge remains ongoing, waiting for another review after 2030. Who will remember what was promised, and who will be given the awards for achievements reached? What quantitative goals exactly have been promised, and what happens if they slip to 2050 or 2070?  

Bernal, B., Murray, L.T., and Pearson, T.R.H. (2018). Global carbon dioxide removal rates from forest landscape restoration activities. Carbon Balance and Management 13, 22. doi: 10.1186/s13021-018-0110-8.

Bonnesoeur, V., Locatelli, B., Guariguata, M.R., Ochoa-Tocachi, B.F., Vanacker, V. et al. (2019). Impacts of forests and forestation on hydrological services in the Andes: A systematic review. Forest Ecology and Management 433, 569-584. doi: 10.1016/j.foreco.2018.11.033.

Falk, Donald A. (2017). Restoration ecology, resilience, and the axes of change. Annals of the Missouri Botanical Garden 102, 201-216, 216. doi: 10.3417/2017006.

Moreno-Mateos, D., et al. (2020). The long-term restoration of ecosystem complexity. Nature Ecology & Evolution 4, 676-685. doi: 10.1038/s41559-020-1154-1.

Silveira, F.A.O., Arruda, A.J., Bond, W., Durigan, G., Fidelis, A., et al. (2020). Myth-busting tropical grassy biome restoration. Restoration Ecology 28, 1067-1073. doi: 10.1111/rec.13202.

Stanturf, J.A. and Mansourian, S. (2020). Forest landscape restoration: state of play.
Royal Society Open Science 7, 201218. doi: 10.1098/rsos.201218.

Temperton, V.M., Buchmann, N., Buisson, E., Durigan, G. and Kazmierczak, L. (2019). Step back from the forest and step up to the Bonn Challenge: how a broad ecological perspective can promote successful landscape restoration. Restoration Ecology 27, 705-719. doi: 10.1111/rec.12989.

Vetter, S. (2020). With Power Comes Responsibility – A rangelands perspective on forest landscape restoration. Frontiers in Sustainable Food Systems 4, 549483. doi: 10.3389/fsufs.2020.549483.

On an Experimental Design Mafia for Ecology

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Ecologist A does an experiment and publishes Conclusions G and H. Ecologist B reads this paper and concludes that A’s data support Conclusions M and N and do not support Conclusions G and H. Ecologist B writes to Journal X editor to complain and is told to go get stuffed because Journal X never makes a mistake with so many members of the Editorial Board who have Nobel Prizes. This is an inviting fantasy and I want to examine one possible way to avoid at least some of these confrontations without having to fire all the Nobel Prize winners on the Editorial Board.

We go back to the simple question: Can we agree on what types of data are needed for testing this hypothesis? We now require our graduate students or at least our Nobel colleagues to submit the experimental design for their study to the newly founded Experimental Design Mafia for Ecology (or in French DEME) who will provide a critique of the formulation of the hypotheses to be tested and the actual data that will be collected. The recommendations of the DEME will be nonbinding, and professors and research supervisors will be able to ignore them with no consequences except that the coveted DEME icon will not be able to be published on the front page of the resulting papers.

The easiest part of this review will be the data methods, and this review by the DEME committee will cover the current standards for measuring temperature, doing aerial surveys for elephants, live-trapping small mammals, measuring DBH on trees, determining quadrat size for plant surveys, and other necessary data collection problems. This advice alone should hypothetically remove about 25% of future published papers that use obsolete models or inadequate methods to measure or count ecological items.

The critical part of the review will be the experimental design part of the proposed study. Experimental design is important even if it is designated as undemocratic poppycock by your research committee. First, the DEME committee will require a clear statement of the hypothesis to be tested and the alternative hypotheses. Words which are used too loosely in many ecological works must be defended as having a clear operational meaning, so that idea statements that include ‘stability’ or ‘ecosystem integrity’ may be questioned and their meaning sharpened. Hypotheses that forbid something from occurring or allow only type Y events to occur are to be preferred, and for guidance applicants may be referred to Popper (1963), Platt (1964), Anderson (2008) or Krebs (2019). If there is no alternative hypothesis, your research plan is finished. If you are using statistical methods to test your hypotheses, read Ioannidis (2019).

Once you have done all this, you are ready to go to work. Do not be concerned if your research plan goes off target or you get strange results. Be prepared to give up hypotheses that do not fit the observed facts. That means you are doing creative science.

The DEME committee will have to be refreshed every 5 years or so such that fresh ideas can be recognized. But the principles of doing good science are unlikely to change – good operational definitions, a set of hypotheses with clear predictions, a writing style that does not try to cover up contrary findings, and a forward look to what next? And the ecological world will slowly become a better place with fewer sterile arguments about angels on the head of a pin.

Anderson, D.R. (2008) ‘Model Based Inference in the Life Sciences: A Primer on Evidence.‘ (Springer: New York.) ISBN: 978-0-387-74073-7.

Ioannidis, J.P.A. (2019). What have we (not) learnt from millions of scientific papers with P values? American Statistician 73, 20-25. doi: 10.1080/00031305.2018.1447512.

Krebs, C.J. (2020). How to ask meaningful ecological questions. In Population Ecology in Practice. (Eds D.L. Murray and B.K. Sandercock.) Chapter 1, pp. 3-16. Wiley-Blackwell: Amsterdam. ISBN: 978-0-470-67414-7

Platt, J. R. (1964). Strong inference. Science 146, 347-353. doi: 10.1126/science.146.3642.347.

Popper, K. R. (1963) ‘Conjectures and Refutations: The Growth of Scientific Knowledge.’ (Routledge and Kegan Paul: London.). ISBN: 9780415285940

On Citations and Scientific Research in Ecology

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Begin with a few common assumptions in science.
(1) Higher citation rates define more valuable science
(2) Recent references are more valuable than older references
(3) Retracted scientific research is rapidly recognized and dropped from discussion
(4) The vast majority of scientific research reported in papers is read by other scientists.
(5) Results cited in scientific papers are cited correctly in subsequent references.

The number of publications in ecological science is growing rapidly world-wide, and a corollary of this must be that the total number of citations is growing even more rapidly (e.g. Westgate et al. 2020). It is well recognized that citations are unevenly spread among published papers, and reports that nearly 50% of published papers never receive any citations at all are commonly cited. I have not been able to validate this for papers in the ecological sciences. The more important question is whether the most highly cited papers are the most significant for progress in ecological understanding. If this is the case, you can simply ignore the vast majority of the published literature and save reading time. But this seems unlikely to be correct for ecological science.

The issue of scientific importance is a time bomb partly because ‘importance’ may be redefined over time as sciences mature, and this redefinition may occur in years or tens of years. A classic example is the citation history of Charles Elton’s (1958) book on invasions (Richardson and Pyšek 2008). Published in 1958, this book had almost no citations until the 1990s. Citations have become more and more important in the ranking of individual scholars as well as university departments during the last 20 years (Keville et al. 2017). This has occurred despite continuous warnings that citations are not valid for comparing individuals of different age or departments in different academic fields (Patience et al. 2017). If you publish in Covid-19 research this year, you are likely to get more citations than the person working in earthworm taxonomy.

Most published papers confirm the general belief that citing the most recent papers is more successful than citing older papers. If this belief could be tested, it would simplify education of graduate students and facilitate teaching. But the simple fact is that in ecology often (but not always) older papers have better perspectives than more recent papers or indicate paths of research that have failed to lead to ecological wisdom. 

Newspapers revel in stories of retracted research, if only to show that scientists are human. Of some interest are studies that show that research which is retracted continues to be cited. Hagberg (2020) cites a case in which a paper was retracted but continued to be cited as much after retraction as before. Fortunately, retracted research is rare in the ecological sciences but not absent, but the various conflicting ways in which scientific journals deal with papers with fraudulent results discovered after they are published leave much to be desired. 

A final comment on references is a warning to anyone reading the discussion or conclusions of a paper. Smith and Cumberledge (2020) have reported a random sample of references in a variety of scientific papers indicated a 25% error rate in ‘quotation’ errors. Quotation errors are distinct from ‘citation errors’ which are minor mistakes in the year of publication, page numbers or names in citations given in papers. Quotation errors are examples of “original paper authors say XX, citing paper says YY, a contradiction to what was originally reported. They used 250 citations from the 5 most highly cited scientific publications of today to determine how many papers contained ‘quotation errors’ and found a 25% error rate. About 33% of these errors could be called ‘Unsubstantiated’ and about 50% of the remaining quotation errors were ‘Impossible to substantiate” category. Their study reinforced early work by Todd et al. (2007) and pointed out to readers a weakness in the current use of references in scientific writing that is often missed by reviewers.

On a more positive note, on how to increase your citation rate, Murphy et al. (2019) surveyed the titles of 3562 papers and their subsequent citation rate from four ecology and entomology journals. They found that papers that did not include the Latin name of species in the title of the paper were cited 47% more often than papers with Latin names in the title. The number of words in the title of the paper had almost no effect on citation rates. They were unable to determine whether the injection of humor in the title of the paper had any effect on citation rates because too few papers attempted humor in the title.   

Elton, C.S. (1958) ‘The Ecology of Invasions by Animals and Plants.’ (Methuen: London.) ISBN: 978-3-030-34721-5

Hagberg, J.M. (2020). The unfortunately long life of some retracted biomedical research publications. Journal of Applied Physiology 128, 1381-1391. doi: 10.1152/japplphysiol.00003.2020.

Keville, M.P., Nelson, C.R., and Hauer, F.R. (2017). Academic productivity in the field of ecology. Ecosphere 8, e01620. doi: 10.1002/ecs2.1620.

Murphy, S.M., Vidal, M.C., Hallagan, C.J., Broder, E.D., and Barnes, E.E. (2019). Does this title bug (Hemiptera) you? How to write a title that increases your citations. Ecological Entomology 44, 593-600. doi: 10.1111/een.12740.

Patience, G.S., Patience, C.A., Blais, B., and Bertrand, F. (2017). Citation analysis of scientific categories. Heliyon 3, e00300. doi: https://doi.org/10.1016/j.heliyon.2017.e00300.

Richardson, D.M. and Pyšek, P. (2008). Fifty years of invasion ecology – the legacy of Charles Elton. Diversity and Distributions 14, 161-168. doi: 10.1111/j.1472-4642.2007.00464.x.

Smith, N. and Cumberledge, A. (2020). Quotation errors in general science journals. Proceedings of the Royal Society. A, 476, 20200538. doi: 10.1098/rspa.2020.0538.

Todd, P.A., Yeo, D.C.J., Li, D., and Ladle, R.J. (2007). Citing practices in ecology: can we believe our own words? Oikos 116, 1599-1601. doi: 10.1111/j.2007.0030-1299.15992.x

Westgate, M.J., Barton, P.S., Lindenmayer, D.B., and Andrew., N.R. (2020). Quantifying shifts in topic popularity over 44 years of Austral Ecology. Austral Ecology 45, 663-671. doi: 10.1111/aec.12938.

On Writing an Abstract for an Ecological Presentation

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There is abundant good general advice for writing an abstract for your thesis, research talk or published paper from the web but it is perhaps useful to add a few points specific to ecological studies. I suggest five points for a good abstract as a condensed version of the traditional writing advice: Who, What, When, Where, How and Why.  

  1. What is the problem, question, or controversy? You must grab the reader in the first sentence or two.
  2. What is your contribution to answering, testing, or changing the question? In a few sentences you should explain what you did, where and when you did it if a field study. If you are testing a hypothesis, you should state the alternative hypotheses as well.
  3. How did you reach your conclusions, what methods did you use? The design of your study should include what species or group of species you included, some general points about sample sizes.
  4. Rotate back to match your conclusions to your prior hypotheses, or the new hypothesis you present.
  5. Finally, state what needs to be done next to further these ecological issues.

The trick is to do all of this in concise sentences, to state clearly your advances in understanding, and equally to state clearly what failed to work the way you had originally postulated.

So, if you can do all of this in 200-300 words, you win the prize. A good abstract is like gold and worth the work.

There is much literature on writing well. Sayer (2019) gives a concise statement of writing for ecological journals. Pollock (2020) emphasizes the responsibility scientists bear for their writing, and Mammola (2020) makes a plea for reducing superlatives in over-selling our conclusions,

If you would like an exercise in a seminar or lab meeting, go through your favourite journal and rank the abstracts in an issue on a scale of 1-10 for both clarity and for enticing you the reader to read the complete details of the rest of the paper.

And go through this same writing routine if you are giving a seminar or lecture and must present a short abstract. We may all be attracted to hear an address on whatever from the Prime Minister or the President, but alas that is not always the case for we mere mortals who must attract an audience to our talks on the basis of our abstract. 

Mammola, S. (2020). On deepest caves, extreme habitats, and ecological superlatives. Trends in Ecology & Evolution 35, 469-472. doi: 10.1016/j.tree.2020.02.011.

Pollock, N.W. (2020). The responsibility of scientific writing. Wilderness & Environmental Medicine 31, 129-130. doi: 10.1016/j.wem.2020.04.005.

Sayer, E.J. (2019). The essentials of effective scientific writing – A revised alternative guide for authors. Functional Ecology 33, 1576-1579. doi: 10.1111/1365-2435.13391.

On a Department of Monitoring Biology

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Begin with the current university structure in North America. Long ago it was simple: a Department of Biology, a Department of Microbiology, a Department of Forestry, and possibly a Department of Fisheries and Wildlife Management. We could always justify a Department of Microbiology because people get sick, a Department of Forestry because people buy wood to build houses, and a Department of Fisheries and Wildlife Management because people fish and hunt. But what are we going to do with a Department of Biology? It rarely deals with anything that will make money, so we divide it into interest groups, a Department of Botany, and a Department of Zoology. All is well. But now a new kid appears on the block, Molecular Biology, and it claims to be able to solve all the issues that were formerly considered the focus of Botany and Zoology and probably several other departments. Give us all the money, the molecular world shouted, and we will solve all your problems and do it quickly. So now we get a complete hassle for money, buildings and prestige, and the world turns on which of the bevy of bureaucrats races to the top to make all the major decisions. If you wish to have proof of concept, ask anyone you can find who teaches at a university if he or she was ever consulted about what direction the university should take.

At this point we begin to proceed based on ‘follow the money’. So, for example if the Department of Forestry gets the most money from whomever, it must get the biggest buildings, the largest salaries, and the newest appointments. So soon you have a system of intrigue that would rival the Vatican. The winners of late are those departments that have most to do with people, health, and profit. So Medical Schools march on, practical matters like economics and engineering do well, and molecular biology rises rapidly.

What has happened to the old Departments of Botany and Zoology? They make no profit; their only goal is to enrich our lives and our understanding of the world around us. How can we make them profitable? A new program races to the rescue, a Department of Biodiversity, which will include everyone in plant, animal and microbe science who cannot get into one of the more practical, rich, existing departments. The program now is to convince the public and the governments that biodiversity is important and must be funded more. David Attenborough to the fore, and we are all abandoning the old botany and zoology and moving to biodiversity.

Now the problem arises for ecologists. Biodiversity includes everything, so where do we start? If we have so far described and named only about 15% of the life on Earth, should we put all our money into descriptive taxonomy? Should we do more biogeography, more ecology, more modelling, or more taxonomy, or a bit of all? So, the final question of our quest arrives: what should we be doing in a Department of Biodiversity if indeed we get one?

If you have ever been involved in herding cats, or even sheep without a dog you can imagine what happens if you attempt to set a priority in any scientific discipline. The less developed the science, the more the arguments about where to put our money and people. Ecology is a good example because it has factions with no agreement at all about what should be done to hasten progress. The result is that we fall back on the Pied Pipers of the day, form bandwagons, and move either forward, sideways, or backwards depending on who is in charge.

So, let us step back and think amid all this fighting for science funding. The two major crises of our time are human population growth and the climate change emergency. In fact, there is only one major crisis, climate change, because as it apparently progresses, everything will be overwhelmed in a way only few can try to guess (Wallace-Wells 2019, Lynas 2020). After some discussion you might suggest that we do two things in biology: first, get a good grip on what we have now on Earth, and second, keep monitoring life on Earth as the climate emergency unravels so that we can respond with mitigation as required. This is not to say we should stop doing other things. We should be more than unifactorial scientists, and it may be a small recommendation to the world of thinkers that we consider endowing at least some universities with a Department of Monitoring Biology and endow it with enough funding to do the job well. (Lindenmayer 2018; Lindenmayer et al. 2018; Nichols et al. 2019). It might be our best investment in the future of biology.

Lindenmayer, D. (2018). Why is long-term ecological research and monitoring so hard to do? (And what can be done about it). Australian Zoologist 39: 576-580. doi: 10.7882/az.2017.018.

Lindenmayer, D.B., Likens, G.E., and Franklin, J.F. (2018). Earth Observation Networks (EONs): Finding the Right Balance. Trends in Ecology & Evolution 33, 1-3. doi: 10.1016/j.tree.2017.10.008.

Lynas, Mark (2020) ‘Our Final Warning: Six Degrees of Climate Emergency’. 4th Estate, Harper Collins, London. E book ISBN: 978-0008308582

Nichols, J.D., Kendall, W.L., and Boomer, G.S. (2019). Accumulating evidence in ecology: Once is not enough. Ecology and Evolution 9, 13991-14004. doi: 10.1002/ece3.5836.

Wallace-Wells, David (2019) ‘The Uninhabitable Earth: Life After Warming ‘ Tim Duggan Books: New York. 304 pp. ISBN: 978-0-525-57670-9.  

How should biodiversity research be directed?

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There are many scientific papers and news reports currently that state that biodiversity is in rapid decline on Earth. No evidence is usually cited for this statement – it is considered to be self evident. What follows from that is typically a panic request for more work on declining populations, more money for conservation NGOs and national parks. Political ecology statements that request more money for ecological research are certainly on the right track if we are to understand how to achieve conservation of our biota. But the question I want to raise here is how to proceed on this broad issue in a logical manner. To do this I will not discuss political ecology or how to gain more donors for conservation agencies, valuable services to be sure. But behind all this advertising is a scientific agenda which needs careful consideration.    

Problem #1 is to determine if there is a problem. In some areas of conservation ecology there is much agreement on principles – we all agree that we are losing natural areas for urban and agricultural development, that we need more protected areas, that most protected areas are not large enough, that there are serious problems with poaching of wildlife and lumber in some protected areas, and that global pollution is affecting much of our biodiversity. In other areas of conservation ecology there is much controversy about details. Is global biodiversity in rapid decline (Vellend et al. 2017, Cardinale et al. 2018)? How can we best identify species at risk, and once we identify them, what can we do to prevent population collapse?

The answer to Problem #1 is that there are problems in some areas but not in others, in some taxonomic groups, but not in others, but overall the data are completely inadequate for a clear statement that overall biodiversity is in global decline (Dornelas et al. 2019). The problems of biodiversity conservation are local and group specific, which leads us to Problem #2.

Problem # 2 is to go back to the ecological details, concentrating on local and specific problems, exactly what should we do, and what can we do? The problems here relate almost entirely to ecological methods – how do we estimate species abundances particularly for rare species? How do we deal with year to year changes in communities? How long should a monitoring program continue until it has reliable conclusions about biodiversity change? None of these questions are simple to answer and require much discussion which is currently under way. How long is a long-term study? It might be something like 30 generations for vertebrate species or even longer, but what is it for earthworms or bark beetles? How can we best sample the variety of insects in an ecosystem in which they might be in decline (Habel et al. 2019)?

We need to scale our conservation studies for particular species, and this has led us into the Species-At-Risk dilemma. We can gather data for a specific geographical area like Canada on the species that we deem at risk. Typically, these are vertebrates, and we ignore the insects, microbes, and the rest of the community. We try to identify threatening processes for each species and write a detailed report (Bird and Hodges 2017). The action plan specified can rarely be carried out because it is multi-year and expensive, so the matter rests. For many of these species at risk and for almost all that are ignored the central problem is action – what could you do about a declining species-at-risk, given funds and person-power? We do what we can on a local scale on the principle that it is better to do something than nothing (Westwood et al. 2019). But too often even if we have a good ecological understanding of declines, for example in mountain caribou in Canada, little or nothing is done (Palm et al. 2020). Conservation collides with economics.

I will try to draw a few possible conclusions out of this general discussion.

  1. It is far from clear that global biodiversity is declining rapidly.
  2. On a local level we can do careful evaluations for some species at risk and take possible action if funding is available.
  3. Setting aside large areas of habitat is currently the best immediate conservation strategy. Managing land use is critical.
  4. Designing strong monitoring programs is essential to discover population and community trends so that, if action can be taken, it is not too late.
  5. Climate change will have profound biodiversity effects in the long run, and conservation scientists must work short-term but plan long-term.

As we take actions for conservation, we ought to keep in mind the central question: What will this ecosystem look like in 100 or 200 years? Perhaps that could be a t-shirt slogan.

Bird, S.C., and Hodges, K.E. (2017). Critical habitat designation for Canadian listed species: Slow, biased, and incomplete. Environmental Science & Policy 71, 1-8. doi: 10.1016/j.envsci.2017.01.007.

Cardinale, B.J., Gonzalez, A., Allington, G.R.H., and Loreau, M. (2018). Is local biodiversity declining or not? A summary of the debate over analysis of species richness time trends. Biological Conservation 219, 175-183. doi: 10.1016/j.biocon.2017.12.021.

Dornelas, M., Gotelli, N.J., Shimadzu, H., Moyes, F., Magurran, A.E., and McGill, B.J. (2019). A balance of winners and losers in the Anthropocene. Ecology Letters 22, 847-854. doi: 10.1111/ele.13242.

Habel, J.C., Samways, M.J., and Schmitt, T. (2019). Mitigating the precipitous decline of terrestrial European insects: Requirements for a new strategy. Biodiversity and Conservation 28, 1343-1360. doi: 10.1007/s10531-019-01741-8.

Palm, E.C., Fluker, S., Nesbitt, H.K., Jacob, A.L., and Hebblewhite, M. (2020). The long road to protecting critical habitat for species at risk: The case of southern mountain woodland caribou. Conservation Science and Practice 2 (7). doi: 10.1111/csp2.219.

Vellend, M., Dornelas, M., Baeten, L., Beauséjour, R., Brown, C.D., De Frenne, P., Elmendorf, S.C., et. al. (2017). Estimates of local biodiversity change over time stand up to scrutiny. Ecology 98, 583-590. doi: 10.1002/ecy.1660.

Westwood, A.R., Otto, S.P., Mooers, A., Darimont, C., Hodges, K.E., Johnson, C., Starzomski, B. et al. (2019). Protecting biodiversity in British Columbia: Recommendations for developing species at risk legislation. FACETS 4, 136-160. doi: 10.1139/facets-2018-0042.

How Should We Test Global Models in Ecology?

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There is an understandable desire to view ecological ideas on an exceptionally large or even global scale. Just as physicists, chemists, and engineers apply their scientific results as correct everywhere, biologists would like to have global hypotheses and global models of ecological principles. There is only one problem – that ecological principles or ‘laws’ are climate contingent. This simple fact has produced a minor mode of panic in the ecological literature. How reliable are our ecological principles? Must we change them as the climate changes? In principle not, since many chemical and physical laws are temperature dependent or moisture dependent, and we just recognize that these laws have a temperature or moisture parameter as part and parcel of how things like chemical reactions can change.

This kind of argument would suggest that if we build the physical-chemical universe into our ecological models we could approach the hard sciences in predictive precision. Alas as we know this is not to be. Why not? The first argument is that ecological systems are composed of many variables – all individuals in a population are not identical, communities and ecosystems contain many interacting species with different physical and chemical requirements. But this does not necessarily let ecologists off the hook because it can be interpreted to mean that we simply have a much harder job to do and it will take much longer but it is in principle achievable. The second argument is that evolution continues to occur and is in principle unpredictable, so that while we know where we are at present, we do not know the future (Ivory et al. 2019).

Let us take a global example of the decline in coral reefs as temperature in the ocean rises. We will ignore for the moment CO2 acidity changes to keep the discussion simple. We can define closely the thermal limits of different coral species, so that should give us good predictability. But we do not know if natural selection will change these thermal limits, or whether or not it can do so rapidly enough. For the most part we project that increasing ocean temperatures will destroy most of our coral reefs and turn them into algal communities. This prediction is partly based on observations of the last 40 years in different parts of the tropics and partly based on measurements in physiological ecology in the lab. But the elephant in the prediction room is evolution and what genetic variation now exists but has not been measured, as well as how far temperature and CO2 will increase (Frank 2019).  

So ecologists are caught in a dilemma – we can in principle define the current state of ecosystems and make short term predictions that we can test with further monitoring, but we cannot make the long term predictions everyone wants to have. As conservation biologists we can make warnings but few of them would stand up in court when push comes to shove. So the consequence is that we live in a world of make believe where, for example in British Columbia the government in its wisdom says yes we must protect old growth forests, and we will do all possible to achieve this goal, as long as new policies do not reduce the annual allowable cut to the forest industry.

We can look to paleoecology to get an overview of how life on Earth has changed in the past on any time scale you wish. If there is a general law coming out of all this research it is that when climate changes, ecological communities and ecosystems change. The simple message that is hard to get across is that, if you like current environmental conditions and desire only small changes in our present ecological communities, it is desirable to reduce the pollution that is causing rapid climate change. No clever and detailed global ecological model will help us overcome the tragedies unfolding with the business as usual models we currently use unless we control rapid climate change (van der Zande et al. 2020). A current popular example is the suggestion that if we plant trees around the world, we can reverse rising CO2 level. That sounds like a good achievable plan but in fact it is impossible (Friedlingstein et al. 2019).

So, my advice is two-fold. First, design and test global ecological models for short term understanding and predictions. Do not pretend they will provide accurate long-term predictions for ecological systems. In some cases, there is little predictability (Geary et al. 2020). Second, do much more long-term monitoring of communities and ecosystems to trace local and global changes quantitatively (Wagner 2020). Then at least we will know how big the ‘wolf’ is before we ‘cry wolf’. 

Frank, P. (2019). Propagation of error and the reliability of global air temperature projections. Frontiers in Earth Science 7, 223. doi: 10.3389/feart.2019.00223.

Friedlingstein, P., Allen, M., Canadell, J.G., Peters, G.P., and Seneviratne, S.I. (2019). Comment on “The global tree restoration potential”. Science 366, eaay8060. doi: 10.1126/science.aay8060.

Geary, W.L., Doherty, T.S., Nimmo, D.G., Tulloch, A.I.T., and Ritchie, E.G. (2020). Predator responses to fire: A global systematic review and meta-analysis. Journal of Animal Ecology 89, 955-971. doi: 10.1111/1365-2656.13153.

Ivory, S. J., Russell, J., Early, R., and Sax, D.F. (2019). Broader niches revealed by fossil data do not reduce estimates of range loss and fragmentation of African montane trees. Global Ecology and Biogeography 28, 992-1003. doi: 10.1111/geb.12909.

van der Zande, R.M., Achlatis, M., Bender-Champ, D., Kubicek, A., and Dove, S. (2020). Paradise lost: End-of-century warming and acidification under business-as-usual emissions have severe consequences for symbiotic corals. Global Change Biology 26, 2203-2219. doi: 10.1111/gcb.14998.

Wagner, D.L. (2020). Insect declines in the Anthropocene. Annual Review of Entomology 65, 457-480. doi: 10.1146/annurev-ento-011019-025151.

On the Use of Statistics in Ecological Research

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There is an ever-deepening cascade of statistical methods and if you are going to be up to date you will have to use and cite some of them in your research reports or thesis. But before you jump into these methods, you might consider a few tidbits of advice. I suggest three rules and a few simple guidelines:

Rule 1. For descriptive papers keep to descriptive statistics. Every good basic statistics book has advice on when to use means to describe “average values”, when to use medians, or percentiles. Follow their advice and do not in your report generate any hypotheses except in the discussion. And follow the simple advice of statisticians not to generate and then test a hypothesis with the same set of data. Descriptive papers are most valuable. They can lead us to speculations and suggest hypotheses and explanations, but they do not lead us to strong inference.

Rule 2. For explanatory papers, the statistical rules become more complicated. For scientific explanation you need 2 or more alternative hypotheses that make different, non-overlapping predictions. The predictions must involve biological or physical mechanisms. Correlations alone are not mechanisms. They may help to lead you to a mechanism, but the key is that the mechanism must involve a cause and an effect. A correlation of a decline in whale numbers with a decline in sunspot numbers may be interesting but only if you can tie this correlation into an actual mechanism that affects birth or death rates of the whales.

Rule 3. For experimental papers you have access to a large variety of books and papers on experimental design. You must have a control or unmanipulated group, or for a comparative experiment a group A with treatment X, and a group B with treatment Y. There are many rules in the writings of experimental design that give good guidance (e.g. Anderson 2008; Eberhardt 2003; Johnson 2002; Shadish et al. 2002; Underwood 1990).

For all these ecology papers, consider the best of the recent statistical admonitions. Use statistics to enlighten not to obfuscate the reader. Use graphics to illustrate major results. Avoid p-values (Anderson et al. 2000; Ioannidis 2019a, 2019b). Measure effect sizes for different treatments (Nakagawa and Cuthill 2007). Add to these general admonitions the conventional rules of paper or report submission – do not argue with the editor, argue a small amount with the reviewers (none are perfect), and put your main messages in the abstract. And remember that it is possible there was some interesting research done before the year 2000.

Anderson, D.R. (2008) ‘Model Based Inference in the Life Sciences: A Primer on Evidence.’ (Springer: New York.). 184 pp.

Anderson, D.R., Burnham, K.P., and Thompson, W.L. (2000). Null hypothesis testing: problems, prevalence, and an alternative. Journal of Wildlife Management 64, 912-923.

Eberhardt, L.L. (2003). What should we do about hypothesis testing? Journal of Wildlife Management 67, 241-247.

Ioannidis, J.P.A. (2019a). Options for publishing research without any P-values. European Heart Journal 40, 2555-2556. doi: 10.1093/eurheartj/ehz556.

Ioannidis, J. P. A. (2019b). What have we (not) learnt from millions of scientific papers with P values? American Statistician 73, 20-25. doi: 10.1080/00031305.2018.1447512.

Johnson, D.H. (2002). The importance of replication in wildlife research. Journal of Wildlife Management 66, 919-932.

Nakagawa, S. and Cuthill, I.C. (2007). Effect size, confidence interval and statistical significance: a practical guide for biologists. Biological Reviews 82, 591-605. doi: 10.1111/j.1469-185X.2007.00027.x.

Shadish, W.R, Cook, T.D., and Campbell, D.T. (2002) ‘Experimental and Quasi-Experimental Designs for Generalized Causal Inference.’ (Houghton Mifflin Company: New York.)

Underwood, A. J. (1990). Experiments in ecology and management: Their logics, functions and interpretations. Australian Journal of Ecology 15, 365-389.

On Three Kinds of Ecology Papers

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There are many possible types of papers that discuss ecology, and in particular I want to deal only with empirical studies that deal with terrestrial and aquatic populations, communities, or ecosystems. I will not discuss here theoretical studies or modelling studies. I suggest it is possible to classify papers in ecological science journals that deal with field studies into three categories which I will call Descriptive Ecology, Explanatory Ecology, and Experimental Ecology. Papers in all these categories deal with a description of some aspects of the ecological world and how it works but they differ in their scientific impact.

Descriptive Ecology publications are essential to ecological science because they present some details of the natural history of an ecological population or community that is vital to our growing understanding of the biota of the Earth. There is much literature in this group, and ecologists all have piles of books on the local natural history of birds, moths, turtles, and large mammals, to mention only a few. Fauna and flora compilations pull much of this information together to guide beginning students and the interested public in increased knowledge of local fauna and flora. These publications are extremely valuable because they form the natural history basis of our science, and greatly outnumber the other two categories of papers. The importance of this information has been a continuous message of ecologists over many years (e.g. Bartholomew 1986; Dayton 2003; Travis 2020).

The scientific journals that professional ecologists read are mostly concerned with papers that can be classified as Explanatory Ecology and Experimental Ecology. In a broad sense these two categories can be described as providing a good story to tie together and thus explain the known facts of natural history or alternatively to define a set of hypotheses that provide alternative explanations for these facts and then to test these hypotheses experimentally. Rigorous ecology like all good science proceeds from the explanatory phase to the experimental phase. Good natural history provides several possible explanations for ecological events but does not stop there. If a particular bird population is declining, we need first to make a guess from natural history if this decline might be from disease, habitat loss, or predation. But to proceed to successful management of this conservation problem, we need studies that distinguish the cause(s) of our ecological problems, as recognized by Caughley (1994) and emphasized by Hone et al. (2018). Consequently the flow in all the sciences is from descriptive studies to explanatory ideas to experimental validation. Without experimental validation ‘ecological ideas’ can transform into ‘ecological opinions’ to the detriment of our science. This is not a new view of scientific method (Popper 1963) but it does need to be repeated (Betini et al. 2017). 

If I repeat this too much, I suggest you do a survey of how often ecological papers in your favorite journal are published without ever using the word ‘hypothesis’ or ‘experiment’. A historical survey of these or similar words would be a worthwhile endeavour for an honours or M.Sc. student in any one of the ecological subdisciplines. The favourite explanation offered in many current papers is climate change, a particularly difficult hypothesis to test because, if it is specified vaguely enough, it is impossible to test experimentally. Telling interesting stories should not be confused with rigorous experimental ecology.

Bartholomew, G. A. (1986). The role of natural history in comtemporary biology. BioScience 36, 324-329. doi: 10.2307/1310237

Betini, G.S., Avgar, T., and Fryxell, John M. (2017). Why are we not evaluating multiple competing hypotheses in ecology and evolution? Royal Society Open Science 4, 160756. doi: 10.1098/rsos.160756.

Caughley, G. (1994). Directions in conservation biology. Journal of Animal Ecology 63, 215-244. doi: 10.2307/5542

Dayton, P.K. (2003). The importance of the natural sciences to conservation. American Naturalist 162, 1-13. doi: 10.1086/376572

Hone, J., Drake, Alistair, and Krebs, C.J. (2018). Evaluating wildlife management by using principles of applied ecology: case studies and implications. Wildlife Research 45, 436-445. doi: 10.1071/WR18006.

Popper, K. R. (1963) ‘Conjectures and Refutations: The Growth of Scientific Knowledge.’ (Routledge and Kegan Paul: London.)

Travis, Joseph (2020). Where is natural history in ecological, evolutionary, and behavioral science? American Naturalist 196, 1-8. doi: 10.1086/708765.

What Do We Need to Know About Covid-19?

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We are currently in a chaotic mess about how to come out of the covid-19 pandemic with minimal casualties and grace. Why should this be? We have had enough examples of pandemics within the last century or two to have some ideas about what will work and what will not, but it would appear that this information is not being used effectively. Part of this can be explained away by the actions of political figures who are incompetent beyond belief, but this is not the only cause of the problem. We have many first-class epidemiologists and modellers around the world working on plans for dealing with covid-19 but there is less coordinated planning than would seem desirable. Perhaps the lack of coordination is highly desirable. We now have experimental situations that any field ecologist would be ecstatic about – cruise ships that are closed systems of potential infections in replicate, states and provinces that practice self-distancing at 1.5 to 2 m and others that ignore this infringement on their liberty or because of poverty do not have the luxury of having enough spacious accommodation to self-distance. Why with all these measurements, good intentions, and data from testing for the virus and antibodies is the picture on what best to do still so cloudy? Given the operational suggestions of social distancing at 2 m, avoiding crowds, washing hands frequently, what ideas need testing to make life less forced? Here are my challenges for some evidence-based questions to answer:

  • Is all covid transmission people to people, and not via door nobs, handrails, and counter tops so that all the cleaning is a waste of resources, time and money? But does cleaning reduce other infections so that it has a net benefit to society?
  • Distance works, but exactly what distance 1m. 1.5 m, 2m? And note 2 m ≠ 6 feet.
  • Are school kids basically immune so that schools should not be closed if teachers can be kept covid free and tested? If we can keep students and teachers safe, it is a colossal waste of resources to close schools, colleges, and universities and pretend that on-line teaching will educate properly (in spite of the clever on-line methods being developed).
  • Given that old people can be protected from covid-19 and given distancing precautions, it is not clear that the mortality from covid-19 for those aged 15 to 60 is much different from the annual flu that runs around year after year. If covid-19 is indeed 5x as toxic as ordinary flu and persists like ordinary flu, how much are we willing as a society to completely reorganize to keep old people safe?
  • Is relying on a vaccine to restore normal life dangerous? Do strategies that are partially effective need further discussion for a Plan B? We may find ourselves in the same situation we have currently with the normal flu virus, partial immunity but not complete and many people refusing vaccinations.
  • Does asymptomatic transmission of covid-19 actually occur, or is it more likely due to poor testing methods and poor patient memory?
  • How much of the covid-19 mortality is ‘natural selection’, how much bad luck, how much is not being self isolated after being warned, how much is the prevailing belief that we can do anything and the doctors will save us?

In my opinion, having 50 or 200 research groups working on covid-19 vaccines when malaria, diphtheria, and TB ravages the poor of the world is more “rich white people are all that matter”. If we wish to put all these resources into one virus, we should provide an equal effort for the poor among us so that our promise is not only “bring covid-19 under control” but rather “bring poverty under control”.