Tuesday, March 29, 2016

What are important directions for ecology?

I was recently asked “what is the most important problem in ecology?”. I was dissatisfied with whatever I ended up answering, so it has been on my mind. I think there is an analogy with medicine here – it’s a little like asking a medical scientist “what is the most important disease to cure?” Similarly, there are multiple possible answers, and the one you give will depend on your area of interest/what type of doctor you are. (I also assume this is a question about basic research, and the answer is not as simple as saying, stop extinctions or prevent habitat loss).

Levels of biological organisation.
The medical analogy breaks down a little because ecology is *far* more complicated than medical science. Medicine has a foundation in anatomy and physiology, which in turn rely on basic sciences like cell biology and genetics. This creates a reasonably constrained framework within which further learning/investigation can be organized. Medicine typically stops at the level of the individual, but ecology inherently involves many additional levels of organization (from individuals, to populations, to species and communities, to ecosystems, and beyond). Within any one of these higher levels of organization (population, community, ecosystem), there can be such an immense amount of variation in outcomes and dynamics that ecologists can lose sight of connections with lower and higher levels. For example, community ecology encompasses so much complexity on its own, that also considering the impacts of population level processes and on ecosystem level processes is a tall order. But, we should also appreciate, given these barriers to understanding, just how far ecology has actually advanced in the last 100 years. The combination of reductionist experiments and descriptive work at all scales has been immensely successful (e.g. see this blog post for a partial list). Many general tools have been developed that we can then use to answer specific ecological questions (the integration with statistics with ecology has been highly successful; the use of specific mathematical models). Still, the ability to reconcile multiple levels of organization and scales still limits ecology.

This is a problem that cell biology has also experienced, and is now approaching via systems biology: "The reductionist approach has successfully identified most of the components and many of the interactions but, unfortunately, offers no convincing concepts or methods to understand how system properties emerge...the pluralism of causes and effects in biological networks is better addressed by observing, through quantitative measures, multiple components simultaneously and by rigorous data integration with mathematical models"(1): to me, this quote rings so true for ecology as well. Systems biology uses mechanistic, mathematical and computational models to attempt to represent multi-scale complexity.

Of course, the optimism about systems biology might be premature in that it hasn’t produced many useful models yet, such that it may be “more of an agenda than a body of results.”. Some of the best “systems ecology” (e.g. meta-ecosystem models) are very system specific and data-heavy (e.g. 2). Can they inform us about generality in ecology?

All of which is to say, I think the most important problems in ecology relate to this need to make the connections between studies and systems and levels of organization. But, doing so may be difficult.

More specific problems

1. The scaling of ecological processes. Many ecologists include a line about being ‘interested in questions of scale’ on their website blurbs. Despite this, our understanding of the aggregate outcome of multiple processes that are occurring at different spatial or temporal scales remains limited, and poorly predictive. There have been a few useful starts (particularly in Peter Chesson’s scale transition papers (3, 4)), but recent theoretical interest seems to be low. We have data at the community scale, and data at the macro-scale. How do we connect these (and can we)? Models describing how processes occurring at smaller scales produce larger scale dynamics can be complex: they may include non-linearities, autocorrelation between regions, the combination of discrete and continuous events, and multiple attractors.

2. Mechanisms maintaining multi-species coexistence in the real world. Hutchinson’s paradox of the plankton remains unsolved*. Community ecologists have invested a lot of time and energy into understanding species interactions as seen in natural communities. To explore the mechanisms behind coexistence, usually (but not always) ecologists have focused on two-species interactions (or maybe 3): understanding coexistence in larger groups tends to be mostly restricted to theory. But fitting the individual pieces into the larger puzzle is exponentially more difficult: in observed large groups of interacting species, what is the relative contribution of the many coexistence mechanisms identified? Which mechanisms are most important, and how do they change through space and time?
*Perhaps not surprisingly, given it is a paradox...

3. Moving farther away from species. In so many ways, focusing on ‘species’ as the unit of measurement is limiting, because ‘species’ is a discrete term and ecology is interested in quantitative measures. Important advances have been made by redefining ecology as the outcome of species traits and species interactions (5). But I think our ability to connect these ideas more closely to species’ multidimensional niches can still improve. In particular, understanding that traits and interactions can change in context-dependent ways (plasticity, ontogeny, environment) will be important (6, 7).

4. Reproducibility of ecological research. This is more of a philosophical question - how do we achieve reproducibility in a science where context-dependence, alternative stable states, chaos and stochasticity all affect results? How do we differentiate between reproducibility (same results under identical conditions) and generality (same results under similar conditions) in results?

References:
1) Sauer, Uwe; Heinemann, Matthias; Zamboni, Nicola. Genetics: Getting Closer to the Whole Picture. Science 316 (5824): 550–551. doi:10.1126/science.1142502. PMID 17463274.

2) Dominique Gravel, Frédéric Guichard, Michel Loreau and Nicolas Mouquet. Source and sink dynamics in meta-ecosystems. Ecology 91(7): 2172-2184.

3) Chesson, Peter. Scale transition theory with special reference to species coexistence in a variable environment. Journal of biological dynamics 3.2-3 (2009): 149-163.

4) Melbourne, Brett A., and Peter Chesson. The scale transition: scaling up population dynamics with field data. Ecology 87.6 (2006): 1478-1488.

5) McGill, Brian J., et al. Rebuilding community ecology from functional traits. Trends in ecology & evolution 21.4 (2006): 178-185.

6) Poisot, T., Canard, E., Mouillot, D., Mouquet, N., Gravel, D. & Jordan, F. (2012) The dissimilarity of species interaction networks. Ecology letters, 15, 1353–61.

7) Siefert, A., Violle, C., Chalmandrier, L., Albert, C.H., Taudiere, A., Fajardo, A., Aarssen, L.W., Baraloto, C., Carlucci, M.B., Cianciaruso, M.V. and L Dantas, V. A global meta‐analysis of the relative extent of intraspecific trait variation in plant communities. Ecology letters 18.12 (2015): 1406-1419.

Wednesday, March 23, 2016

The evolutionary canary in the coal mine*

*note -this post originally appeared on the Applied Ecologist's blog

Like canaries in coal mines, species can provide important information about deteriorating environmental conditions. A whole sub-discipline of environmental biomonitoring has emerged to provide the necessary tools to evaluate biological responses to changes in environmental conditions. While historically biomonitoring focused on contaminant concentrations in sentinel species –such as heavy metals in clams; modern biomonitoring uses information across multiple biological levels of organisation, from tissues, to organism behaviour, to the abundances and distributions of species. Since it is impossible to assess every aspect of an ecosystem’s response to pollution, scientists and practitioners still need to make decisions about which elements of an ecosystem should be monitored.
A coal miner with a canary –the classic sentinel species (url for photo: http://www.academia.dk/Blog/wp-content/uploads/CanaryInACoalMine_2.jpg)

In freshwater systems, diatoms are often the preferred organisms for monitoring since they have high diversity and diatom communities are structured strongly by local environmental conditions. Because of their long use in biomonitoring, freshwater biologists have sensitivity and indicator values for thousands of diatom species. Thus, in principle, you should be able to sample diatom communities in lakes and rivers of interest, and then assess the water quality based on the presence and abundance of different diatom species. While such proxies should always be validated and interpreted carefully (Stephens et al. 2015), there is a long and successful history of using diatoms for environmental monitoring.
Image of diatoms from a scanning electron microscope. (By Kostas Tsobanoglou - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=45315566)
The difficulty in practice is to identify diatom species, which requires expert training and can be time consuming. A number of researchers have pursued proxies and surrogates, for example using life form (e.g., diatom shape) or higher taxonomic groupings, instead of identifying species (Wunsam, Cattaneo & Bourassa 2002). In a recent article in the Journal of Applied Ecology, Francois Keck and colleagues (Keck et al. 2016) take this one step further, by using diatom evolutionary relationships as the biomonitoring tool.

Keck et al. employ novel statistical methods to create clusters of species based on their evolutionary relatedness from a phylogenetic tree and species’ sensitivity to pollution and show that these clusters, when delineated by short to moderate phylogenetic distances, do a good job of replicating species-level community pollution sensitivity indices.

This may seem like a onerous task, to assign diatoms to a correct position on a phylogenetic tree, but with the availability and now widespread use of DNA barcoding techniques, it is becoming easier to get genetic data for microscopic assemblages than to identify cells to species. This means that samples can be fit to the phylogenetic clusters without needing to shift through samples. Further, if species are observed, which have not been properly assessed for their sensitivity, they can be assigned an expected sensitivity value based on their relatedness to assessed species.
The phylogenetic tree and species’ sensitivities (Fig. 2 in Keck et al.).
While diatom evolutionary history may not have been strongly influenced by environmental pollutants in the past –because they are relatively recent stressors; it is clear from Keck et al.’s results that closely related species are similarly sensitive to pollution. Other fields of applied management have also begun to incorporate evolutionary history in the design and assessment of applied actions –for example, restoration (Hipp et al. 2015). Evolutionary history can provide important insights and management tools for dealing with the consequences of environmental change.


References

Hipp, A.L., Larkin, D.J., Barak, R.S., Bowles, M.L., Cadotte, M.W., Jacobi, S.K., Lonsdorf, E., Scharenbroch, B.C., Williams, E. & Weiher, E. (2015) Phylogeny in the Service of Ecological Restoration. American Journal of Botany, 102, 647-648.
Keck, F., Bouchez, A., Franc, A. & Rimet, F. (2016) Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms (microalgae). Journal of Applied Ecology.
Stephens, P.A., Pettorelli, N., Barlow, J., Whittingham, M.J. & Cadotte, M.W. (2015) Management by proxy? The use of indices in applied ecology. Journal of Applied Ecology, 52, 1-6.
Wunsam, S., Cattaneo, A. & Bourassa, N. (2002) Comparing diatom species, genera and size in biomonitoring: a case study from streams in the Laurentians (Quebec, Canada). Freshwater Biology, 47, 325-340.


Wednesday, March 9, 2016

Debating limits on diversity in class

I wrote a while ago about the debate on whether global diversity has ecological limits, based on two papers from Harmon and Harrison, and Rabosky and Hurlbert. This was in turn based on a debate from the ASN meeting (aside: there should be more formal debates at conferences). I decided to try replicating this debate in the Advanced Ecology class I'm teaching with Kendi Davies, and I was pleasantly impressed with the outcome. The class is mostly upper year students and small (~25 people), and the focus is on reading the primary literature and exploring key topics in ecology using active learning techniques (e.g. 1, 2). Since we're reading about patterns and processes of diversity through space and time, the debate topic was fitting.

The debate was split over two classes - in the first, students were split into two groups and they prepared their opening and closing statements and their supporting arguments. I've tried having students use Google documents and slides for these kind of group collaborative activities, and it seems to work well. (This is in part because there are 'lender laptops' available from the department's IT, which means that all students can participate, even without owning a personal laptop). What is great about Google docs is that when anyone adds or removes or edits text, the other members of the group can see it in real time, which seems to encourage more students to be actively involved than if, say, a single student is taking notes. Each group decided who would present the opening statement, each supporting argument, the rebuttal statement, and the closing statement, and who would take notes and prep the rebuttal.

To raise the stakes a bit, the winning team would get a pass on one homework assignment (the other motivator presumably being fear of letting their group down). What impressed me was how engaged students were during prep and during the actual debate. (For example, during prep, students were watching videos on how to debate, and expressed some concerns about espionage by the other teams ;-) ) More seriously, they took the time to understand the arguments presented in the source literature, and went beyond that to integrate support from other primary literature. I think at times students (okay, most of us) can get away with skimming papers for the key points: this rewarded them for reading carefully and thoughtfully.
Current US political debates provided instruction
on what not to do (from cnn.com).

The judges were a few generous postdocs (motivated by the promise of free food), who not only scored the debates, but gave some feedback to the teams. Ironically, the winning team had argued that “Species Diversity Is Dynamic and Unbounded at Local and Continental Scales” (after Harmon and Susan Harrison), but the class was nearly unanimous that they personally felt that there likely were ecological limits on diversity.

What I would do differently next time:

  • Plan some redundancy - a couple of people were sick, etc, who had roles in the debate. This left team members scrambling a bit. 
  • Group sizes: 12 people is a bit big for a group and makes coordination difficult. It might be possible to have smaller groups and do 2 sets of debates. Or, alternatively, to assign half the class as judges (or press - another prof here uses students as press who have to prepare questions for the debaters).
  • Consider not randomly assigning people to groups - it might be better to try to balance teams.
  • Public speaking and argument logic - interestingly, most of the students have little experience in constructing convincing and well supported arguments. We talk a lot about hypothesis construction with STEM students, but persuasive speech and writing receive less attention. Things like 'signposting' important points could use more practice.

Friday, March 4, 2016

Pulling a fast one: getting unscientific nonsense into scientific journals. (or, how PLOS ONE f*#ked up)

The basis of all of science is that we can explain the natural world through observation and experiments. Unanswered questions and unsolved riddles are what drive scientists, and with every observation and hypothesis test, we are that much closer to understanding the universe. However, looking to supernatural causes for Earthly patterns is not science and has no place in scientific inquiry. If we relegate knowledge to divine intervention, then we fundamentally lose the ability to explain phenomena and provide solutions to real world problems.

Publishing in science is about leaping over numerous hurdles. You must satisfy the demands of reviewers and Editors, who usually require that methodologies and inferences satisfy strict and ever evolving criteria -science should be advancing. But sometimes people are able to 'game the system' and get junk science into scientific journals. Usually, this happens by improper use of the peer review systems or inventing data, but papers do not normally get into journals while concluding that simple patterns conform to divine intervention.

Such is the case in a recent paper published in the journal PLOS ONE. This is a fairly pedestrian paper about human hand anatomy and they conclude that anatomical structures provide evidence of a Creator. They conclude that since other primates show a slight difference in tendon connections, a Creator must be responsible for the human hand (well at least the slight, minor modification from earlier shared ancestors). Obviously this lazy science and an embarrassment to anyone that works as an honest scientist. But more importantly, it calls into question the Editor who handled this paper (Renzhi Han, Ohio State University Medical Center), but also PLOS ONE's publishing model. PLOS ONE handles thousands of papers and requires authors to pay for the costs of publishing. This may just be an aberration, a freak one-off, but the implications of this seismic f$@k up, should cause the Editors of PLOS to re-evaluate their publishing model.  

Wednesday, March 2, 2016

What explains persistent species' rarity in communities?

Someone asked me what is the most important or lingering issue in community ecology recently. (There’s probably a whole post to answer that question (to come...)). One answer is the mystery of species coexistence: for more than 50 years (from Hutchinson’s paradox of the plankton through today) we have tried to explain the immense and variable diversity on earth by understanding what allows two or more species to coexist. There are many ways to explain coexistence, and yet the details and the specifics for any given system are also still usually incompletely understood.

A good and fascinating example is that of persistent rarity. Why are so many species in communities rare? What allows species to remain rare for long periods of time, given that small populations should be at greater risk for stochastic extinction? A new preprint from Yenni et al. (1) considers the empirical evidence for one potential explanation for persistent rarity: asymmetric negative frequency dependence (see also Yenni et al. 2012 (2)).

Coexistence theory (Chesson 2000) considers stabilizing mechanisms to be those that allow intraspecific competition to be greater than interspecific competition (often defined as ‘niche’ mechanisms). The strength of such stabilizing mechanisms can be estimated by looking at how a species’ population growth rate is limited by the frequency of conspecifics compared to the frequency of heterospecifics in the community. Negative frequency dependence is expected when stabilizing mechanisms are strong. This allows species to increase when rare, since limitation by conspecifics is low, followed by a decline in growth rates as conspecific frequency increases.

Asymmetric negative frequency dependence may explain persistent rarity, since it suggests especially strong conspecific limitation. As a species’ frequency increases, their growth rate greatly declines and intraspecific interactions, rather than interspecific competition, determine abundances. Species are rare, but also less likely to experience extinctions through competition with other species. The authors suggest that as a result of this, we should expect rare species to have stronger negative frequency dependence, in comparison to more common species. They look for evidence for asymmetric frequency dependence using data from 148 communities collected across multiple taxonomic groups (birds, fish, herpetofauna, invertebrates, mammals, and plants), 5 continents, and 3 trophic levels. The data represented time series of species abundances, which the authors used to estimate negative frequency dependence as the relationship between a species’ frequency in the community and their annual per capita population growth rate.

Several aspects of the results are particularly interesting. First, the authors had to omit rare species that are not persistent, since other processes likely explain the presence of such ephemeral members of communities. The frequency of ephemeral species (not stably coexisting at a local scale), for example, was quite high, particularly in plant communities (average of 82 species per community, of which only 22.6 species were on average identified as ‘persistent’). This may suggest the importance of spatial mechanisms for coexistence or co-occurrence. Their overall prediction of stronger negative frequency dependence in rare species appeared to holds in 46% of the communities they examined, consistently for all of the taxonomic groups but one (herps!). Additionally, the opposite pattern (common species having stronger negative frequency dependence) was never observed.

Rarity in nature is common :-) but not well predicted using most coexistence theory. Many interesting and important questions arise from it, and from results like those shown in Yanni et al. For example, do rare species have rare traits or rare niches? Is the frequency dependent growth rate context dependent (i.e. can a species be strongly limited by conspecifics in one environment but not another)?

*Note I haven’t reproduced any figures here, since this is a preprint. However, it is openly available, so do have a look (link 1 below). I’m not certain if there is a rule of thumb on blogging about preprints, but I imagine it is much like blogging about conference talks. The work may not have been peer reviewed/published yet, but the broad results and ideas remain interesting to discuss.

References:

1. Glenda Yenni, Peter Adler, Morgan Ernest. Do persistent rare species experience stronger negative frequency dependence than common species? doi: http://dx.doi.org/10.1101/040360. Preprint.

2. Yenni, Glenda, Peter B. Adler, and S. K. Ernest. "Strong self‐limitation promotes the persistence of rare species." Ecology 93.3 (2012): 456-461.

Wednesday, February 17, 2016

Grad school is like...

This post exists for no reason other than that I heard some fantastic analogies for graduate school/academic endeavours too good not to share... :-)

Starting grad school is like being dropped into a jungle with a machete and being told "find something new". Maybe (video game-like) you have a supportive supervisor, and so you are given a crude map. If you have labmates or fellow students, you can fend off the predators together. A good funding source allows you to travel faster. Best of all, maybe you come across some Tilley-hatted explorer who is so excited about the jungle that they give you detailed directions. There are infinite paths through the jungle, but some are harder than others.

The other analogy was for how to be a good supervisor, which is like a parent teaching a child to ride a bike. The parent can push a child off, and say "peddle!". This will be followed by lots of crashes and scraped knees and maybe the odd close call with traffic. Maybe the child figures it out, and is a fearless cyclist. But they might give up on biking all together, too. Or, the parent can hold the handles the whole time and say "great work! you're riding a bike all by yourself!" The result is a confident little cyclist who will probably crash when they finally get the opportunity to ride without help. A good supervisor probably holds on at first, then graduates you to training wheels and then takes them off. There will still be a few crashes, but the result is a cyclist not afraid to go alone, and without too many cuts and bruises.
Or maybe you've heard better ones?

Saturday, February 13, 2016

The vanishing pangolin: How do you change the value of an endangered species?

Extinction is forever. Extinction reduces the biological heritage of the Earth and is something that we cannot undo.

While living in China, and traveling around Asia, I have said something to my children I have never said before: “I want you to take a really good look, these animals will go extinct in your lifetime”.  I said this as we were watching 8 of the 60 remaining Hong Kong pink dolphins.

Hong Kong pink dolphin (photo by Shirley Lo-Cadotte)

Species become rare and endangered for many reasons, like habitat destruction, pollution, human facilitated spread of problematic species (rats for example), and direct harvesting. While all of these factors are subject to laws and regulations that attempt to control them, it is the last one, harvesting, that relies most on altering peoples' wants and desires. I don’t know why, but to me it is also the saddest cause, the idea that a species dies out because we desire it and kill it or chop it down, just doesn’t seem right.  

Walking through the market alley near my apartment in Guangzhou, China, I saw something that both intrigued and horrified me: a dead and quartered pangolin. You may not be familiar with pangolins –also called scaly anteaters; they are mammals about the size of a large cat or medium-small dog (like a cocker spaniel), with a very long and thick prehensile tail that they use in trees. Their most unique feature is that they are covered in large flat scales that are made of keratin –the same as your fingernails. 

A Chinese pangolin, Manis pentadactyla (https://commons.wikimedia.org/wiki/File:Pangolin%27s_tail.jpgsted to Flickr by verdammelt cc-by-sa-2.0) 
Pangolins are critically endangered. They also have the distinction of being one of the most trafficked animals in the world. In China and Vietnam there is high demand for pangolins because they are considered a delicacy and more importantly their scales are used in traditional medicine. These scales are believed to provide a cure for a number of diseases, including cancer. The incidence of cancers in China is skyrocketing, which is not surprising given the level of pollution, and couple this with increasing affluence, the desire and ability to pay for pangolin parts has never been greater.

Obviously pangolin scales do not cure cancer. You might as well save your money and suck on your fingernails instead, but evidence and logic are not likely to sway mortal fear. There are groups in Asia dedicated to protecting endangered animals and educate citizens about wildlife. Such organizations have an opportunity to capitalize on recent attitude shifts in China and elsewhere, where animal wellbeing is increasingly seen as important. In China, pet ownership has increased dramatically over the past decade and pets are now seen as companions –which I suspect was partially a result of the one-child policy. But the demand for pangolins still exists. When we visited the Angkor Conservation Centre in Cambodia, which works tirelessly to rehabilitate animals and educate people, they were recovering from the theft of one of their pangolins from an enclosure, which they knew was transported to China.

The Chinese authorities are coming down hard on the illegal pangolin trade. They now routinely arrest individuals selling pangolins and seize large shipments. While such seizures and arrests show that the Chinese government is taking pangolin protection seriously, there is only so much they can do while demand is high.

Police confiscating a large illegal pangolin shipment bound for China (photo originally from news.163.com) 

My Mother-in-law, who is from southern China, said it best when I told her about the dead pangolin in the alley: “people just need to be educated”. That is really where the answer lies. Laws can only change peoples’ behaviour so much; education campaigns are desperately needed. Currently, there is an internationally funded billboard campaign in China to stop people from buying elephant ivory. Ivory demand is high in China. Despite the importance of reducing ivory purchases, I would argue that this type of education campaign needs to focus a little closer to home, and Pangolin conservation efforts are in desperate need of help. 

When we were visiting the conservation centre in Cambodia, I told my children that the Pangolin would go extinct in their lifetime. I really hope that I am wrong.




Monday, February 8, 2016

New ways to address an old idea: rethinking the regional species pool

Like many concepts in ecology (metacommunity, community), the idea of a regional species pool is useful, makes conceptual sense, and is incredibly difficult to apply to real data. Originally, the idea of a species pool came from the theory of island biogeography (MacArthur and Wilson, 1967), where it referred to all the species that could disperse to an island. Today, the regional species pool appears frequently, across null models, studies of community assembly both empirical and theoretical, and metacommunity theory. 

Understanding how particular processes shape community membership—whether the environmental, competition, or dispersal limitation—depends on knowing the identity of all the species that could have potentially assembled there. The species pool as defined by the research provides the frame of reference against which to consider a community's composition. Most null models of community assembly rely on correctly identifying this set of species, and worse, tend to be very sensitive to bias in how the regional pool is defined. If you include all species physically present in a region, in your species pool, environmental filtering may appear to be particularly important simply because many of those species can’t actually survive in your community (the narcissus effect). Given the importance of null models to community ecology, defining the species pool appropriately is an ongoing concern.

There are many decisions that can be made when asking 'which species could potentially be members of a community'? You could include all species that can physically arrive at a site (so only dispersal or geographic distance limits membership), or only include those species that can both arrive and establish (both dispersal and environmental conditions limit membership). Further, the availability of data is key: if you use observational data used to determine the environmental limitations, you may also incorporate the outcome of biotic interactions indirectly. If some species are rare and have low observation likelihoods, they will be under-represented. Abundances may be useful but inaccurate depending on how they are measured. Finally, it is common to define species as either present or not present for a species pool; this binary approach may conceal ecologically important information.
The 'filtering' heuristic for understanding community membership. Species groups 1-3 could each be defined as a regional species pool, depending on the definition applied.
A number of recent papers provide alternative approaches to constructing species pools, meant to avoid these pitfalls. Researchers can define multiple contrasting species pools, each pool representing an ecological process (or perhaps multiple processes) of interest. Each species pool can be modified further to reflect the strength of a particular process in constraining membership. The regional pool is not seen as a single entity but as a number of possible configurations whose utility is in comparison.

Lessard et al. (2016) illustrates how to produce this kind of process-based species pool with various constraints (figure below). Their three-step approach is to:
  1. Define absolutely all possible members of regional pool. This is determined by identifying all assemblages in the region containing at least one species also found in the focal community (creating a 'dispersion field') (figure below, section A). This delineates a large region and identifies all species within it.
  2. Calculate the probability of resampling a species from the focal community elsewhere in the dispersion field. This is done in the context of the process of interest. For example, the probability of observing a species in the focal community and another community might be determined based on the geographical or environmental distance between those sites. Every site in the dispersion field would now have a probability (or distance really) associated with it, representing some similarity with the focal site.
  3. Finally, apply constraints to the calculated probabilities. You might choose to consider only the species within communities that are at least 50% similar to the focal community, for example. Such constraints would reflect the strength or importance of filtering by the process of interest.
Another recent paper (Karger et al., 2016) takes an approach with a number of commonalities to the Lessard et al. method. However, rather than resampling to produce potential pools of species (with species being defined as present or absent), they advocate a probabilistic approach to species pools. They suggest that species pools should be thought of as a set of probabilities of membership, which may be more reflective of ecological reality. In some ways, this is a simply a formalization of probabilistic sampling from Lessard, but instead of applying constraints, the researcher acknowledges that probabilities vary for different species. “Hence, a species pool can simply be defined as a function of probabilities of a species’ occurrence in the focal unit given the unit’s environmental and biotic conditions, geographical location and the time frame of interest”.

Both comparative and probabilistic approaches to defining species are logical advances, and one way of dealing with the untidy concept of the species pool. If this topic is of interest, a few other papers, albeit slightly less recent, are definitely worth reading: Pigot and Etienne 2015; Lessard et al. 2012, Carsten et al., 2013.
From Lessard et al., 2016. The three steps to build a species pool.

Saturday, February 6, 2016

Reining in traffic –looking to China for solutions?

Human impacts on landscapes are immense. Urban areas represent complete transformations of the geological, hydrological and ecological norms in landscapes. But while urban effects are concentrated to relatively small areas, the roads and rail lines feeding cities create a pervasive and diffuse network of negative impacts. Roads funnel rain runoff and can cause local flooding and this runoff also concentrates pollutants. Further, roads alter wildlife movement. For example, the fragmentation of formerly continuous forest in Florida is worsened by large busy roads, and black bears there are unable to move long distances to find mates. The result of this is that the Florida Black bear populations are getting smaller and more genetically inbreed.

Roads are created to meet traffic demands. The more people drive and the further they drive, the more roads we build. Cities around the world are growing, meaning that more cars are concentrated in small areas. The increase in automobile use also has direct environmental consequences. Cars, thanks to their internal combustion engines, add pollution to our local environments –carbon monoxide, particulate matter, and other toxins create smog, exacerbate respiratory ailments, and contribute to global warming.

More cars also means more traffic congestion and greater difficulty in getting from A to B, meaning that we spend more time travelling to, instead of being, somewhere. Heavy reliance on automobiles directly affects our quality life in both positive and negative ways.

1950s traffic jam in Los Angeles (from Wikipedia)
Given the undesirable consequences of cars, many cities try to reduce car use. In North America, cities employ a number of strategies, including: minor improvements to public transit (while often passing on the costs to riders), creating car free zones (which have been very modest in North America, whereas European cities have been much more successful –Montpellier, France is a great example), introducing tolls, and limiting parking in the city core. It is safe to say that the North American approach to dealing with traffic has been less than spectacular –just drive through Toronto or Los Angeles during rush hour.

Living in China for the past several months, I have been intrigued by how Chinese jurisdictions have dealt with traffic. And traffic was something that needed dealing with here. In the late 1990s and early 2000s, thousands of new cars were added to roads every single day.  The air quality in China is abysmal and having hundreds of millions of cars driving at the same time only make things worse. So governments in China decided to experiment with ways to reduce automobile use.

In China, much of the power to control automobiles resides with municipalities –they are the ones who set local traffic laws and issue license plates. From conversations with scientists from different regions of China, I have compiled ways different municipalities deal with traffic and reduce automobile use. Here are some of the ways that municipalities try to reduce automobile traffic:

1) Massive investments in public transit

There can be no real traffic solutions without building fast, efficient and affordable public transit. China has been a world leader in public infrastructure development over the past ten years. For example, Shanghai has one of the largest metro systems in the world, and has opened a new line every other year since 1999! They are currently building two new lines, which will give Shanghai 18 metro lines and about 400 stations. In Guangzhou, where I currently live, they also have a very modern and rapidly expanding metro system. Guangzhou currently has 8 lines with 4 more under construction! In all the Chinese cities I’ve been in, the metro systems are modern, efficient, heavily used, and very affordable. In Guangzhou, a bus ride works out to be about 35 cents US and a metro trip to the airport (the longest trip you can take in Guangzhou I believe) is about $1.15 US.

In Toronto, where I normally live, and like most other large North American cities, subway construction has not been sufficient to keep up with population growth. Local politicians seem to be unable to make the tough decisions to get public transit infrastructure built. But this infrastructure is the linchpin for any successful reduction in automobile usage.

2) Driving days

During the 2008 summer Olympics, Beijing created a system where cars were allowed on the roads only on certain days. Which days people could drive their cars depended on the last number of their license plates. This scheme was successful in reducing traffic congestion and air pollution. Since then, they have periodically reinstated this policy, especially during extremely bad air pollution days. I was there in early December, and road sharing was in effect then.

3) Making license plates really, really expensive (or difficult to get).

In Guangzhou, Beijing, and Shanghai, getting a car is easy, but getting a license plate, now there is the real hurdle. Since 2012, Guangzhou and other cities have severely limited the number of license plates issued, and now people can get a plate in one of two ways in these cities: by joining a lottery or going to an auction. In the lottery, a person submits an application and waits for the results. One person told me it took them three years to get their plate in the lottery. In the auction, the plates go to the highest bidder and the price for a license plate at auction has sky rocketed. A person told me that plates at auction now go for more than 60,000 RMB (about  $10,000 USD), which costs more than an economy car here! This person also quipped that the plates have become more of a status symbol than the actual car.

4) Your license plate will die

In Guangzhou and other cities, license plates expire. No, not like they expire in North America where you pay an annual license fee. They expire after 10 years and are no longer valid, and the driver must re-enter the lottery. 

5) Pay the toll

Many of the intercity highways have tolls here. While this is not a policy that affects travel behaviour within cities, it does influence driver choices traveling outside the city. Tolls only work when there are decent alternatives, and the rail system in China is excellent. There are frequent trains and many high speed lines in operation (where the trains go faster than 250 km/h). We don't have many toll roads in Ontario, but the one we have near Toronto, hwy 407, doesn't go into the city (so doesn't influence commuter decisions), and does not have viable options for alternative travel. This highway is an example of poor government policy and it was one of the worst policy decisions by a government who thought private companies should run public infrastructure. Its nothing more than a cash grab that doesn't serve the broader good. But I digress.

I have been struck by the variety of approaches and the experimental nature of policy making. What I mean by experimental, is that some policies seem to be ‘test run’ to see how people respond and if the policies result in the desired effects. China is able to institute creative and extreme measures because of the government’s unique ability to change policy without public debate. Often these policies are instituted overnight with little warning. In China, people seem to take government edicts with a “well, what can you do?” attitude. But if there is a country that can change the automobile culture, China is a good candidate. They did change what a family was with the one-child policy.

While most North Americans would certainly have a problem with the lack of transparency and seemingly impulsive nature of government decisions, China is providing the world with working examples of how to reduce the number of automobiles. It is clear to most, that without strong governmental leadership, a robust set of policies, and massive infrastructure investment, heavy automobile traffic will be unavoidable.