Sunday, March 18, 2018

Don't be Ranunculus... Little known plant behaviours

Guest post by Agneta Szabo, MEnvSci Candidate in the Professional Masters of Environmental Science program at the University of Toronto-Scarborough

Through the scientific study of plant behaviour, we continue to discover new ways in which plants interact with their environment in animal-like ways. Words like “listening”, “foraging”, and “parenting” may seem odd to associate with plants, and yet plants show evidence of all of these behaviours. Here are some of the many ways in which plants behave.

As it turns out, plants are listening! A study by Heidi Appel and Rex Cocroft published in 2014 describes their discovery that plants can detect their predators acoustically and ramp up their defenses as a response. Appel and Cocroft recorded the sound vibrations of caterpillars chewing on Mouse‑ear Cress leaves, and played these recorded vibrations to previously unaffected Mouse-ear Cress plants over several hours before allowing caterpillars to attack the plants. The researchers found that, compared to plants that were primed with recordings of silence, those who were primed with recordings of chewing produced much higher levels of the oils glucosinolate and anthocyanin, which are toxic to caterpillars. Furthermore, Appel and Cocroft found that the plants were able to distinguish the sound vibrations caused by chewing from recordings of wind or other insect noises.
In addition to listening for their predators, plants can also listen for water. In 2017, Monica Gagliano and her colleagues published a paper showing that the Garden Pea was able to locate water by sensing the vibrations generated by water moving inside pipes. Garden Pea seedlings were planted in pots shaped like an upside-down Y, and each arm of the pot was treated with different experimental conditions. When one arm was placed in a tray of water and the other was dry, plant roots grew towards the arm with water. Seems obvious enough. However, when one arm was placed above a tube with flowing water and the other was dry, the plant roots still grew towards the water, even though there was no moisture. When given a choice between a tray of water and the tube with flowing water, the Garden Pea seedlings chose the tray of water. This led Gagliano to hypothesize that plants may use sound vibrations to detect water at a distance, but that moisture gradients allow the plants to reach their target at close proximity.
Garden Pea water acoustics experimental set-up (Gagliano et al., 2017)

Plant roots forage for food in a similar way to animals. In his 2011 review, James Cahill explores plant root responses to varying nutrient cues in the soil. Cahill explains that plant roots are responsive to both spatial and temporal nutrient availability. For example, when a nutrient patch is placed in the soil at a distance from the plant, there is a substantial acceleration in root growth in the following days. This growth is directed precisely towards the nutrient patch, and as the root approaches its target, the rate of growth slows as the nutrient patch is consumed. Furthermore, plants develop greater root biomass in richer nutrient patches, and they allocate more root biomass to patches with increasing nutrient levels.

Other foraging plants include the parasitic Dodder vine. This plant has no roots and lives off a host plant. In 2006, Consuelo De Moraes and her team published a study demonstrating that the Dodder plant uses scent, or volatile chemical cues, to locate and select its host plant. De Moraes experimentally planted Dodder seedlings between a Tomato and Common Wheat plant, the Tomato being its preferred host. Using a time lapse camera, De Moraes captured the circling movement of the Dodder plant as it approached both host options repeatedly, before settling on the Tomato plant 90% of the time. Through further experimentation by giving the Dodder seedlings a choice between the condensed chemical odour of the Tomato plant and a live Tomato that has been covered to prevent giving off odour, it was determined that the Dodder uses the chemical signals to select its host. Without being able to “smell” the live Tomato plant, the Dodder chose to attach to the vile containing the condensed chemical odour. 
Dodder vine attaching to a Tomato plant

(PBS, 2014:


One of the most fascinating aspects of plant behaviour is parental care and kin recognition. Suzanne Simard’s work studying forests as a complex, interconnected organism has been featured on several popular media outlets including the TED Talk series and the Radiolab podcast. Through her research, Simard discovered that through a network of mycorrhizal fungi, adult trees were nurturing their young with a targeted exchange of nutrients such as carbon and nitrogen, as well as defense signals and hormones. Through experimental plantings of Douglas Fir seedlings that were directly related to the adult trees and unrelated Douglas Fir seedlings, she found that the “mother trees” recognized and colonized their kin with larger networks of mycorrhizal fungi, and sent more carbon to these seedlings. Furthermore, there was a reduction in root competition with the related seedlings. When injured, the adult trees sent large amounts of carbon and defense signals to their young, which increased the seedlings’ stress resistance.
Tree mycorrhizal network schematic 
(Medium, 2017:

Similar recognition of kin was observed by Susan Dudley and Amanda File in a 2007 paper. In this study, Dudley and File planted related “sibling” Sea Rocket plants together in pots, as well as unrelated “stranger” Sea Rocket plants together in pots. After several weeks, the roots were cleaned and assessed. The study found that kin groups allocated less biomass to their fine roots, while stranger groups grew larger roots in order to compete for resources. The same responses were not observed when kin and stranger groups were grown in isolated pots, which suggests that the mechanism for kin recognition was through root interactions.

Although we still don’t fully understand the mechanism by which plants process information, it is clear that the way plants interact with their environment is far more complicated than we previously thought. The concept of plants as inanimate organisms, blindly competing for resources is now outdated. Continued discoveries in plant behaviour demonstrate, once again, how little we understand about the natural environment—a humbling thought in an age when humankind thinks itself superior to our fellow species.

Appel, H.M. & Cocroft, R.B. (2014). Plants respond to leaf vibrations caused by insect herbivore chewing. Oecologia, (2014)175: 1257–1266.
Cahill, J.F. & McNickle, G.G. (2011). The behavioral ecology of nutrient foraging by plants. Annual Review of Ecology, Evolution, and Systematics, 2011(42): 289–311.
Dudley, S.A. & File, A.L. (2007). Kin recognition in an annual plant. Biology Letters (2007)3: 435–438.
Gagliano, M., Grimonprez, M., Depczynski, M. & Renton, M. (2017). Tuned in: plant roots use sound to locate water. Oecologia (2017)184: 151–160.
Runyon, J.B., Mescher, M.C. & De Moraes, C. (2006). Volatile chemical cues guide host location and host selection by parasitic plants. Science, 313(5795): 1964–1967.
Simard, S. (2016). Suzanne Simard: How trees talk to each other [Video file]. Retrieved from

Monday, March 12, 2018

Gained in translation: translational ecology for the Anthropocene

A recent evaluation of the state of science around the world run by 3M found that 86% of the 14,000 people surveyed believed that they knew 'little to nothing' about science. 1/3 of all respondents also said they were skeptical of science and 20% went farther, saying that they mistrust scientists and their claims.

Those attitudes wouldn't surprise anyone following US politics these days. But they're still troubling statistics for ecologists. Perhaps more than most scientific disciplines, ecologists feel that their work needs to be communicated, shared, and acted on. That's because modern ecology can't help but explicitly or implicitly include humans – we are keystone species and powerful ecosystem engineers. And in a time where the effects of global warming are more impactful than ever, and where habitat loss and degradation underlie an age of human-caused extinction, ecology is more relevant than ever.

The difficulties in converting primary ecological literature into applications are often construed as being caused (at least in part) by the poor communication abilities of professional scientists. Typically, there is a call for ecologists to provide better science education and improve their communication skills. But perhaps this is an 'eco-centric' viewpoint – one that defaults to the assumption that ecologists have all the knowledge and just need to communicate it better. A more holistic approach must recognize that the gap between science and policy can only be bridged by meaningful two-way communication between scientists and stakeholders, and this communication must be iterative and focused on relevance for end-users.

William H. Schlessinger first proposed this practice - called Translational Ecology (TE) - nearly 8 years ago. More recently an entire special issue in Frontiers in Ecology and the Environment was devoted to the topic of translational ecology in 2017. [The introduction by F. Stuart Chapin is well worth a read, and I'm jealous of the brilliant use of Dickens in the epigraph: “It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity.”]

Although applied ecology also is focused on producing and applying ecological knowledge for human problems, translational ecology can be distinguished by its necessary involvement of the end user and policy. Enquist et al. (2017, TE special issue) note: "Ecologists who specialize in translational ecology (TE) seek to link ecological knowledge to decision making by integrating ecological science with the full complement of social dimensions that underlie today's complex environmental issues."
From Hallet et al. (2017, TE special issue)

The essential component of translational ecology is a reliance on people or groups known as boundary spanners, which are the key to (effectively) bridging the chasm between research and application. These people or organizations have particular expertise and skill sets to straddle the divide between "information producers and users". Boundary spanners are accountable to the science and the user, and generally enable communication between those two groups.

Boundary spanners likely have interdisciplinary backgrounds, and integrate knowledge and skills from ecology and biology, as well as disciplines such as anthropology, human geography, sociology, law, or politics. The key issue in that boundary spanners can overcome is the lack of trust between information users and producers. Translational ecology – through communication, translation, and mediation – is especially focused on developing relationships with stakeholders and boundary spanners are meant to be particularly skilled at this. 

For example, academics publish papers, and then the transmission of information to potential users is usually allowed to occur passively. At best, this can be slow and inefficient. At worst, potential end users lack access, time, and awareness of the work. Boundary spanners (including academics) can ensure this knowledge is accessibly by producing synthetic articles, policy briefs and white papers, by creating web-based decision-support tools, or by communicating directly with end users in other ways. A great example of existing boundary spanners are Coop extension offices hosted at US land grant universities. Coops are extensions of government offices (e.g. USDA) whose mission is to span the knowledge produced by research and to bring it to users through informal education and communication. 

For working academics, it may feel difficult to jump into translational ecology. There can be strong institutional or time constraints, and for those without tenure, fear that translational activities will interfere with other requirements. Institutions interested in working with ecologists also often face limitations of time and funding, and variable funding cycles can mean that boundary-spanning activities lack continuity.

But what's hopeful about the discussion of translational ecology in this issue is that it doesn't have an individualistic viewpoint: translational ecology requires teams and communities to be successful, and everyone can contribute. I think there is sometimes a very simplistic expectation that individual scientists can and must be exceptional generalists able to do excellent research, write and give talks for peers, teach and lecture, mentor, and also communicate effectively with the general public (in addition to taking care of administration, human resources, ordering and receiving, and laboratory management). We can all contribute, especially by training boundary spanners in our departments and labs. As F.S. Chapin says, "The key role of context in translational ecology also means that there are roles that fit the interests, passions, and skills of almost any ecologist, from theoreticians and disciplinarians to people more focused on spanning boundaries between disciplines or between theory and practice. We don't need to choose between translational ecology and other scientific approaches; we just need to provide space, respect, and rigorous training for those who decide to make translational ecology a component of their science.

From Enquist et al. (2017, TE special issue).

Special Issue: Translational ecology. Volume 15, Issue 10. December 2017. Frontiers in Ecology and the Environment

Thursday, March 8, 2018

The Gender-Biased Scientist: Women in Science

Guest post by Maika Seki, MEnvSci Candidate in the Professional Masters of Environmental Science program at the University of Toronto-Scarborough

In November of 2017, Nature Ecology & Evolution published “100 articles every ecologist should read” by Courchamp and Bradshaw, sparking a social media outrage. Rightfully so, because the list of first authors only included two women. There remains a pervasive perception that women lack the skills to practice science, and that there simply are not enough women in the field for them to have made a significant contribution, referring to the male-dominated history of the sciences. Many of us have come across studies highlighting gender bias in science education - which people have attempted to use to explain gender gaps in STEM fields. However in 2011, neuroscientist Melissa Hines found no significant difference between the mathematical, spatial, and verbal skills of boys and girls. But of course that finding did not receive much attention. In light of the emerging discourse of vital inclusivity in science, now is the time to confront our own social biases with the goal of achieving gender equity in the scientific community.

Instead of rehashing these outdated arguments, why don’t we talk about the barriers that women face in science? Why don’t we talk about the sexism in the publishing and peer-review process? In 2015, evolutionary geneticist Fiona Ingleby submitted a research paper to PLOS ONE, where the peer-reviewer suggested that she work with male biologists in order to strengthen the study, stating, “It would probably … be beneficial to find one or two male biologists to work with (or at least obtain internal peer review from, but better yet as active co-authors).” The under-recognition of women scientists has been so rampant in the fabric of science that it has been coined the Matilda effect; named after the first women scientist to comment on the phenomenon, Matilda Jocelyn Gage.
Why don’t we talk about the barriers women face in accessing employment in science, even while possessing the same qualifications as their male counterparts? At Yale University, a study was conducted wherein over 100 scientists assessed a resume for a job posting. The only difference between the resumes were the names; half of them were given recognizably male names, and the other half recognizably female names. The resumes submitted under the female names were deemed significantly less competent and employable, and were offered lower salaries. Clearly there is work to be done.

And then there was Tim Hunt, a Nobel laureate who made outright sexist comments at the World Conference of Science Journalists stating, “Let me tell you about my trouble with girls … three things happen when they are in the lab … You fall in love with them, they fall in love with you and when you criticize them, they cry.Twitter responded with the hashtag #DistractinglySexy, where women scientists shared unglamorous photos of them doing their research work. Hunt subsequently resigned from his honorary post at the University College-London. We may think that this is an exceptional and isolated event, but studies show that we are not immune to these kinds of social forces of gender discrimination, even if we like to think so — especially as scientists. These seemingly minor micro-aggressions translate to devastating and tangible effects, such as the gender pay gap. 

Photo by @STEPHEVZ43 on Twitter, as a response to Tim Hunt’s sexist comments.

Within scientific fields, we like to pride ourselves in being as close to bias-free as possible with our empirical, quantitative, and reproducible data. But scientists are people, and as such, we must confront the cultural and social influences that may permeate our objectivity. As scientists, we do not like to admit to this. But if we are going to arrive as close to the truth as possible, we need to capitalize on the emerging discourse of gender issues in science.
As of 2015, Canadian women represented only 22% of the STEM workforce. Not only are women under-represented in the workforce despite 62% of undergraduate students being women, but they are under-compensated. According to Statistics Canada, the wage gap persists across all fields, with the women median income of a bachelor’s degree being $68,342, and $82,083 for men. This is not a “third world” problem. This is a global issue. It is indisputable that there are systemic barriers that women face when pursuing careers in science. So why can’t scientists consider the confounding social factors at play that create these patterns? In science when somebody denies a phenomenon after many analyses point to the same mechanism, we would likely consider that as being irrational. With this in mind, is the denial of gender bias in science not irrational? By acknowledging these biases and promoting change, we take aim at the lack of objectivity in the discipline of science. It should also be encouraged to confront the sexism, racism, and all other intersectionalities of power imbalance within the science community. Some may argue that there is no place for politics in science, but we must face the reality that the two can not be separated. Addressing the sexism would bring us better, more balanced science. 

Statistics Canada graph on the Canadian men and women in STEM fields.

How can we aspire towards a world of innovation and ground-breaking research when roughly half of the population is held back? And how can we address it? To start, we need to hold institutions more accountable. It is disheartening to know that had people not reacted to the all-male panels, it would not be seen as a problem. Furthermore, it is not enough to tweet about it. It’s a start, but not nearly enough — because how many of these types of stories repeat themselves in the media? We need it to be written in the mandates of institutions, and this is not enough. We need it to be enforced. We also need women to be more involved and hold power in these decision-making panels; it is not enough to throw in a token white woman and call it a day. It is not enough for women to be given a seat on the board as a corporate marketing tool under the guise of inclusivity. They must also be afforded the same power that men have. We need to hold each other more accountable. We need to confront our own prejudices, no matter how uncomfortable that may be. If not for women, then do it for practical and selfish reasons; do it because there are studies that show that women have to be more productive than men to be deemed equally scientifically competent (feeling the pressure to prove themselves). And do it because it is better for the economy, and because diversity in the workplace increases productivity

Graph by The Star on the income of full-time men and women in Canada, who have a bachelor’s degree.

There is no good reason to continue to exclude women from the same influential roles that men have, and it is time that we each consider our own sexist views (whether sub-conscious or not). It is time to challenge the systemic biases in powerful institutions in order to let women claim their full potential as true peers to men; as colleagues, partners, scientists, and in all other walks of life. In order to increase scientific literacy, we can not afford to continue to exclude women from science, because science needs women. In the spirit of the United Nations’ International Day of Women and Girls in Science day, which passed on February 11th, and International Women’s day today, let us commit to empowering women to reach political, social, and economic equality to men. And let us make changes in our own lives, begin conversations with those around us, and become more active in our communities to progress towards gender equity.

Friday, February 23, 2018

Moving on up to the regional scale

Like the blind men and the elephant, perspective drives understanding in ecology. The temporal and spatial scale of analysis (let alone the system and species you focus on) has major implications for your conclusions. Most ecologists recognize this fact, but consider only particular systems, scales or contexts due to practical limitations (funding, reasonable experimental time frames, studentship lengths). 

Ecologists have long known that regional processes affect local communities and that local processes affect regional patterns. Entire subfields like landscape ecology, metapopulations, metacommunities, and biogeography (species area relationships) highlight these spatial dependencies. But high-profile ecological research into biodiversity and ecosystem functioning ('BEF') primarily considers only local communities. Recently though, the literature has started to fill this gap and asking what BEF relationships look like at larger spatial scales, and how well local BEF relationships predict those at larger spatial scales.

'Traditional' BEF experiments were done at relatively small spatial scales (often only a few meters^2). Positive BEF relationships were commonly observed, but often were quite saturating – that is, only a few species were necessary to optimize the function of interest. If the impact of biodiversity saturates with only a few species, it would seem that surprisingly few species are necessary to maintain functioning. True, studies that considered multiple ecosystem functions are more likely to conclude that additional diversity is required for optimal functioning (e.g. Zavaleta et al. 2010). But a simplistic evaluation of the facts that a) ecosystem functioning rapidly saturates with diversity, and b) locally, diversity may not be generally decreasing (Vellend et al. 2017), could lead to overly confident conclusions about the dangers of biodiversity loss. Research on BEF relationships, as they transition from local to larger spatial scales, is increasingly suggesting that our understanding is incomplete, and that BEF relationships can grow stronger at large spatial scales.

A number of recent papers have explored this question, and in considering the essential role of spatial scale. Predictions about how BEF relationships will change with spatial scale vary. On one hand, in most systems there are only a few dominant species and these species may disproportionately contribute to ecosystem functions, regardless of the spatial scale. On the other hand, species-area relationships tend to increase rapidly at small scales, as community composition turns over. If that is the case, then different species may make important contributions in different places. Winifree et al. (2018) contrasted these predictions for three crop species that rely on natural bee pollinators (cranberries, blueberries, and watermelons). They censused pollinators at 48 sites, over a total extent of ~3700 km^2. Though at local scales very few bee species were required to reach pollination goals, the same goals at larger spatial scales required nearly an order of magnitude more bee species. These results in particular appeared to be driven by species turnover among sites--perhaps due to underlying environmental heterogeneity.
From Winifree et al. "Cumulative number of bee species required to maintain thresholds of 25% (orange), 50% (black), and 75% (purple) of the mean observed level of pollination, at each of n sites (16). Horizontal dashed lines indicate the total number of bee species observed in each study. Error bars represent 1 SD over all possible starting sites for expanding the spatial extent. For all three crops combined, each x-axis increment represents the addition of one site per crop".

Another mechanism for increased BEF at larger scales is insurance effects. The presence of greater diversity can interact with spatial and temporal environmental variation to increase or stabilize ecosystem functioning. Greater diversity should maximize the differential responses of species to changing conditions, and so buffer variation in ecosystem functioning. Such effects, when they occur through time are temporal insurance, and when they occur via dispersal among sites, spatial insurance. Wilcox et al. (2018) considered the role of synchrony and asynchrony among populations, communities, and metacommunities to ask whether local asynchrony affected stability (see Figure below for a nice conceptual explanation). Across hundreds of plant data sets, they found that asynchrony of populations did enhance stability. However, the degree to which it affected stability varied from very weak to very important (e.g. by 1% to 300%). Maximizing species or population differences at local scales apparently can have implications for dynamics, and so potentially stability of functioning, at much larger scales.

From Wilcox et al. "Conceptual figure showing how stability and synchrony at various spatial scales within a metacommunity combine to determine the stability of ecosystem function (here, productivity). In (a), high synchrony of species within and among local communities results in low stability at the scale of the metacommunity. In (b), species remain synchronised within local communities, but the two communities exhibit asynchronous dynamics due to low population synchrony among local patches. This results in relatively high gamma stability. Lastly, in (c), species exhibit asynchronous dynamics within local communities through time, and species-level dynamics are similar across communities (i.e. high population synchrony). This results in relatively high gamma stability. Blue boxes on the right outline stability components and mechanisms, and the hierarchical level at which they operate. Adapted from Mellin et al. (2014)."
Finally, Isbell et al. (2018) describe ways in which ecosystem functioning and other contributions of nature to humanity are scale-dependent, laying out the most useful paths for future work (see figure below).

From Isbell et al. 2018.
These papers make nearly identical points worth reiterating here: 1) we have done far too little work beyond the smallest spatial scales (~3 m^2) and so lack necessary knowledge of the impacts of losing of biodiversity, and 2) policy decisions and conservation activities are occurring at much larger scales – at the scale of the park, the state, or the nation. Bridging this gap is essential if we are to make any reasonable arguments as to why ecosystem function figure into  large-scale conservation activities.

Sustaining multiple ecosystem functions in grassland communities requires higher biodiversity. Erika S. Zavaleta, Jae R. Pasari, Kristin B. Hulvey, G. David Tilman. Proceedings of the National Academy of Sciences Jan 2010, 107 (4) 1443-1446; DOI: 10.1073/pnas.0906829107. 

Plant biodiversity change across scales during the Anthropocene. Vellend, Mark, et al. Annual review of plant biology 68 (2017): 563-586.

Species turnover promotes the importance of bee diversity for crop pollination at regional scales. RACHAEL WINFREE, JAMES R. REILLY, IGNASI BARTOMEUS, DANIEL P. CARIVEAU, NEAL M. WILLIAMS, JASON GIBBS. SCIENCE16 FEB 2018 : 791-793

Asynchrony among local communities stabilises ecosystem function of metacommunities. Kevin R. Wilcox, et al. Ecology Letters. Volume 20, Issue 12, Pages 1534–1545.

Isbell, Forest, et al. "Linking the influence and dependence of people on biodiversity across scales." Nature 546.7656 (2017): 65.

Thursday, January 18, 2018

A general expectation for the paradox of coexistence

There are several popular approaches to the goal of finding generalities in ecology. One is essentially top down, searching for generalities across ecological patterns in multiple places and at multiple scales and then attempting to understand the underlying mechanisms (e.g. metabolic scaling theory and allometric approaches). Alternatively, the approach can be bottom up. It may consider multiple models or multiple individual mechanisms and find generalities in the patterns or relationships they predict. 

A great example of generalities from multiple models is in a recent paper published in PNAS (from Sakavara et al. 2018). It relies on, links together, and adds to, our understanding of community assembly and the effects of competition on the distribution of niches in communities. In particular, it adds additional support to the assertion that both combinations of either highly similar or highly divergent species can coexist, across a wide variety of models.

Work published in 2006 by Scheffer and van Nes played an important early role towards a reconciliation of neutral theory and niche-based approaches. They used a Lotka-Volterra model to highlight that communities could assemble with clusters of coexisting, similar species evenly spaced along a niche axis (Figure 1). Neutrality, or at least near-neutrality, could result even when dynamics were determined by niche differences. [Scheffer, van Nes, and Remi Vergnon also provide a nice commentary on the Sakavara et al. paper found here].
Fig. 1: From Scheffer and van Nes, emergent 'lumpiness' in communities.
One possibility is that Scheffer and van Nes's results might be due to the specifics of the L-V model rather than representing a general and biologically realistic expectation. Sakavara et al. address this issue using a mechanistic consumer-resource model in "Lumpy species coexistence arises robustly in fluctuating resource environments". Under this model, originally from Tilman's classic work with algae, coexistence is limited by the number of resources that limit a species' growth. For 2 species, for example, 2 resources must be present that limit species growth, and further the species must experience a tradeoff in their competitive abilities for the 2 resources. Coexistence can occur when each species is limited more by the resource on which it is most competitive (Figure 2). Such a model– in which resources limit coexistence—leads to an expectation that communities will assemble to maximize the dissimilarity of species.
Fig 2. From Sakavara et al. (2017).
Such a result occurs when resources are provided constantly, but in reality the rates of resource supply may well be cyclical or unpredictable. Will community assembly be similar (resulting in patterns of limiting similarity) when resources are variable in their supply? Or will clumps of similar species be able to coexist? Sakavara et al. considered this question using consumer-resource models of competition, where there are two fluctuating limiting resources. They simulated the dynamics of 300 competing species, which were assigned different trait values along a trait gradient. Here the traits were the half-saturation coefficients for the 2 limiting resources: these were related via a tradeoff between the half saturation constants for each resource.

What they found is strikingly similar to the results from Scheffer and van Nes and dissimilar to the the results that emerge when resources are constant. Clumps of coexisting species emerged along the trait axis. When resource fluctuations occurred rapidly, only fairly specialized species survived in these clumps (R* values that were high for either resource 1, or resource 2, rather than intermediate). But when fluctuations were less frequent, clusters of species also survived at intermediate points along the trait axis. However, in all cases the community organized into clumps composed of very similar species that were coexisting (see Figure 3). It appears that this occurs because the fluctuating resources result in the system having non-stationary conditions. That is, similar sets of species can coexist because the system varies between those species' requirements for persistence and growth. 

Fig. 3. "Lumpy species coexistence". The y-axis shows the trait value (here, the R*) of species present under 360 day periodicity of resource supply.  
Using many of the dominant models of competition in ecology, it is clearly possible to explain the coexistence of both similar or dissimilar species. This is true across approaches from the Lotka-Volterra results of Scheffer and van Nes, to Tilman's R* resource competition, to Chessonian coexistence (2000). It provides a unifying expectation upon which further research can build. Perhaps the paradox of the planktons is not really a paradox anymore?

Thursday, January 4, 2018

Some of the best advice on the internet: several years of links

I started off the New Year with a much-needed bookmark reorganization and deletion, which also gave me a chance to re-read some of the links I've held onto (sometimes for years). There's an ever-increasing amount of useful content on the internet, but these have proven some of the most helpful, concrete, and lasting guides for navigating a scientific life.

I thought I'd collate the list here with the hope others might find some of these useful.

How to make it as early career researcher and new faculty: 
Identity and academia:
  • I think most of us took different and often interesting routes to science (for example, I grew up in an evangelical Christian family, took a number of years to finally start my undergrad, and had no particular knowledge of ecology when I started my BSc. I wanted to be a vet, but now I'm an ecologist. Close enough :) ) and so I like to hear the many different routes by which scientists found science (SEAS).
  • Overcoming imposter syndrome - there are many websites devoted to the topic, but this one provides particularly concrete steps to overcoming this common problem. 
  • No one is perfect, and feedback can hurt - why feedback hurts and how to over come that. And no, it isn't enough to say, 'grow a thicker skin' (The Thesis Whisperer).
  • Diversify EEB - a useful list of women and minorities working in EEB, worth keeping in mind when making nominations, selecting reviewers, and making various invitations. 
  • And it's worth remembering that there is a dark side (one slightly bitter take on it). (Fear and Loathing in Academia)
Mentoring and leadership:
Computing/Data management:
Data visualization:
  • There are some really beautiful infographics about science from Eleanor Lutz here (Tabletop Whale).
  • Information is Beautiful - infographics for inspiration
  • Show me Shiny - some great examples of how R Shiny has transformed data visualization and interaction.
  • If you are familiar with Edward Tufte's influential work on data visualization, you can use R to produce similar plots here. (Lukasz Piwek)
Miscellaneous links:

Monday, December 18, 2017

Holiday caRd 2017!

Here is this year's card, with best wishes from both of us at the EEB & Flow!

It gets a little harder every year to figure these out. R's plotting capabilities improve every year, but usually via specialized packages. I've tried more and more to use as few additional packages beyond base, and to produce a script that is hopefully compatible across platforms.
  • For best performance, users must install the 'deldir' package and the 'RCurl' package. This lets you download the necessary data file with as little effort as possible. 
  • If you have trouble accessing the file via the URL, you can just download the data file from Github directly, making sure to load the file into R using the hashed out code in Lines6-7.
Then to run, copy the full code (below), OR download the source file from github ,
OR, the easiest way, run this quick code directly:

Full script here.
(Bonus points for those who can guess which species of McArthur's warblers these are meant to be ;) )

Wednesday, December 13, 2017

More authors, more joy?

It seems that ecologists have been complaining that no one writes single author manuscripts anymore since at least the 1960s. de Solla Price predicted in 1963:
"…the proportion of multi-author papers has accelerated steadily and powerfully, and it is now so large that if it continues at the present rate, by 1980 the single-author paper will be extinct”
Fortunately, an interesting new editorial in the Journal of Applied Ecology has the data (from their archives of published and submitted papers) to evaluate to ask whether this disastrous outcome has actually occurred.

It turns out that Price was wrong about single-author extinction, although he hadn't misread the trends. Since the 1970s, the proportion of single-authored papers at the journal have declined to less than 4% and the mean number of authors has risen to more than 5 (Figure 1).

Fig 1. 
It's also notable that single-authored papers are cited significantly less often and are 2.5x less likely to be accepted (!). (If that statistic doesn't make you want to gather some coauthors, nothing will). These trends agree with others reported in the literature.

The authors hypothesize that a number of factors drive this result. Ecology has gotten 'bigger' in many ways - analyses are less likely to focus on single populations or species and more likely to be replicated through space and or time. This increased breadth requires more students or assistants to aid with experimental or field work, or collaborations with other labs to bring such data together. Similarly, ecological data collection and analyses often require multiple types of specialized knowledge, whether statistical, mathematical, technological, or systems-based. And by relying on multiple researchers to play specialized roles, the overall quality of a manuscript might be higher (as compared to a jack-of-all trades). The authors also suggest that factors including the growing number of ecologists, the more international scope of many research activities, and more democratic approaches to authorship have increased the mean number of co-authors.

What makes these results particularly interesting is that I think there is still something of a cachet for the sole-authored paper. The conceit is that writing a sole authored paper means that you have a fully realized research plan, and you're accomplished enough to bring it to fruition by yourself. But these stats at least seem to suggest that you're better off with a few friends :)

Barlow, Jos, Stephens, Philip A., Bode, Michael, Cadotte, Marc W., Lucas, Kirsty, Newton, Erika, Nuñez, Martin A., Pettorelli, Nathalie. On the extinction of the single-authored paper: The causes and consequences of increasingly collaborative applied ecological research. J Appl Ecol. 55(1): 1365-2664.

Wednesday, November 22, 2017

Of course we need to save endangered species: a response

I spend a lot of time thinking about the related topics of conservation, biodiversity, and evolution, so I was interested to see an editorial in the Washington Post on precisely those issues. The article, "We don’t need to save endangered species. Extinction is part of evolution" by Alex Pyron, presents a misrepresentative and potentially harmful position about the future of the earth's biota.

Pyron begins by stating that "Evolution loves death." Selection necessarily means the success of one variant at the expense of others, and today's living creatures are the survivors of an ongoing battle for existence. Extinction is not a modern phenomenon by any means. There have been five mass extinctions, including the glaciation of Gondwana and the impact of an asteroid that lead to the loss of the dinosaurs.

But the 6th great extinction (the Anthropocene extinction - the one we are currently living in) shares little in common with these past events. This is the only extinction that a single species (humans) are primarily responsible for, through activities from habitat conversion or degradation, land fragmentation, warming climate, ocean acidification, and human consumption of natural resources. In this context, Pyron's argument seems to be that we ought to retain an anthropocentric viewpoint of conservation as well. That is, we are simply selecting for species that can survive in our wake, and we should feel concern only for those species that we need.
"But the impulse to conserve for conservation’s sake has taken on an unthinking, unsupported, unnecessary urgency. Extinction is the engine of evolution, the mechanism by which natural selection prunes the poorly adapted and allows the hardiest to flourish. Species constantly go extinct, and every species that is alive today will one day follow suit. There is no such thing as an “endangered species,” except for all species. The only reason we should conserve biodiversity is for ourselves, to create a stable future for human beings. Yes, we have altered the environment and, in doing so, hurt other species. This seems artificial because we, unlike other life forms, use sentience and agriculture and industry. But we are a part of the biosphere just like every other creature, and our actions are just as volitional, their consequences just as natural. Conserving a species we have helped to kill off, but on which we are not directly dependent, serves to discharge our own guilt, but little else."
This is hardly an original viewpoint (hastening to the Bible's 'Then God said, “Let Us make man in Our image, according to Our likeness; let them have dominion over the fish of the sea, over the birds of the air, and over the cattle, over all the earth and over every creeping thing that creeps on the earth.'). But it is a short-sighted one. Ignoring more philosophical arguments about the intrinsic value of all species, the arguments presented are problematic and incomplete, and the potential cost could be huge.

Pyron notes that we may be over-estimating the loss of species:
"According to some studies, it’s not even clear that biodiversity is suffering. The authors of another recent National Academy of Sciences paper point out that species richness has shown no net decline among plants over 100 years across 16,000 sites examined around the world."
The study cited by Pyron here does not support the assertion that biodiversity is fine. In fact, Vellend et al (2013) show that at local scales, plant diversity (i.e., the number of plant species; species number being only way of characterizing biodiversity) has been stable. This isn't the same as saying species are not being lost at a global scale. In a follow-up piece (Vellend et al. 2016), the same author notes that at the global scale, "Nonetheless, if we take 142 and 592 as somewhere in the ballpark of extinctions that have occurred between 1600 and 2016, we get extinction rates of 0.98–4.1, 1–2 orders of magnitude higher than the background rate." Outside of plants, Pimm et al. (2014)'s comprehensive review of extinctions in birds, amphibians, and mammals show extinction rates have at least doubled since 1900. These are rates much higher than considered 'natural'. Even when no extinctions have occurred yet, populations are declining rapidly (Ceballos and Ehrlich 2014, Ceballos et al 2017).

An anthropocentric approach also requires complete understanding and control of our environment. Preventing the loss of the species we need or the ecosystems we rely on is not straightforward (as seen by the rarity with which species become 'non-endangered'). Humans are still under-informed about ecosystem services and goods, and what biotic and abiotic interactions are essential to maintain them. The existence of IPBES is a good indicator of how essential and lacking this information is. To confidently state that "Conserving a species we have helped to kill off, but on which we are not directly dependent, serves to discharge our own guilt, but little else" ignores the indirect linkages that might matter, and our lack of knowledge of them.

Further, the philosophy that humans will survive somehow, in the face of losses of biodiversity and changing planetary climate is probably mostly true for the richest members of the planet. Elsewhere, food shortage associated with climate change (eg.) and water shortages (eg.) already threaten individuals in less wealthy countries.

Ironically, Pyron suggests that all we need to make this reality is "moderation".
"The solution is simple: moderation. While we should feel no remorse about altering our environment, there is no need to clear-cut forests for McMansions on 15-acre plots of crabgrass-blanketed land. We should save whatever species and habitats can be easily rescued (once-endangered creatures such as bald eagles and peregrine falcons now flourish), refrain from polluting waterways, limit consumption of fossil fuels and rely more on low-impact renewable-energy sources....We cannot thrive without crops or pollinators, or along coastlines as sea levels rise and as storms and flooding intensify."
But the anthropocentric view of the world that he presents is the opposite of moderation. It favours only humans. In many ways it's the other extreme of the Half-Earth proposal that suggests we set aside half the planet made free of humans. Having been told we don't need to value species beyond our current needs and interests assumes that we will capably and correctly identify those needs and goals, including for time frames beyond our own myopic lifespans. This uncertainty means that a human-centric view may be just as harmful to humans as approaches that ascribe value for biodiversity more value. And humans have proven willing and capable of taking much broader and more effective actions, that accommodate both humans and other organisms. (As FDR said and did: "We have fallen heirs to the most glorious heritage a people ever received, and each one must do his part if we wish to show that the nation is worthy of its good fortune.")

It's frustrating to see this kind of description of biodiversity as though the earth is simply a plus-minus ledger of species – a few lost here, a few gained there.

A conservation baseline is meant to capture an idealized Eden is of course unreasonable. But Pyron's view looks like Hell. ("If this means fewer dazzling species, fewer unspoiled forests, less untamed wilderness, so be it. They will return in time.")

Edit (Nov. 24): the TL:DR is that 
a) I thought the author cherrypicked the ecological literature and downplayed what we know about the loss of biodiversity and the complex/negative effects of human actions; 
b) if the argument is that we should think about biodiversity over timescales of millions of years, humans don't matter anyways; 
c) if we do care about humans, utility values of biodiversity are an acceptable focus of conservation. But it would be misguided to think that we have a perfect understanding of how ecosystems work or a perfect ability to forecast our impacts. For reasons of uncertainty, sampling effects and option value argue that we preserve as much diversity as we can;
d) Non-economic utility values (aesthetic, cultural values) are a good argument for conservation too. Most of us want to leave our children a beautiful planet that is full of life. 

Thursday, November 16, 2017

Decomposing diversity effects within species

The relationship between biodiversity and ecosystem functioning is so frequently discussed in the ecological literature that it has its own ubiquitous acronym (BEF). The literature has moved from early discussions and disagreements about mechanism, experimental design, and species richness to ask how different components of biodiversity might contribute differentially to functioning. The search is for mechanisms which hopefully will lend predictability to biodiversity-function relationships. One approach is to independently manipulate different facets of biodiversity – whether species, phylogenetic, trait-based, or genetic diversity – to help disentangle the relative contribution of each.

A new paper extends this question by considering how within-species diversity – including genotypic richness, genetic differences, and trait differences – contribute to functioning. Abbott et al. (2017, Ecology) use a field-based eelgrass system to explore how independent manipulations of genotypic richness and genetic relatedness affected biomass production and invertebrate community richness. They collected 41 unique genotypes of eelgrass (Zostera marina), and used 11 species-relevant loci to determine the relatedness of each genotype pair. The authors also measured 17 traits relevant to performance including "growth rate, nutrient uptake, photosynthetic efficiency, phenolic content, susceptibility to herbivores, and detrital production ".
Eelgrass meadow.

Each of these of these measures are inter-related, but not necessarily in clear, predictable fashions. Genotypes likely differ functionally, but some traits and some genotypes will vary more than others. Genetic distances or relatedness between species similarly may be proxies for trait differences, but this depends on the underlying evolutionary processes. The relationship between any of these measures and functions such as biomass production are no doubt varied and dependent on the mechanism.

The authors established plots with two levels of genotypic richness, either 2 genotypes or 6 genotypes, where genotypes varied among the 41 available. Fully crossed with the genotypic richness treatment was a genetic relatedness treatment: genotypes were either more closely related than a random selection, less closely related, or as closely related as random. At the end of the experiment, above and belowground biomass were collected, and epifaunal invertebrates were collected, and modelled as a component of the biodiversity components.

Because of early die-offs in many plots, planted genotype richness differed from final richness greatly (very few plots had 6 genotypes remaining, for example). For that reason, final diversity measures were used in the models. The relationship between aboveground biomass or belowground biomass and biodiversity were similar: both genotypic richness and genotypic evenness were positively related to total final biomass, but genetic relatedness was negatively correlated. That is, plots with more related genotypes were less productive. Other variables such as trait diversity was not as important, and in fact they did not find any relationship between trait differences and degree of genetic relatedness between genotypes. Since relatedness seemed unrelated to functional similarities, between genotypes, the authors suggested that possibly that reduced biomass among related genotypes is due to self-recognition mechanisms. Most interestingly, the best predictors of invertebrate grazer diversity were opposite -  – the best predictor was trait diversity, not genotypic richness or genetic relatedness.

Even in this case, where Abbott et al. were able to separate different diversity components experimentally, it's clear that simplistic predictions as to how they contribute to functioning are insufficient. The contributions of genotypic versus trait diversity were not strongly related. Further, trait diversity performed best on the function for which genotypic diversity performed worst. Understanding what this means is difficult - are the traits relevant for understanding intraspecific interactions (resource usage, etc) so incredibly different from those relevant for interspecific interactions with herbivores? Are the 17 traits too few to capture all differences, or too many irrelevant traits? Do we expect different biodiversity facets have unique independent effects on ecosystem functions, or does the need to consider multiple facets simply mean we have an imperfect understanding of how different facets are related?