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.

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.