Insect herbivory in fragmented forests: it’s complicated

March 15, 2016 / Chris Buddle / 1 Comment

I’m excited to announce a recent paper to come out of the lab, by former PhD student Dorothy Maguire, and with Dr. Elena Bennett. In this work, we studied the amount of insect herbivory in forest patches in southern Quebec: the patches themselves varied by degree of fragmentation (ie, small versus large patches) and by connectivity (ie, isolated patches, or connected to other forest patches). We studied herbivory on sugar maple trees, both in the understory and canopy, and at the edges of the patches. Our research is framed in the context of “ecosystem services” given that leaf damage by insects is a key ecological process in deciduous forests, and can affect the broader services that forest patches provide, from supporting biodiversity through to aesthetic value. Dorothy’s research was part of a larger project about ecosystem services and management in the Montérégie region of Quebec.

Dorothy Maguire sampling insects in the tree canopy (Photo by Alex Tran)

The work was tremendously demanding, as Dorothy had to select sites, and within each site sample herbivory at multiple locations, including the forest canopy (done with the “single rope technique). Dorothy returned to sites many times over the entire summer to be able to assess trends over time. Herbivory itself was estimated as damage to leaves, so after the field season was completed, thousands of leaves were assessed for damage. The entire process was repeated over two years. Yup: doing a PhD requires a suite of skills in the field and lab, and there is no shortage of mind-numbing work… Dedication is key!

As with most research, we had high hopes that the results would be clear, convincing, and support our initial predictions – we certainly expected that forest fragmentation and isolation in our study landscape would have a strong effect on herbivory – after all, our study forests varied dramatically in size and isolation, and herbivory is a common and important ecological process, and insect herbivores are known (from the literature) to be affected by fragmentation.

The landscape of southern Quebec. Lots of agriculture, some patches of forest.

However, as with so much of ecological research, the results were not straightforward! “It’s complicated” become part of the message: patterns in herbivory were not consistent across years, and there were interactions between some of the landscape features and location within each patch. For example, canopies showed lower levels of herbivory compared to the understory, but only in isolated patches, and only in one of the study years! We also found that edges had less herbivory in connected patches, but only in the first year of the study. Herbivory also increased as the season progressed, which certainly makes biological sense.

So yes, it’s complicated. At first glance, the results may appear somewhat underwhelming, and the lack of a strong signal could be viewed as disappointing. However, we see it differently: we see it as more evidence that “context matters” a great deal in ecology. It’s important not to generalize about insect herbivory based on sampling a single season, or in only one part of a forest fragment. The story of insect herbivory in forest fragments can only be told if researchers look up to the canopy and out to the edges; the story is incomplete when viewed over a narrow time window. In the broader context of forest management and ecosystem services, we certainly have evidence to support the notion that herbivory is affected by the configuration of the landscape. But, when thinking about spatial scale and ecosystem processes, careful attention to patterns these processes “within” forest patches is certainly required.

We hope this work will inspire others to think a little differently about insect herbivory in forest fragments. Dorothy’s hard work certainly paid off, and although the story is complicated, it’s also immensely informative and interesting, and sheds light on how big landscapes relate to small insects eating sugar maple leaves.

Reference:

Maguire et al. 2016: Within and among patch variability in patterns of insect herbivory across a fragmented forest landscape. PlosOne DOI: 10.1371/journal.pone.0150843

Natural history of canopy-dwelling beetles: More than just ‘Fun Facts’

March 11, 2016March 11, 2016 / Chris Buddle / Leave a comment

This is the second post by undergraduate student Jessica Turgeon – she’s doing an Honour’s project in the lab; here’s her first post that introduces the project. Since that first post, Jessica has spent a LOT of time at the microscope, and has identified over 120 species of spiders and beetles from forest canopies and understory habitats.

Every species has a different story to tell and each one of these is equally interesting. I sometimes think about natural history as ‘fun facts’: something interesting about an organism (or species) to tell children so that they can appreciate nature. As my time at McGill progressed and my knowledge of the natural world deepened, I realized that the ‘fun facts’ are actually built upon a very strong scientific foundation, and can help us understand results of research projects. Natural history can sometimes be reduced to ‘fun facts’ but it’s a whole lot more than that!

The European Snout Beetle on a pin.

I decided that perhaps I should look at the natural history of some of my species and maybe this would shed light on some patterns that I’m seeing within the data. The most abundant beetle species was Phyllobius oblongus (Curculionidae) with 69 individuals. Interestingly, we only collected this species in the first half of our sampling season and they were mainly collected on black maple and sugar maple trees. To try and understand why this is so, I turned to the species’ natural history, and to the literature.

These weevils tend to eat fresh leaf shoots and prefer the soft leaves found on maple trees. Once the maple’s leaves are fully-grown, P. oblongus moves on to plants with indeterminate growth, like raspberry bushes (Coyle et al. 2010). This corresponds exactly to our data: the beetles were found on our black and sugar maples during the beginning of summer and then they taper off as the season progressed!

Beetle data: the European Snout Beetle was only collected during the beginning of the season.

To make this even more interesting, P. oblongus is an invasive species. Its common name is the European Snout Beetle and was accidentally introduced into North Eastern North America in the early 1900s. While most invasive species are a cause for concern, both the Canadian and American governments largely ignore this species. It may inflict some damage to trees but not enough to be worried about. They’re more annoying to researchers than anything since they congregate in the trees in large numbers!

The second most abundant beetle species in the collections was Glischrochilus sanguinolentus (Nitulidae). This species is native to Canada and rather abundant. Species in this genus are called sap beetles but this species in particular is more commonly called a picnic beetle. Large groups of G. sanguinolentus swarm to picnics since they are attracted to sweet food, which ruins the picnics. In nature, they feed on the sap produced by injured trees – hopefully not an indication that the trees we were climbing were damaged!

The natural histories of species open new doors to understanding how organisms live and interact with one another. I thought that it was strange that P. oblongus completely disappeared from my samples midway through the sampling season and its natural history explained why this was so. Picnic beetles eat the exuding sap of an injured tree so in the future I’ll be on the lookout so that I don’t accidentally climb a broken tree! So really, natural history is more than just ‘fun facts’; it helps us understand patterns and to better understand how our natural world works.

References

Coyle, D.R., Jordan, M.S. and Raffa, K.F., 2010. Host plant phenology affects performance of an invasive weevil, Phyllobius oblongus (Coleoptera: Curculionidae), in a northern hardwood forest. Environmental entomology,39(5), pp.1539-1544

Evans, A.V., 2014. Beetles of eastern North America. Princeton University Press.

Tips for managing a research lab

February 18, 2016 / Chris Buddle / 1 Comment

Running a research lab* isn’t easy. I learned this the hard way last fall when I performed rather poorly on my lab safety inspection. At the time it seemed to be a low priority: cleaning up the lab always seemed less important compared to, for example, having a lab meeting. We have since done a major lab clean-up, and we are back on track (phew!), but the experience has made me think about the skills needed to run a lab. Hopefully this is of interest to some of you, especially early career researchers (ECRs), but I would also like experienced researchers to wade with comments and tips. This post will be more about the “nuts and bolts” of running a lab, but perhaps a future post can be about broader philosophies around being the head of a research lab.

Part of my lab – AFTER cleaning.

Human resources

There are people in a lab. This means, as the head of a lab, you need to pay attention to human resources. This might be practical kind of stuff, like signing expense reports, or making sure students are getting paid when they are supposed to. But there are also many more complex things to think about, such as helping resolve arguments, or helping students through difficulties. You need to learn to listen, you need to navigate social dynamics, and be a good communicator. Make your expectations clear, and be sure that everyone is well aware of their roles and responsibilities. Work on ways to have a productive AND fun lab. Be sensitive to everyone’s different needs, and be open to change – operate on a principle of kindness. You will likely find yourself navigating some tricky situations so be sure to get help when you need it: there may be training available, or perhaps ask your Chair or a colleague about advice on being a good manager of human resources.

Organization

Running a lab is very much about being organized. There has to be a “plan” for all the different supplies, and space for everyone to store their samples, find the ethanol, or grab new Petri dishes. From the start it’s important to think about space needs in the long-term – anticipate how the lab might change in the future, and make sure there is room to grow. People need to feel that they have a “home” in the lab, whether it’s a desk or piece of a lab bench, and this requires careful assessment of space. I personally struggle with sample storage, and seem to squeeze old samples into various drawers, with a promise of getting rid of them (or putting them in long-term storage) after students have published their work. That promise is mostly broken, as it it easier to just store stuff and forget about it. ECRs: avoid this mistake! Stuff accumulates far too quickly. Be sure to label things too, including where to put supplies.

OrganizedLab

Safety and training

Don’t drink from the beakers; broken glass is dangerous. Stay on top of the safety rules at your institution: it’s easy to miss those emails, but as I learned, they are important. Top-down guidance about safety will show the lab members that safety is a priority not an afterthought. Know where to store chemicals, know about the eye wash stations, and make sure the first aid kit is stocked and ready. Know what needs to get stored where, and be ready when there is a call for hazardous waste disposal. Learn about MSDS, and be on top of the chemicals that may be present in your lab. As the head of a lab, you are indeed responsible for making sure your lab members have the appropriate training in the context of lab safety: whether it be WHIMIS, research ethics, or wilderness first aid, get your students signed up, and pay for the training. Don’t shirk this essential responsibility.

Permits

As the head of a lab, your name will likely be on all the research permits, and depending on your field of study, this can be a very big deal, and complicated. From collecting permits to animal care to biohazards, you need to guide your students through the permit process, from application to final reports. You have to be aware of deadlines, and know the ins and outs of the different requirements, especially when your work might cross jurisdictions. This can take an inordinate amount of time, but it requires the time commitment: lacking a permit can stall an entire research program. It’s essential to be proactive and prepared for permits. I certainly get my students to write the bulk of their own research permits, but a manager of a lab needs to facilitate this process.

Budgets and supplies

Running a lab means making sure there is a budget (i.e., you need a research grant!) to buy light bulbs for the microscope, flagging tape for field work, or medium for the agar plates. You need the money, and you need to know the process. The latter is not trivial: at my University some supplies are best bought using an internal purchasing system. Other places need just a credit card, or perhaps a purchase order. There are so many systems to learn, and each one probably needs a different password. It’s confusing and frustrating, and you have to stay on top of it. I keep a special file with all the details written out, and a hard-copy folder with old invoices – this way I can make sure to but the right sizes of things. Consistency is supplies is rather important!

Troubleshooting

Here are some things that have occurred in my lab over the years: weird smells from the sink. Lack of heat. Leaks from the ceiling. Power failures. Spider escapes**. Failing fridge. Failing freezer.

And the list goes on… Running a lab can be a lot about troubleshooting – you need to figure out who to call for what problem, and find a speedy resolution – otherwise you let down your grad students. Make a list of key people to get to know, from facilities to the local safety officer. Even better, post the list up in the lab, next to the telephone.

Ok, so there are certainly more things to know about running a lab, but hopefully the list provided is a start. Here’s the catch: almost everything I learned about running a lab was learned on the job. Despite attending some required workshops at the start of my career, I did not learn any real skills about running a lab. I was not trained to run a lab. Scientists must be taught to manage a lab.

That is a problem because a failure to run a lab properly has significant consequence for a lot of people! My students depend on the supplies that I have to buy, and they need to know what to do if there’s a chemical spill. Thankfully I had some good mentors when I was a grad student, and I managed to figure a lot of things out. However, I do think Universities need to do a better job helping hone the skills needed to run a lab; in many research fields, a successful academic career really depends on having a smooth-running lab, anything that can be done to help prepare ECRs for this would pay off.

In sum, I’m certainly a work in progress. Although I have some skills in research, I know that running a lab can be a real challenge for me, whether it’s forgetting to order supplies or checking the eyewash station weekly. I have learned to delegate a bit, and my grad students help me immensely at maintaining a safe and clean lab environment. I sure hope some of you can learn a bit from my own trials and tribulations… And please educate yourself, plan ahead, and know what it takes to run a lab well before you get the keys.

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Here are some other resources I’ve come across, related to managing a lab: from Genome Web, ASBMB, a post by Matt Welsh, and a Reddit thread on the topic

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*Note: my experiences are from a mid-size University entomology lab. I don’t have a post-doc or technician in my lab. Bottom line: some of what I wrote may not be generalizable to other contexts

**Sometimes we work with live spiders, on various projects. There have been times when they haven’t been where we left them. Oops.

Bog spiders: a serendipitous research project

January 22, 2016January 22, 2016 / Chris Buddle / 2 Comments

This is a guest post, written by an Honour’s undergrad student in the lab, Kamil Chatila-Amos. It’s the first of two posts about his work, and the goal of this post is to introduce Kamil and his research project.

Research can be serendipitous and spontaneous, and that’s certainly the story of how my honour’s project started! I spent last winter working on howler monkeys in Panama (which is a story in itself) and although I adored every second of it, it certainly made me out of touch with the McGill world. When I came back, most of my friends had found themselves a summer research job and even an honours supervisor for the upcoming semester.

So there I was, barely a week after my return, erratically filling out online job applications in the lobby of one of our buildings. I was looking at all kinds of opportunities: herbarium employee in Edmonton, ichthyology assistant in Wisconsin, plant surveying in Vaudreuil, bird surveys in Ontario, insectarium employee in Montreal. I was applying to anything and everything that was still available. Little did I know that the arthropod ecology lab is right next to the lobby… Chris walked by, saw me and stopped to chat. (Well it’s more accurate to say he talked to me while quickly walking to his next meeting)*. Turns out, a student of Terry Wheeler (another entomology Prof. at Macdonald campus), Amélie Grégoire Taillefer, was going to post a job online that very afternoon! She was looking for a field assistant to help her catch flies in bogs in the James Bay area.

A couple days later I was northern-bound! A 15 hour drive north of Montreal is the town of Matagami and about 30 km north of there is Lake Matagami, along which we were staying. In a yurt. A yurt!!! Basically, a large round tent of Mongolian origins. They’re big and this one had a minimal kitchen and shower. But the fact remains that it’s a tent with the isolative properties of canvas. It got pretty cold those first couple weeks and dropped below freezing a few nights. At least it had a fireplace. (It’s actually a great place for people wanting to explore that area of Québec and the owners are wonderful. Go check them out at ecogiteslacmatagami.ca)

Kamil_Yurt

The work itself was great. The first week, we explored the area for suitable bogs to install her pantraps. That’s when I realized how awesome bogs are. There are so many things to eat in bogs! Cattails, cranberries, Labrador tea, cloud berries, chanterelles, boletes, black flies…

For the remainder of the trip two days a week were spent visiting our five sites and harvesting the pantraps filled with flies, dragonflies, crickets, spiders and the occasional putrid mouse. The following two or three days we would sort through the samples, separating the lower flies (Nematocera) from the rest.

Ready for some serious bog-sweeping.

After the first week I couldn’t help but notice just how many spiders we were catching. Mostly out of pity I think, I decided to sort out the spiders as well. I felt bad throwing them out… Fast forward to five weeks later and I’m heading back to Montreal with a bagful of vials filled with dead spiders. (My roommates were not very fond of having them in our freezer).

A few weeks later I set up a meeting with Chris and essentially barged into his office with the spiders to ask to work in his lab. It took a while (and quite a bit of convincing) but here I am, sorting through spiders and writing blog posts!

The research project we structured has two components. The first part will look at how the community composition of spiders varies between the five sampled bogs. Second, I’m lucky enough to have the opportunity to try DNA barcoding using COI markers. This part remains very blurry right now**, but I’m very excited to see where it leads.

Kamil hard at work in the lab!

If it weren’t for serendipity I would not have gone to James Bay this summer. And if it weren’t for being spontaneous, I would not have sorted out the spiders and would not be working in Chris’ lab right now. But spontaneity does have its down sides. I didn’t plan far enough ahead** and in hindsight, I should have collected some insect orders to be able to do a more in depth ecological analysis.

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* um, yes, I spend a LOT of time in meetings, and often have discussions and chats with student on my way to and from those meetings!

** for what it’s worth, research is often blurry, and planning ahead isn’t always possible!

Summer in the trees: Undergrad research on canopy spiders and beetles

December 10, 2015December 10, 2015 / Chris Buddle / 1 Comment

Note: this post is written by undergraduate Honour’s student Jessica Turgeon, who is a member of the arthropod ecology laboratory. This post is part of the requirements for her project, and is an introduction to her research.

I’ve always been interested in nature and the environment but was never a big fan of insects. As time went on and I learned to appreciate all organisms big and small I realized that I didn’t really have a preferred “pet taxon” but rather was interested in ecology and community structure. I found others that my interests were shared with other members of the arthropod ecology lab, and I was able to start an Honour’s project in the lab earlier this fall.

Using a beat-sheet in the tree canopy, to collect arthropods

I was given an opportunity to do an internship at Kenauk Nature, a 65,000-acre plot of land near Montebello, Quebec. This property is primarily used for the hunting and fishing industries, but they are branching into scientific research. Kenauk was keen to support three McGill interns to complete the Black Maple project, the pilot project for Kenauk Institute.

The Black Maple project revolves around black maples, since Kenauk is the only area in Quebec to have a black maple stand. The project consisted of three sub-projects, one for each intern and each project dealing with a different taxon. While the two other students worked on plants and birds, my project was about arthropods and their diversity in Kenauk. We wanted to characterise the community structures of beetles and spiders based on vertical stratification and tree species: this involved tree-climbing!

Jessica – getting ready to climb up!

During the summer, I looked at abundance data and concluded that beetles were more abundant in the upper canopy and that spiders were more abundant in the understorey. This internship transitioned into my Honour’s project, where I plan to look at species richness and functional diversity to answer my questions on community assemblages. To my knowledge, this has never been done at Kenauk Nature and would provide great baseline data for the owners of the property.

We sampled in three sites, each containing three trees. Each site had one sugar maple (Acer saccharum), one black maple (Acer nigrum) and one American basswood (Tilia americana). Within each tree we sampled five times: twice in the understorey, once in the middle canopy and twice in the upper canopy. We also used two different types of traps: beat sheets, an active technique, and Lindgren funnels, a passive technique. Both trap types are specialized, with beating more tailored towards spiders and Lindgren funnels invented to collect beetles. When beating a branch, the arthropods fall on a 1m² sheet and are then collected whereas Lindgren funnels are hung in a tree and passively collect arthropods that fly into it.

As part of our job, we learned how to use a single ropes climbing system, a one-person method of using ropes to climb a tree. All three interns caught on quickly and it easily became our favourite part of the job. However, we did have to sort through the samples, a job requirement that wasn’t nearly as fun as climbing trees. But this is what happens in ecology: you romp around in the woods to collect your data then spend time in the lab analysing them. It was nice to experience this first-hand and I must say, I liked it and am looking forward to future projects like this.

Now that the summer is over and collection is completed, I spend all of my free time in the lab identifying beetles and spiders. All of the beetles are identified and about half of the spiders are identified. From this work, Kenauk Nature can proudly say that the property supports 24 families representing 117 species of beetles! Once the Kenauk Institute officially launches, more rigorous research can be done to try and increase these numbers.

Learning Taxonomy… spider drawings (of male palps) help.

All in all, from the sampling in the summer to the identification in the lab, this has been a great experience. Here’s to hoping the second half of my honours project will be as equally fun and challenging as the first half was! Stay tuned for a blog post to be published in the spring of 2016: it will summarize the main results from this Honour’s project.

Vouchers? What vouchers? Revealing a crisis in arthropod-based research

August 25, 2015August 25, 2015 / Chris Buddle / 14 Comments

Here’s a hypothetical scenario:

Q: “Hey I see you published a paper that shows the wolf spider Trochosa ruricola occurs up in the Ottawa Valley – I didn’t realize it had reached that far. It’s an invasive species, so tracking its distribution is quite important”

A: “Yeah, we too were surprised it was up that far: to our knowledge, only Trochosa terricola was in that part of Ontario”

Q: “It is tricky to tell apart those two species! What museum did you deposit specimens in? I’d like to take a look at them to verify the identification.”

A: “Um, we didn’t get around to depositing specimens in the museum. There might still be some in the lab. I’ll have to get back to you...”

Not cool. And also much too common.

Bottom line: when specimen-based research is done with arthropods, whether it is a biodiversity inventory, a community ecology study, or a taxonomic revision, the researchers must deposit voucher specimens in a research museum or institutional collection. This is only way to truly verify that the work is accurate, that people are calling things by the same name, and it puts a stamp in time for the research. Without deposition of these voucher specimens (somewhere that is publicly accessible and curated, and along with data about time, place and collector) the research cannot be verified, and this goes against the principle of repeatability in science.

Beetles in drawers: a great example of specimens in a curated museum, and shows how such specimens can be used for all kind of research!

This is a no-brainer, right? It’s time to test whether or not scientists actually bother to deposit voucher specimens…. As part of a graduate-level* class in Entomology last winter, we surveyed the literature to find out the frequency of voucher deposition with arthropod-based research. We looked at papers to see what percentage actually report on vouchers, assessed whether the frequency of voucher deposition varied by research type, study organisms, institution (of researcher), and whether voucher deposition has changed over time.

We published the results a few weeks ago, in the Open Access journal PeerJ, and our work has revealed a crisis in arthropod-based research. Overall, rates of voucher specimen deposition were very low, as only 25% of papers report on the deposition of voucher specimens. This is horrible, and essentially means that the specimens from the majority of papers published cannot be traced to a collection, and cannot be verified.

Some disciplines were worse than others, as crustacean researchers deposited vouchers only 6% of the time, as compared to the relatively higher rate of voucher deposition by entomologists, at 46%. Here is a summary of the main findings:

The main findings of our research: the asterisk illustrates a significant difference relative to a global mean. Figure from our paper, published here.

Is there any good news? Perhaps so… when looking at rate of voucher deposition over time, more papers are reporting about vouchers in 2014 (35%) compared to 1989 (below 5%).

At the end of our paper we provide some conclusions and recommendations, and these are repeated here:

PIs must be responsible and proactive on the process of voucher specimen deposition, from the start of any project.
Graduate students need to be mentored appropriately about the importance of voucher specimen deposition.
It needs to be recognized that voucher specimens are important for all branches of arthropod research – there is no reason that entomologists should do better than, say, crustacean biologists.
Close collaboration between Universities/Research Centres and Museums is required, so that there is an agreed up, and easy process for all researchers to deposit vouchers.
Everyone involved with arthropod-based research needs to work together to push for long-term, sustainable funding for institutional collections/museums so that proper curation of vouchers can be done.
Publishers and editorial boards need to have clear policies about voucher specimens, so that any papers published are required to report on vouchers.

I recognize that the title of this post is provocative. Is it *really* a crisis?

I think it is: I think that even the best rate of voucher deposition that we report on is too low. We must aim to be closer to 100%. It’s important as we work to describe the world’s biodiversity, understand what is happening to our species in the face of climate change, or track the distribution of invasive species. It’s important that our hard work is more than a publication: our hard work is often a specimen, and that specimen needs to be accessible for future generations.

Voucher for critters than need to be stored in liquids looks something like this.

Reference:

Turney S, Cameron ER, Cloutier CA, Buddle CM. (2015) Non-repeatable science: assessing the frequency of voucher specimen deposition reveals that most arthropod research cannot be verified. PeerJ 3:e1168 https://dx.doi.org/10.7717/peerj.1168

* A most sincere thanks to my graduate students Shaun, Elyssa and Chris – these students did the lion’s share of this project, and took on this graduate class with great enthusiasm, maturity and motivation. You all inspire me!

Meet Shaun Turney and Fuzzy Cognitive Mapping

February 9, 2015February 9, 2015 / Chris Buddle / Leave a comment

This is another in the series of “Meet the arthropod ecology lab“: Meet PhD student Shaun Turney, and a neat project he’s been working on…

I joined the lab in September and I’ve been really enjoying my first months as a PhD student. I haven’t done any field work yet so that means no specimens to ID or field data to crunch. Instead I’ve been occupying my time very happily playing on the computer. I recently released an R package on CRAN for Fuzzy Cognitive Mapping called “FCMapper”, in collaboration with Michael Bachhofer. It is based on FCMapper for Excel, distributed at http://www.fcmappers.net/joomla/, developed by Michael Bachhofer and Martin Wildenberg. Fuzzy Cognitive Mapping is really cool and you should try it out!

Shaun, in the lab, thinking about food-webs.

Recently I’ve become interested in graph theory and all that it has to offer to ecology. Anything that can be represented as boxes and arrows (or lines) can be represented as a graph (in the graph theory sense) and can be analyzed using graph theory tools. I LOVE box and arrow diagrams. Like, maybe an inappropriate amount. Any paper that I’ve printed out and read has at least two or three box and arrow diagrams scribbled into the margins. My notebook is filled with box and arrow diagrams from lectures that I’ve attended or random thoughts that have passed through my mind while I’m sitting on the train. Some people think in words, some in pictures, but I think in boxes and arrows. So you can imagine my enthusiasm as I’ve discovered over the past year that there exists a whole body of mathematics that can represent and analyze box and arrow diagrams.

My latest favourite graph theory tool is called Fuzzy Cognitive Mapping. It can be understood by breaking down the term into its component words. A “cognitive map” in this case is when you represent a system as interconnected concepts. Boxes and arrows, in other words. The “fuzzy” part refers to fuzzy logic. Fuzzy logic is logic that deals with approximate rather than exact values. So to make a fuzzy cognitive map, you make a box and arrow diagram and assign approximate values to the arrows (positive vs negative, weak vs strong relationship). The concepts are then allowed to affect each other until they come to an equilibrium. The exciting part is that then you can try out scenarios! For instance, you could fix one (or more!) concept to be a high or low value and see how it affects the rest of the system. In the context of ecology, one use is to explore potential ecosystem management scenarios (ex, http://en.vedur.is/media/loftslag/Kok_JGEC658_2009.pdf).

If Fuzzy Cognitive Mapping sounds interesting to you (and it should!), you can download the package from CRAN. Michael Bachhofer and I plan to create a tutorial in the spring, but until then you are welcome to email me if you can’t figure out how to use the package.

Download here: http://cran.r-project.org/web/packages/FCMapper/

A graphics output for a toy example I was playing with the other day. It is a cognitive map of things which might affect spotted owl abundance. FCMapper uses igraph for visualization. The thickness of the arrows represents the strength of the relationship and the color represents the direction (red=negative, black=positive), as assigned by me. The size of the circles represents the “size” of each concept at equilibrium, as determined using the nochanges.scenario function in FCMapper. Think of the fun maps you could make for your favourite study system!

Leading a discussion of a scientific paper

January 21, 2015 / Chris Buddle / 3 Comments

I’m teaching a graduate class in Entomology this term, and part of that class involves students leading discussions about scientific papers in our discipline. These discussions are typically between 60 and 90 minutes, with a small group (4-6 individuals). This post provides some advice and guidelines around how to go about doing this. That being said, this is not a ‘one size fits all’ kind of world, especially when talking about science: you may have better or alternative approaches when discussing scientific papers – please comment, and share your ideas!

1. Provide a (quick) summary of the paper:

In most cases, you want to first provide the audience a brief but accurate overview of the paper. It’s often useful to do a little research about the authors – this provides a context that may be very helpful and may prove insightful later on. For example, do the authors have a publication record that aligns with the current paper? Are the authors graduate students or post-doc (not that it matters, but it does provide context!).

The focus on the summary should be about the Research Questions / Hypothesis, and to explain these you will also need to discuss an overall conceptual framework. This means you need to know this conceptual framework very well. After providing the broader context and framework, you should quickly go over the main methods, and the key results. You should act as a guide for your audience, and take them through the key results. Try not to spend a lot of time on more trivial aspects of a paper. In general, your summary should not delve too deeply in the discussion part of the paper.

Don’t forget: you are assuming everyone in the room has read the paper, so your overall introduction should be relatively short (no more than 10 minutes). More time may be required if a concept or methodological approach is particularly complex. Try not to provide opinions or critiques of the paper at this point in time – save this for the general discussion.

2. Ask for points of clarification:

Before proceeding with detailed discussion of the paper, you should ask the audience if they require clarification on anything in the paper. You are leading a discussion and therefore considered an ‘expert’ on the paper, and as such, should be prepared to handle these points of clarification – this will most likely require you to do a bit of research on areas of the paper that you do not understand! It’s important you you make it clear that you are not starting a detailed critique (yet); you are first making sure that people all understand the critical ‘nuts and bolts’ of the paper.

3. Leading a discussion:

The majority of the time should be spent on the actual discussion. There are many ways to do this, but here are some tips:

Try not to let your own opinion of the paper distract or take over – your goal is to get other people to reveal their own views; these may or may not agree with your own views! Be welcoming and accommodating to other people’s opinions and viewpoints. Never make anyone feel small or stupid, even if they make a goofy mistake.
That being said, make sure that you do have an opinion, and be willing to share it at some point
Prepare a list of questions that you could ask other people if the discussion needs help to get started. Always try to find positive points in a paper, even if the paper is, overall, very weak. Similarly, try to bring out negative features even if the paper is strong. This means you have to sort out strong and negative parts of a paper for yourself (well ahead of time)
It’s sometimes a good idea to first go around the room and ask for something that people felt was strong and positive about the paper, and then do this again but ask for points of constructive criticism about the paper.
Don’t hesitate to ask people (specifically) for their views on some sections of this paper: a gentle push may be needed to get started on discussing the specifics, but this can be fruitful.
Since you are chairing the discussion, don’t be afraid to take control if the discussion wanders too far from where it needs to be, and/or if the discussion gets too trivial or mired in the weeds
Related, whenever possible, draw the discussion back to the actual research objectives, and try to broaden the discussion out to the overarching concenptual framework: are the results generalizable to other fields? Does the paper make broad and meaningful conclusions that will be long-lived and significant?
Towards the end of the discussion, it may be useful to ask people how they might have done the work differently. Or, stated another way, what could have been improved?

4. Summarize the discussion:

Spend the last five minutes of your time reminding people abou the actual research objectives, and provide a concise summary of the discussion that just wrapped up. Do this in an inclusive way, and give a nod to everyone in the room: make everyone feel that their points of views and opinions are taken seriously. Try to get an overall consensus about the general quality of the paper, and one litmus test may be whether or not you would cite the paper in your own work, and in what context.

Meet the lab: Elyssa Cameron

January 2, 2015 / Chris Buddle / 1 Comment

Here’s another in the “Meet the lab” series – written by Master’s student Elyssa Cameron.

Like many in my field, my love of nature and the creatures which inhabit it began much earlier than I can remember. From camping trips to day camps to museums and everything in between, I have always been passionate about understanding the world around me. Whether I was catching butterflies, trying to identify an elusive bird, exploring a new place or simply basking the in the beauty and wonder of an unaltered landscape, I knew that I wanted to be an advocate for nature.

Elyssa Cameron, with a furry friend.

In 2011, this led me to pursue an undergraduate degree at McGill University in Environmental Biology, specializing in wildlife. Here I learned the skills and thought processes that would help guide me on my journey. This is also where I feel in love with ecology and ecosystem dynamics. I was humbled by the enormous web of complexity which governs our world and sought to discover where exactly my interests lay. My search took me to South Africa, where I spent 3 week learning about wildlife management, game ranching, governance of national parks, and the challenges in maintaining healthy, safe, sustainable populations and ecosystems. It was during this trip that I realised that the management and conservation of any ecosystem needed to rest upon a solid understanding of the ecology of the system as well as the interactions of individual species, between different species and between species and their environment. Without this basic knowledge of how something works, one cannot hope to protect it.

With this newfound drive for management and conservation through a better understanding of ecosystem ecology, I signed on to do a Master’s project with Chris Buddle (McGill University) on arctic arthropods in 2014. Having never truly worked on insects and spiders before, I knew such an undertaking would be a challenge; but one that I was excited to take on! The aim of this project is to establish a more comprehensive long-term ecological monitoring program in Cambridge Bay, Nunavut, by linking patterns of vegetation and habitat diversity to arthropod diversity. In this way, we can examine the arctic ecosystem in a more complete way and not as a series of individual pieces. This will allow for more effective management in this rapidly changing ecosystem and will hopefully provide more predictive power for models and policies.

However, to obtain these baseline conditions, we must first collect the data. This took me on my second great adventure – a summer in Canada’s high arctic! For those of you who have not yet experienced the vast and diverse beauty of Canada, it is something I cannot recommend enough. But be forewarned, there are LOTS of bugs – which was great for the Bug Team! Working in association with CHARS (Canadian High Arctic Research Station) the Bug Team was part of a unit of researchers set on better understanding the arctic ecosystem and promoting interdisciplinary collaboration. We sampled spiders, flies, beetles, wasps and others to try and get the most complete view of the species diversity and community structure as we could in such a short summer.

Elyssa’s Arctic Adventures!

While there, we also did a number of community outreach programs to try and get the locals interested in science. We participated in a science night, made insect and butterfly collections to leave at the high school and Sarah Loboda (one of my wonderful lab mates!) organized day camp activities for the kids.

Now back at McGill, I spend most of my days in the lab looking through a microscope. With the general sorting of samples now complete, I am about to embark on my biggest challenge yet: species identifications! Both scary and exciting; but with the great support system here, I’m not worried.

As of January, I will also be co-supervising an intern from the Vanier Wildlife Technicians program with Chris Cloutier (the lab’s resident mosquito expert).

Meet the lab: Sarah Loboda

November 20, 2014 / Chris Buddle / 1 Comment

This is the second in a series of posts that will introduce the members of the arthropod ecology lab. This one is about Sarah Loboda:

I am not one of those people who can reflect back on my childhood with memories of chasing butterflies with a net. Instead, I could be found shouting loudly when seeing a spider in the bathtub. Things change… today I study community ecology of Arctic arthropods, and have a deep passion for arthropod of all kinds, from spiders to butterflies and flies.

Sarah, with a butterfly net.

My interest in entomology began as a challenge, and I love challenges! When I was an undergrad at Université du Québec à Rimouski, Québec, a tackled the big challenge of learning to identify insects. During my undergrad, I participated in several research projects where I could encounter biodiversity of insects and spiders and I developed a curiosity and a fascination about arthropods, particularly those living in extreme Arctic environments. Arthropods are ectotherms, yet they survive, year-round, in a region where the climate is very harsh. I quickly realized that the taxonomy was not the only interesting aspect in entomology. I wanted to identify arthropods in order to do research on community ecology. During the final year of undergrad in Rimouski, I decided to do a research project on the community ecology of spiders in salt marshes. As part of this project, I met Chris Buddle who encouraged my passion for entomology and the Arctic and I was lucky to do a Master’s project on spiders in the Canadian North as part of the Northern Biodiversity Program.

I take all opportunities to do outreach, and talk about insects and spiders with anyone who is interested. I am also involved in different societies, including the Entomological Society of Canada, and the Entomological Society of Québec, for which I’m the student representative. I love to volunteer and organize activities for members. Being the mother of two children, I also like to share my passion about arthropods with my kids, their friends and classmates in schools or daycares.

Sarah in front of her awesome poster at an Entomological Society of Canada meeting. This poster was a runner-up for a prize!

I have just started the second year of my Ph.D. I work with the veritable goldmine of data that has been collected from Zackenberg (northeast Greenland), where a long term monitoring program of arctic biodiversity has existed since 1996. My primary research objective is to assess temporal changes of the Arctic fly communities in this region, using the Muscidae and Phoridae families as model study taxa. The second objective of my research project will be to assess phenotypic and genetic changes over the last two decades in two species of Arctic muscids from Zackenberg. For this project, I am co-supervised by Jade Savage, a muscids expert from Bishop’s University, and Toke Høye from Aarhus University.

Arthropod Ecology

Writings about arthropod ecology, arachnids & academia at McGill University

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