Meet Shaun Turney and Fuzzy Cognitive Mapping

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.

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!

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!

Take the active learning challenge

Dear Instructors,

Here’s your challenge: Include active learning activities in every lecture.

Just do it.

Active learning is a philosophy and approach in which teaching moves beyond the ‘podium-style’ lecture and directly includes students in the learning process. There is certainly a big movement out there to include active learning in the classroom, there is evidence that it works, and active learning strategies have been around for a long time. Active learning can make learning experience more interactive, inclusive, and help embrace different learning styles. Active learning places the student in a more central role in a classroom, and allows students to engage with the course and course content in a different way.

So, why doesn’t everyone embrace active learning?

Without a doubt, it can take a bit of extra work. This post by Meghan Duffy provides an excellent case study, and illustrates the benefits and drawbacks of embracing a ‘flipped classroom’ in a large biology class, and part of that involves heaps of active learning strategies.

Active learning also involves some risk-taking, and perhaps risks that pre-tenure instructors should avoid. The strategies can remove some of the control of the instructor, and this can be uncomfortable for some teachers. For any active learning strategies to work, the instructor, and students, need to be on board, and each strategy brings some challenges, takes time to prepare, and certainly takes time in the classroom.

This term, in my 70+ student ecology class, I decided to take the active learning challenge, and, every lecture, include active learning*. I want to share a few of the things I have done so far, and hopefully show that some ideas are easy and doable, for pretty much any teaching context (note: I do use this book to help generate ideas)

1) The teacher becomes the student: for the last five minutes of class, I pretended to be a student, and asked the students to become the teacher. I then asked them some questions about the course content, drawing upon material from the last couple of lectures. Because I have taught the course for many years, I had a good sense of where some ‘problem areas’ may be, and thus formulated questions that got to the more difficult material. Students then were able to respond to my questions, and share their own expertise with the whole class.

2) Clear and muddy: at the end of one lecture, I asked the students to write down one part of the content they really understood well (the clear), and one area that might be “the muddiest point” (i.e., what they are struggling with). Students handed in the pieces of paper, and I went through and sorted them, and then spent part of the next lecture re-explaining common muddy areas. This was a terrific way to get anonymous feedback, helped reinforce areas that I perceived to be going well, and allowed me to target problem areas in the course.

Here's a "muddy" - this student's comment reflects a common concern around how I teach some of the content.

Here’s a “muddy” – this student’s comment reflects a common concern around how I teach some of the content.

3) Gather in groups: many active learning strategies work best when students are in groups. To quickly set up groups during class, each student holds a ‘card’ with different symbols, letters, numbers, and drawings, and when I call out one of these, the students form groups. I made the cards so students get sorted into groups of different sizes, depending on the activity.

 

Cards given to students, for quick abilities to arrange into groups.

Cards given to students, for quick abilities to arrange into groups.

An easy and effective active learning strategy with groups is to have student discuss among themselves a particular problem or question. After a few minutes, a spokesperson can report back their findings to the whole class. I’ve also had some students come to the front and present the result to the class. This does depend on having ‘enthusiastic’ volunteers, but I have not found this a barrier.

4) IF-AT cards: this term, I am trying to use Instant-feedback assessment-techniques for multiple choice questions. These cards allow students to scratch off answers on a card, and they immediately know if they are right and wrong, and can scratch a second or third time to receive partial points. I have used these in the classroom, for group work, and then students can work on problems (presented by me on the blackboard or screen), debate and discuss the answers, and then scratch off to reveal the correct answer. This activity therefore includes group work, problem solving, discussion and debate, and instant feedback. It does take a little bit of time (20 minutes or so, for a few questions), but is an effective active learning strategy that combines learning with an instant-feedback style of assessment.

5) Pair and share: this is also a simple and effective way to get discussions happening in lecture. I pose a question or idea, and simply have students turn to their neighbour to discuss the answer. I then ask some of the pairs to share their answers or ideas, and I also divide the lecture hall into different sections and ask pairs from each section to report back. This allows full use of the space in the classroom and students at the backs, fronts, or sides are able to feel included.

All of the abovementioned strategies don’t actually take that long and do not require a major overhaul to the course or course content. I believe they are relatively risk-free and easy, and suitable for any instructor, pre-tenure or not. I see these kinds of active learning strategies more as ‘value added’ activities, and as small steps that can increase student engagement in the classroom.

I also teach with chalk, as I find that's a great way to make the classroom more active, for everyone.

I also teach with chalk, as I find that’s a great way to make the classroom more active, for everyone.

 

——–

* Full disclosure: so far I have succeeded in all but one lecture, and I’m eleven lectures in. I’ll post an update at the end of term, to let you know if I’m successful all term!

Trophic cascades in fragmented forests

Many birds eat insects and spiders. Some of these insects and spider are themselves predators, feeding on critters lower down in the food web. Some of the insects that are fed upon by birds, or other predators, also play important roles in forest, such as munching upon the fresh, green leaves of young trees (here’s a reminder).

Munch, munch, munch. The hungry caterpillar. (photo by Sean McCann, reproduced here with permission)

Munch, munch, munch. The hungry caterpillar. (photo by Sean McCann, reproduced here with permission)

These interactions are ongoing, all the time, in forests around the world. These forests, however, are changing in important ways. Some of them are getting smaller and smaller as humans continue to encroach on the land, via urbanization or agriculture. This results in a ‘fragmented’ landscape. A landscape with small forest patches, perhaps no bigger than your back yard. A landscape with larger forests, perhaps one in which you could get lost in. These forests are themselves connected to each other –sometimes directly by a corridor or hedgerow.

This is the context for PhD student Dorothy Maguire’s research. Within that context, Dorothy tackled a fascinating project, one that was just recently published. In this work, Dorothy and co-authors (including me, an undergrad at that time, Thomas Nicole, and McGill Professor Elena Bennett) put cages around small trees in different types of forests SW of Montreal. The cages (made of chicken wire) were in place to test the effects of ‘predator exclusions’ on the insects and spiders occurring on saplings. The prediction is that if you exclude larger predators, such as birds, this may allow a ‘release’ of other insects and spiders. In turn, this release may have trickle-down effects on an important process occurring in young trees: herbivory. For example, if a predator is more common because it’s not being eaten by birds, perhaps it will eat more caterpillars, which may mean the leaves on trees will be eaten less frequently. In ecology this is dubbed a ‘trophic cascade’. Dorothy did this work in the context of fragmented forests, and she worked in forests that were either small and isolated from other forests, or in forests that were large and connected to other forests. This was done because there’s an expectation that these ecological effects will be different depending on the degree of fragmentation happening on the landscape. For example, insectivorous birds may decrease in abundance in small, isolated patches, which means their effects on insect prey (and perhaps herbivory) may be reduced relative to effects in larger patches of forest.

Dorothy Maguire, working in a forest fragment.

Dorothy Maguire, working in a forest fragment.

During one summer field season, Dorothy and Thomas wrapped up some small sugar maple trees in chicken wire, left some alone as controls, counted insects and spiders over the summer months, and measured herbivory on the trees themselves. As expected, the effects of the ‘cage’ was significant: when you put a cage around a tree, you end up with more arthropods living on those trees. This confirms other papers which report a similar effect: insectivorous birds (and perhaps other vertebrate predators) have a significant, and meaningful impact on the insects and spiders living on trees. Or, stated another way, birds eat critters living on trees, and without these birds, there would certainly be more arthropods around!

Dorothy did not uncover a strong effect on the process of insect herbivory: although more insects and spiders were living in the trees protected by chicken wire, the leaves themselves were not affected. This could be because more insect predators were around, and thus compensating for the lack of birds, and eating just as many herbivorious insects (e.g., caterpillars) as the birds might have eaten.

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

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

Scaling up to the landscape context, there were no overall significant effects of the cage treatments in relation to the forest type, nor was the level of herbivory dependent on the landscape context. The general results for large, connected patches were no different than for small, isolated patches. However, the magnitude of the effect was marginally affected by the landscape context for the cage exclusion: vertebrate predator may have a more significant impact in smaller, isolated patches.

As with all research projects, this work resulted with as many questions as answers, which is equally frustrating and fascinating. It’s clear that vertebrate predators are important in these systems, but more work is needed to fully assess whether these effects are truly affected by the degree of forest fragmentation on the landscape. The lack of effects on the process of herbivory itself was equally intriguing – there are clearly many complex interactions occurring on small maple trees. Some of these interactions involve top-down predation events, but there are likely a suite of ‘bottom-up’ effects that are also influencing the system.

Reference:

MAGUIRE, D. Y., NICOLE, T., BUDDLE, C. M. and BENNETT, E. M. (2014), Effect of fragmentation on predation pressure of insect herbivores in a north temperate deciduous forest ecosystem. Ecological Entomology. doi: 10.1111/een.12166

Meet the lab: Crystal Ernst

This is the first in a series of posts where each Arthropod Ecology lab member can introduce themselves. First up is PhD student Crystal Ernst:

I’m a Ph.D. candidate in the final stages of my program: these days I’m crunching out analyses and writing papers as I prepare to submit my thesis at the end of the term. As a community ecologist, I spend a lot of time thinking about how and why different species assemble together in space and time. These questions are foundational to the study of ecology and provide the overall framework for my research program, which uses beetles and other ground-dwelling arthropods to study the structure and determinants of terrestrial animal assemblages.

PhD student Crystal Ernst installing pan traps along the Dempster Highway (Yukon)

PhD student Crystal Ernst installing pan traps along the Dempster Highway (Yukon)

I have spent my summers conducting field research in gorgeous, remote regions of our northern territories, including Kugluktuk Nunavut and the Dempster Highway in the Yukon. My colleagues, members of the Northern Biodiversity Program, have contributed to the collection efforts as well, resulting in specimens being obtained from twelve different locations in the boreal forest, the subarctic and high arctic, spanning Canada coast to coast. I’m now neck-deep in the joy of interpreting the stories contained in my collection of specimens.

Specimens in pan trap (photo by C Ernst)

Specimens in pan trap (photo by C Ernst)

 

Sorting specimens back in the lab

Sorting specimens back in the lab

I’ve taken two approaches with this work. First, I’ve used a fairly traditional taxonomic approach to studying these animals: by identifying them morphologically (with a microscope and identification keys), I can associate each individual with a known insect species – although some new species have also been discovered! With this information I can describe the species richness (diversity) and distributions of different beetles in the north, and see which species are associated with each other at different northern locations. Secondly, I’ve looked at my arthropods from the perspective of their ecological functions – their roles in their environments. For example, some insects are responsible for pollenating plants, others are important decomposers, and others still are predators; arthropod assemblages can therefore be described in terms of the diversity and dominance of different functional groups. I am in the process of comparing taxonomic and functional assemblages found across northern Canada, and working to determine what aspects of their ecosystems (things like: temperature, wind, and sunlight; the diversity and structure of the plant community in which they live; soil characteristics) are associated with the way these assemblages are structured, and how they change over time and across space.

Three color morphs of Blethisa catenaria, a rare subarctic species (H. Goulet)

Three color morphs of Blethisa catenaria, a rare subarctic species (H. Goulet)

A fun complementary topic I’ve researched is the relationships between some high arctic ground beetles and a fascinating group of parasites called hairworms. I found a number of beetles from different locations to be infested with these worms; in one instance almost a quarter of the beetles were infected! The parasites are aquatic as adults and must first infect an aquatic insect (like a mosquito larva) before being transmitted to a terrestrial host (like a beetle) via the predation of the aquatic host by the terrestrial insect. To complete their life cycles, the worms somehow compel the beetles to enter the water, effectively forcing them to drown themselves so that the worms can emerge safely into their aquatic habitat. This discovery suggests an important link between the creatures living in terrestrial habitats and those in aquatic habitats and tells us about the arctic food chain: beetles must be eating mosquitos or other insects that have aquatic larval/immature stages. These prey items may, in fact, be a very important source of food. More work needs to be done to confirm this! In the meantime, I am excited to have found these associations – the fact that these particular species of beetles can be hosts for hairworm parasites is new information, and it appears that the parasite itself is a new species!

Pterostichus caribou with hairworms (C. Ernst)

Pterostichus caribou with hairworms (C. Ernst)

When I’m not writing my thesis or putting obscure little black beetles on pins, you can probably find me working at McGill’s Teaching and Learning Services, enjoying my time as a teaching assistant, networking on Twitter, mucking around in my vegetable garden (or putting said veggies in jars), walking my dogs, enjoying nature while canoe tripping with my partner, poking wildlife, or lifting heavy things at the gym. I’m on the hunt for a fantastic postdoctoral position that will allow me to continue studying different communities of living things in other ecosystems, and that factors that affect how they’re put together, and I’m excited about the many opportunities out there!

Lunch in the tree-tops for the birds and the bugs

A few weeks ago, our laboratory published a paper in PeerJ (an open-access journal) titled “Vertical heterogeneity in predation pressure in a temperate forest canopy“. This work resulted from a project by former Master’s student Kathleen Aikens. She graduated a little while ago, and although we published one of her thesis chapters in 2012, it took another year to get this paper out, in part because Kathleen and I both become too busy.  Thankfully, post-doc Dr. Laura Timms agreed to help us finish up the paper, and she worked with me and Kathleen to re-analyze the data, re-write some sections, and whip it into shape.

As is now traditional for my laboratory, here’s a plain-language summary of the paper:

Tree canopies, including those in deciduous forests in southern Quebec, are important for many different animals, including insects and spiders. These small, marvelous creatures crawl up and down trees with regularity, feed upon the leaves of trees, feed upon each other, and are food for animals such as birds and bats. Past research has shown that many species of insects and spiders live in tree canopies, and in general, more insects and spiders are found closer to the ground compared to the very tops of the trees. This makes sense, since deciduous tree canopies often need to be recolonized each spring, and tree canopies are relatively harsh environments – they are windy, hot, and often-dry places as compared to the forest floor.  What we don’t know, however, is whether the insects and spiders avoid the tree canopies because they may be eaten more frequently in the canopy as compared to the understory. The objective of this research was to test this question directly, and find out whether insects and spiders are arranging themselves, vertically, because predators may be preferentially feeding on them along this vertical gradient. This is a very important area of study since biodiversity is highly valued and important in forests, but we cannot fully appreciate the status of this diversity without discovering what controls it.

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Our mobile aerial lift platform. TO THE CANOPY!

We did this work by using two experiments that involved manipulating different factors so we could get at our question in the most direct way possible. In the first experiment, we made ‘cages’ out of chicken wire and enclosed branches of sugar maple trees in the cages. We did this at the ground level all the way to the tops of trees, using a ‘mobile aerial lift platform’. These cages acted to keep out large predators, such as birds, but allowed insects and spiders to live normally on the vegetation. We counted, identified, and tracked the insects and spiders both within these cages, and in adjacent branches that did not have cages (the ‘control’). By comparing the control to the cage, we could find out whether feeding activity by larger vertebrate predators affected insects and spiders, and whether this differed when comparing the ground to the top of the trees. In the second experiment, we used small pins and attached live mealy worms (larvae of beetles) to the trunks of trees, and we did this in the understory all the way up to the canopy. We watched what happened to these mealy worms, and compared what happened during the day and overnight. This is called a ‘bait trial’, and let us figure out what sort of predators are out there in the environment, and in our case, whether they fed more often in the canopy compared to the ground-level. This second experiment was designed for seeing the effects of insect and spider predators along a vertical gradient whereas the first experiment was focused more on vertebrate predators (e.g., birds).

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Munch munch. Carpenter ants feeding on mealworms.

Our results from the first experiment showed that the cages had an effect: more insects and spiders were found when they were protected from predation by birds. Birds are playing a big role in forest canopies: they are feeding on insects and spiders, and in the absence of vertebrate predators, you might speculate more insects and spiders would occupy trees. Our second experiment showed that ants were important predators along the tree trunks, and overall, the most invertebrate predators were found in the lower canopy. Both experiments, together, confirmed that the understory contained the most insects and spiders, and was also the place with the highest amount of predation pressure.  The take-home message is that there is an effect of predation on insects and spiders in deciduous forests, and this effect changes if you are in the understory as compared to the top of the canopy. We also learned and confirmed that insects and spiders remain a key element of a ‘whole tree’ food web that includes vertebrates such as birds, and that predators in trees tend to feed on insects and spiders along a gradient. Where there is more food, there is more predation pressure! Our work was unique and novel because this is the first time a study of predation pressure was done along a vertical gradient in deciduous forests. It will help better guide our understanding of forest biodiversity, and the processes that govern this diversity.

A more detailed discussion of this work is posted on the PeerJ blog.

Arctic reflections (Part 2)

I started a post last week about my recent field trip to the Arctic – I was situated in Cambridge Bay (Nunavut) for a week, and here are a few more reflections from that trip.

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Wildlife

Walking across the tundra brings sights of circling rough-legged hawks and the sounds of jaegers. We were able to find spots where the hawks like to sit (at higher elevations, on a pile of rocks and boulders). The vegetation is particularly rich under these perches, as the nutrient inputs are very high! We could also find feathers, and pellets – these pellets are a tidy package – a mass that represents the undigested parts of a bird’s food, regurgitated. These pellets can be dissected and you can find the tiny bones of small mammals. While in Cambridge Bay it was a particularly good year for lemmings, and thus a particularly good year for hawks, and snowy owls. Each day on the tundra, about a dozen different snowy owls were sighted. They were always just the right distance away, perched beautifully and peacefully on slight rise – a close look with the binoculars showed the owls staring right back, tracking our movements as we were tracking theirs. If you walk little closer, the owls take off, flying low and fast over the tundra.

Bird food. Aka lemming.

Bird food. (otherwise known as lemming).

At times, off in the distance, it was also possible to see black, slow-moving shapes – unusual creatures, shaggy, and foreign to a boy from the south. These were muskoxen – chewing their way across the tundra. While in Cambridge Bay I spent some time with graduate students working on Muskox health, and I learned of the serious disease, lungworm, that is affecting these stunning mammals. Lungworm has been known from the mainland for some time, but only more recently on Victoria Island – climate change is a possible reason for this change in distribution. These nematodes use slugs or snails as intermediate hosts. Yes, there are slugs and snails in the Arctic!  Finally, it’s pretty difficult to talk about Cambridge Bay without mentioning the fish. The traditional name for this place, in Inuinnaqtun, is “good fishing place“, and that is an apt description. We ate fresh fish every day, enjoying Lake trout, Greenland cod, and the most delicious of all, Arctic Char. We were blessed with amazing weather during my week in Cambridge Bay, and our Sunday afternoon fishing trip on the ocean was picture-perfect.

Good fishing place.

Good fishing place.

Landscape and light

It’s hard to explain the North to people who have never experienced it, but let me try:

The landscape is breathtaking in its starkness.  The tundra rolls out like a grey/green/brown carpet, as far as the eye can see. It’s broken up by ponds, streams, and lakes, and broken up by slight changes in elevation. This results in a landscape that ripples with shadows and colours; a landscape that meanders, curls and curves depending on the underlying bedrock, sediment, glacial till, and permafrost. 

At first glance, the Arctic tundra appears homogenous, but after walking for hours upon hummocks and through cotton grass, you start to see the diversity of ecosystems, and the heterogeneity in microhabitats. It’s a landscape that is forever changing and providing plants and animals opportunities as well as challenges. I was in Cambridge Bay in early August, and it was evident that the summer season was ending.  In addition to the signs from the plants (lack of flowers) and wildlife (geese were moving in, in flocks; butterflies were seldom seen), the strongest evidence was the light. During the week I was in Cambridge Bay, there was about 18 hours of daylight each day, but the land is losing about 5 minutes of light each day – it’s a rapid change. Since Cambridge Bay is above the Arctic circle, it gets 24 hours light in June and early July, but by mid-August, summer is winding down. This means, however, that you can experience the most stunning sunsets – you can sit for hours and watch the sun approach the horizon from a remarkably shallow angle. The “magic” light is with you for hours. The kind of low light that makes everything slow down.  The kind of light that creates long, dancing shadows, and warms everything in a soft, gentle glow.

Arctic reflections

Reflection

To finish, I wanted to write a little bit about perspective. The Arctic makes you feel close to the earth. When standing on the tundra, the land before you contains no telephone lines, roads or apartment buildings. It’s very much like it was hundreds or thousands of years ago. You could start walking and you won’t likely see anyone else. The Arctic causes you to reflect and slow down. And most importantly, the Arctic makes you feel small. I think that’s an important feeling to have every now and then. The land is vast and old; we are small and young. Let’s remember we are here for a short while, and some of our time is probably well spent out in a forest, on a lake, or hiking the tundra.  Time on the land is time well spent, in part because it causes you to pause and reflect. I think the world would be a better place if we spent a little more time breathing in nature, and remembering what the earth is giving us and on how we ought to respect it a little more.  We owe it everything.

The Arctic makes me think of these things and for that I am grateful.

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Labels tell stories: natural history and ecology from dead spiders in vials

Earlier this week I was back in Ottawa at Canada’s National Spider collection with a couple of enthusiastic students from the lab. We were doing more databasing, which involves reading old labels and entering the information into a database.

Sound boring?  Nothing is further from the truth. It’s an amazing way to spend time, here’s an example:

Spiders as prey

Yes, that label for a jumping spider species provides more than a name, locality and date. It provides a story. It confirms that spiders are hosts for parasitoid wasps, and it documents an ecological interaction; one that is stamped in time and place.

Every single specimen in a museum or research collection tells a story. There are untold riches on little pieces of paper linked to biological specimens. In addition to the usual name, place, and time, label data gives us varied and fascinating ecological stories. Here’s another one:

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Yes, more evidence of one spider species preying upon another species. Intraguild predation, recorded and placed in a vial.

I love this next one – in part because you now know that bluebirds eat jumping spiders and that Arachnologists can identify the species based only on the male palp (that is all that was in the vial, it’s the little spider ‘bit’ at the bottom left). Um, I suppose the bird got the rest of the specimen!:

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Label data can tell incredible stories!  Here’s a nice set of labels that show how Phidippus jumping spiders really, really get around:

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Planes, automobiles, and boats.  (um, boats in Saskatchewan! A Province of relatively limited water, by Canadian standards).

Label data also provide insights into the characters of scientists. Below is an example of three different individuals all identifying the specimen as the same species. The three scientists, by the way, are preeminent Arachnologists in North America – I would trust any one of their identifications, but clearly they were not entirely sure, and all three had a look to confirm the identification. Three votes from Dondale, Maddison & Edwards, in three different decades! Yes, it’s Phidippus audax:

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Label data provide an important historical context.  I was thrilled to see this label from 1917 collected by none other than Norman Criddle (Criddle is well known to Entomologists in Canada):

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Label data provide opportunity to discuss, imagine and be inspired by biodiversity. I identified a species of jumping spider from a place called Sable Island. The species is one of the most attractive spiders in North America, Habronattus decorus

Sable Island is here:

Sable Island

So… the questions start. How did it get there? Presumably ballooning? Are these lovely critters still on Sable Island? What is the fauna of Sable Island? Is is a stable fauna? An old vial, stuck in a cabinet in Ottawa, opens to door to questions of dispersal, biogeography and biodiversity.

I think the message is clear: databasing provides a rich opportunity to paint a picture of a species, over time and over space.  

But here’s the problem: there are about 2700 vials of jumping spiders to database. Each one takes about 3 minutes to database, meaning it would take about 135 hours of work to database only 1 family of spiders, in one collection! And working in the collection is not free – paying students, travel time, lodging, etc. all take time and resources.

So far our laboratory got through about 400 specimens (15% of the Salticidae). We have barely made a dent.

This is an undeniable problem: We must capture these data and make them available for scientists to use.

How can we understand biodiversity change when most of our historical data are not yet digitized?

How can we begin to understand biodiversity patterns without knowing what is where, and when? 

When I wrote my previous post about the Canadian collection, I was pointed to Notes from Nature – an on-line resource where databasing is crowdsourced. This is a pretty neat idea – label data (and specimens) are photographed, uploaded to the site, and anyone in the world can transcribe the data.  It allows anyone with an interest in biodiversity to reach into a collection and learn the stories from the specimens.

I am hoping to try this out with spiders from Canada’s national collection. While in Ottawa, I tried taking photos of specimens, and tracked how much time it takes. It turns out it takes about 2 minutes to photograph the specimens and label. You must take out the spider, the label(s), arrange everything carefully and take photo(s). It then takes about 1 minute to edit the photo, and about 1.5 minutes for someone to enter data into a computer from a photograph instead of from the specimen itself. So, total time for databasing is 1-2 minutes longer than sitting in the collection and doing the databasing. The benefit, of course, is that there is good potential to actually get a collection databased from afar. Here’s an example of a photographed label and specimen, after editing:

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Question: would YOU help database if you could go on-line and see these kinds of images? Does it grab your attention? Even if 20-30 people agreed to database 75 or so specimens, each, the Salticidae would be done! (and, of course, someone would have to take images, and edit them beforehand).

I am keen to have your feedback…. I want to know if it’s an idea worth pursuing.

Do you want to learn stories from specimens? 

How I traded field biology for a desk job

As I was looking at my summer schedule, it occurred to me that my time out in the field (here defined as outside, collecting data, probably wearing zip-off pants and carrying a field book, insect net and a set of vials) has been getting less and less, every year. As a PhD student I spent most of my summer collecting data. I loved it – the rugged joys of bumpy back-roads in Alberta, the sticky and smelly combination of sweat and bug spray, the cold beer at the end of a long field day.  As I moved on to a post-doc in Ohio, I still spent a lot of time collecting spiders in soybean fields, helping other graduate students in the field, although the summers also included some lab work, and substantial time writing manuscripts.

When starting at McGill over 10 years ago, I kick-started my research program by spending weeks in the field, and seemed to manage a lot of time with each of my graduate students during the field season.  However, time in the field was measured as weeks, and not months.  Now, as I look at my schedule, I’m “maybe” going to get one full week in the field this summer, and a fews days here and there helping with other projects going on in the lab. My time doing field work, actively collecting data, is minimal.

Deep thoughts: field work in the Arctic. Are these days long gone...?

Deep thoughts: field work in the Arctic. Are these days long gone…?

Wait a second. One reason I got into this business was because I like to figure out neat stuff about nature, while being in nature. As a child, I always enjoyed beingin the field‘ (this is also known as ‘playing outside‘) and wanted to continue this as an adult. What happened?

Academics in my discipline of study (let’s call it ‘field ecology‘) and at my career stage (i.e., some years into the job) spend relatively little time in the field and the bulk of their time is a desk job, click-click-clicking away on a keyboard. Staring at a monitor. I know there are exceptions (and BIG congratulations on those of you who do manage to get outside to collect data, regularly!), but when I look around to my colleagues, most of them spend more looking out a window instead of being out that window. The time gets chewed up by other (important) priorities: grant writing, editing manuscripts, writing manuscripts, answering emails, reading papers, attending meetings, chairing meetings, going to conferences, preparing talks for those conferences, writing lectures, delivering lectures and so on. These are all the current demands on our time, and they are the things that the job requires! (for other relevant discussions about this, have a peek at this post by Sarah Boon, and I’ve previously written about how I spend my time).

Bottom line: most of my work duties are indoor activities. I am fortunate in that some of my teaching occurs outside, but that is not the norm.  The other thing that happens is ‘life’ – time with family is important to me, and time away from family is difficult. One reason I’ve spent less weeks away is because it’s tough on all of us and I like being around when the kids are growing up. There’s also that thing called a vacation – Academics typically their vacation time during the summer. (related to this is a post over at Dynamic Ecology titled “how often do you travel”, by Meg Duffy)

That is how I have traded field biology for a desk job.

I’m not alone: here are some responses from folks on Twitter when I asked about their experiences, and whether they have traded field biology for a desk job:

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This is not a lament; this is not a sob story. In fact, perhaps many of us are OK with this transition from field biologist to ‘research manager’:

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There is an important message here for people moving up through the Academic system: current PhD and MSc students need to recognize that the idea of landing an Academic job that gets you ‘out in the field’ a lot is probably a pipe dream.

I’ll end with some optimism: Even though things have changed, I think I can still call myself a  ‘field ecologist’ and here’s why:

1) “Field Trips” can be short. It’s possible to capture an hour outside over lunch and collect data on Agelenopsis spiders in a hedge near the picnic table, or stop off at a bird banding station in the AM before work, or swing by a forest to check a pitfall trap on the way home. I have come to realize that field work need not be ‘weeks away’.  In many cases, it’s worth starting up a project that takes you outside regularly, at a local field site. This makes the field work an easier part of the day and you don’t need to schedule weeks away (nor will you need to schedule it months in advance). Keeping it simple, and keeping in manageable is important for me, given the other constraints on time.

2) Trade-offs: I spend time in the field instead of attending a lot of conferences. I have always enjoyed going to scientific conferences, but given the difficulties in getting away for extended periods of time, I realized that I could do field work, or attend conferences, but doing both is not always possible. One of my academic mentors discussed this with me soon after I had started my job at McGill (ironically, at a conference!); he said that when the weather is good, time was better spent collecting flies rather than sitting in a hotel basement. Good point. (By the way, summer-conference are kind of annoying because of this conflict!).  Networking at conferences is very valuable, but that face-to-face networking may not be as essential later in a career. Thanks to social media, it’s also possible to attend conferences virtually.

3) Live vicariously through students: My thoughts about field work are somewhat nostalgic and dreamy, and I forget about the problems. I forget about the flat tires, encounters with bears, the biting flies, and the exhaustion. I’m reminded of these things when my graduate students come back from the field, and sometimes I am happy I wasn’t with them. I can, instead, spend a day or two with them in the field, troubleshoot, help but not have to suffer through it all. I’m a ‘gentleman field biologist’ now. Is that lame? Is that pathetic? Nope. I’ve put in my time and can now have my field trips field with all the fun parts and less of the annoying parts.

4) Mixing vacations with field biology: I’ve not been all that successful at this, but I do know colleagues who manage to mix extended vacation time with field work. I do this on a smaller scale, and it typically includes carrying vials along with every trip, whether it is to the family cottage, or just a walk in the local forest. I’m always after records of pseudoscorpions, and have managed some nice finds while on vacation.  My family does, however, gives me strange looks when I go chasing after spiders or butterflies during lunch break while on a road trip. I can handle the ridicule –> it’s for science!

Although I have largely traded field work for a desk job, there are still glimmers of exciting field work, and still opportunities to get outside and be reminded of the reasons why I originally got into this line of work. I am not depressed or sad about my desk job – I have the best job in the world, despite the the fact that I stare out the window and sometimes dream of field work. I also maintain that these things come in cycles – a few years ago I was away for a few weeks in the field, even if this year is less intensive. It’ll come around again, and perhaps I will write a post in the future that discusses how it’s possible to be a gritty, smelly, rough and tough field biologist again. For now, though, I must stop typing. It’s hard work and my fingers are a little sore.

Ecology and Mathematics: perspectives from undergraduate students

Post written by Chris Buddle and Carly Ziter (MSc student at McGill – you can follow her on twitter)

Population and Community Ecology is an introductory undergraduate course at McGill University and each lecture typically starts with an x-axis and a y-axis drawn on the chalkboard – something like this:

Chalk board, with x- and y-axis. The start of every lecture.

Chalk board, with x- and y-axis. The start of every lecture.

The course is taught from a quantitative perspective, and it uses equations, models and graphs to cover concepts ranging from logistic population growth, to metapopulation ecology and estimating species diversity.  The class uses Gotelli’s “A Primer of Ecology” as the text – a book that walks through many ecological concepts from first principles. It includes calculus, probability theory, statistical distributions, and null models.

It was therefore fitting that the ‘E.O. Wilson versus Math” debate was discussed during lecture last week.  Students were asked to read Wilson’s piece in the Wall Street Journal, and read some of the blog posts that reacted to this, including Jeremy Fox and Brian McGill‘s posts on dynamic ecology. Students were also asked to look at some of Terry McGlynn’s writing over at small pond science, and to come to lecture prepared – to have opinions and be willing to discuss these opinions.

For those not fully aware of this debate, here it is in a nutshell: Wilson argued that a ‘deep’ understanding of math may not always be prerequisite for doing great science, or at least may not be required for generating big ideas and concepts. Wilson was in part trying to encourage people who are ‘math phobic’ that this phobia needs not be a reason to stay out of science.  Not surprisingly, this stirred up a lot of debate (and some of it was rather harsh!), and the debate was particularly interesting from the perspective of Ecology since this discipline has always struggled with this topic (see Terry’s excellent post about tribalism in ecology for some perspectives on this).

Here is a summary of the key points that were discussed during lecture – and let’s just say that a 50 minute lecture slot was NOT enough time for this topic! (by the way, there were between 50 and 60 students who attended this  lecture, and the class is comprised primarily of students studying environmental biology).

Many of the students were surprised at the tone and overall discussion points that emerged from Jeremy Fox’s post – they argued that when they read Wilson’s piece, they didn’t feel the intended audience was ‘established’ ecologists – but rather the post was meant for students at the start of their careers. Some of them found the blog posts way over the top, and the academic discussions took away from the main message.  Some felt that Wilson was arguing in part about the need for freedom to think without any boundaries (mathematics, or anything else).  Creative thought need not be constrained, and students coming up through the system, whether they are math literate or not, should never fear heading into science (indeed, some confessed that an increase in math courses may have driven them away from biology altogether).  Related to this, mathematical models all require assumptions (we talked a LOT about this when working through Gotelli’s book!), and any assumptions are limiting and could distract from thinking out of the box about any topics, including ones that are ecological. These students worried that the constraints imposed by math could force ecologists to view the world through a particular lens.

That being said, many of the students also agreed that a deeper understanding of mathematics was absolutely required for ecology – especially since the world is complex, with complex problems – problems that require multiple disciplines to solve.  However, while these disciplines include mathematics and biology, they also include literature, history, environmental policy, and more.  What a solid argument! And it was great to see that argument expressed by 20 year-olds.  Yes, math is important, but it is one tool that we need in this world, and it’s not necessarily more important than other tools.  While some ecologists are strong in math, others may prefer to hone their policy skills, for example. Ecology’s strength, in part, is in its ability to bridge different disciplines and students expressed how ecology is actually a ‘great uniter’ of biology and math (and other fields, certainly some areas of ecology draw upon a range of ideas from sustainability science, medicine, economics, history, etc).

The students also expressed concern about how mathematics is taught, from elementary school all the way to University – they expressed how learning mathematics in isolation of other topics is ‘ok’ for individuals with an intuition and natural ability with math – but many students felt that a better way to learn about math was applying it to the ‘real world’. The application of mathematics is the best route to learn mathematics. Ecology was again touted as a perfect example of a discipline in which application of mathematics is clear – from predicting distribution of invasive species to modelling species richness in fragmented forests.  For some students, math was not a subject they initially enjoyed, or strove to learn – it was ultimately through their study of ecology that they began to value math as a tool they could use to support their discoveries, and lend credibility to their work.

By in large, students agreed that mathematics was required for ecology, but there was certainly debate about how much was enough – whether it was enough to use mathematics as a tool, or that perhaps mathematics was more like a language.  A language in which fluency is required so all the nuances can be understood and that the full meaning is in place.  From those advocating mathematical “fluency”, there was a strong opinion that like languages, mathematics can be learned with hard work and focus (yes, they agree with Wilson on this point!) – this opinion comes with a wealth of experience in the classroom at McGill since many of the students are mother-tongue French and have learned English after coming to McGill.  In other words, if you can learn a language you can also learn math.

The final argument put forward by students was that this entire discussion about Ecology was from a very narrow perspective – what about the role of traditional ecological knowledge?  Ecology is a much older discipline than Clements, von Humbolt, Haeckel, or even Aristotle. Throughout history, humans have been interacting with their environment, and have been observing nature.  By this act, humans have been counting, developing models, and making predictions… for thousands of years.  Linking mathematics to nature is very, very old.  Ecologists ought to pay more attention to other ways of looking at the natural world, other ways to visualize, predict, observe and count. Although this is certainly not the same kind of math as presented by Gotelli, perhaps it could be as insightful.

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In sum, the discussion with undergraduate students on this topic was insightful, fascinating and important. There was clearly a strong appreciation for the role of mathematics in ecology, but also different ideas about the degree to which a deep understanding of math is required – which often related back to the students own struggles with, or aptitude for, math earlier in their studies. It was validating to hear that they appreciated using Gotelli’s book to learn the foundations of ecology, and recognized that ecological models can be both limiting and liberating.


Seasonality of Arctic Beetles

I’m excited to report on paper written by Crystal Ernst, PhD student in my lab, and well known as the “Bug Geek“. This paper is a product of the Northern Biodiversity Program (yes, it sure is great that the papers from this project are starting to appear!), and will be one of Crystal’s PhD thesis chapters. The paper is titled Seasonal patterns in the structure of epigeic beetle (Coleoptera) assemblages in two subarctic habitats in Nunavut, Canada

A very nice Arctic beetle! (photo by C. Ernst, reproduced here with permission)

A very nice Arctic beetle! (photo by C. Ernst, reproduced here with permission)

Here’s a plain-language summary of the work:

Although we often think of Arctic systems as cold and lifeless, Canada’s tundra habitats are home to a high diversity of arthropods (insects, spiders and their relatives). Beetles are important insects on the tundra – filling ecological roles as predators (feeding on other insects), herbivores (feeding on plants), mycophages (feeding on fungi), and necrophages (feeding on dead or decaying animals). In this research, we wanted to find out what happens to ground-dwelling Arctic beetles as a function of seasonality. We were curious about whether different species occurred at different times during the short Arctic summer, and whether the functions of the beetles changes over the summer. This is an important area of study because beetles perform important ecological functions, and knowing how these functions change over time may have broader implications for northern ecosystems. This is especially relevant in the Arctic since these systems have a short ‘active season’, and climate change is disproportionally affecting northern latitudes. If climate change alters an already short summer, what might happen to the beetles?

This research was done as part of the Northern Biodiversity Program (NBP) – a broad, integrative project about the diversity of insects and spiders across northern Canada. The NBP involved collecting samples at 12 sites in the Arctic, but at one of these sites (Kugluktuk, in Nunavut) we had an opportunity to do a more detailed collection over the entire summer of 2010. This involved setting out traps for the entire active season, from June through to August. These traps were plastic containers sunk into the ground – beetles that wander along the tundra fall unawares into these traps, which contain preservatives, and are trapped until a researcher collects the samples. Traps were placed in wet and (relatively) dry habitats so that we could compare the two habitats. After the collections were returned to our laboratory, the beetles were identified to species, counted, and the biomass of the beetles was estimated – biomass lets us determine what happens to the ‘amount of beetles’ on the tundra in addition to figuring out ‘how many’ (abundance) and ‘what kind’ (species) were in the traps. The beetles were also classified into their key ecological roles. The data were then compared as a function of when traps were serviced to let us assess what happens to beetles as a function of seasonality.

We collected over 2500 beetles, representing 50 different species – remarkably, 17 of these species represented new Territorial records. This means that 17 of the species that were identified had never before been recorded in all of Nunavut! Although many ecological functions were represented by the beetles we collected, most were predators. We documented that wet habitats had different kinds of beetle species than the drier tundra habitats, even though the actual number of species between the habitats did not differ. We also uncovered a seasonal affect on the functions of beetles in the system – as the season progressed, the beetles tended to be represented more by predators compared to earlier in the season, which was dominated by beetles representing a diversity of functions. The mean daily temperature also related to the seasonal change that was observed in the beetles.

PhD student Crystal Ernst, happily working on the Arctic tundra.

PhD student Crystal Ernst, happily working on the Arctic tundra.

This work is one of the first to carefully quantify how beetles change during short Arctic summers. We found a diverse assemblage of beetles, filling a range of ecological roles. These ecological roles, however, do not stay the same all summer long, and the shifts in the beetles were related to mean daily temperature. Given that Arctic systems will be significantly affected by climate change, this is worrisome – if temperatures increase, or become more variable, this may affect ecosystem functions that are mediated by beetles. This is more evidence supporting the need to track climate change in the Arctic, and play close attention to the small animals of the tundra.

Reference:

Ernst, C., & Buddle, C. (2013). Seasonal patterns in the structure of epigeic beetle (Coleoptera) assemblages in two subarctic habitats in Nunavut, Canada The Canadian Entomologist, 145 (02), 171-183 DOI: 10.4039/tce.2012.111