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

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!

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.

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:

  1. PIs must be responsible and proactive on the process of voucher specimen deposition, from the start of any project.
  2. Graduate students need to be mentored appropriately about the importance of voucher specimen deposition.
  3. 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.
  4. 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.
  5. 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.
  6. 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.

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

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!

Leading a discussion of a scientific paper

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

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

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.

giraffe

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.

Arctic

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

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.

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!

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.

What is the motivation for pursuing graduate school?

Last week an interesting hashtag was floating around twitter:  #whyididaphd.  It was great to see reflections on this topic, and during our most recent lab meeting, I asked my students why they were pursuing advanced research-based degrees, and here are some of their responses:

  • Graduate school allows an opportunity for freedom to do the things you find interesting, every day.
  • Doing research means you can follow your interests and curiosity.
  • Doing a MSc is a perfect transition between an undergraduate degree and whatever might come next!
  • Doing research is an opportunity to work independently, and this is important to me.
  • Research is about gaining knowledge and learning on  your own. It’s like the best kind of drug: you can get hooked and it’s good for you, and it never ends.
  • Graduate school develops my network of collaborators, and I need this as I enter the work force.
  • I want to do things that are relevant, and are my ‘own’. Research allows this.
  • Doing an advanced degree was an important career stage, because I need it in order to do what I really want to do into the future (i.e., academic position).

These reflections were insightful, and showed that the students had wonderful motivations for pursing advanced degrees in a research-based laboratory. I agree that doing a MSc or PhD is perfect for people who are curiosity-driven, and who appreciate the independent nature of the work.

I had two responses to #whyididaphd. The first one certainly reflects my thinking now:

Screen Shot 2014-10-08 at 1.12.23 PM

The second response is a little more honest, and reflects my thinking at the time I decided to continue with research, about 20 years ago:

Screen Shot 2014-10-08 at 1.13.21 PM

Is it wrong to pursue a MSc or PhD “just because there’s nothing better to do”, or “because I don’t have another plan and I like University”?  We had a heated debate about this, and the lab was divided. One argument is that it’s a total waste of time, energy, money and resources to pursue a MSc or PhD “just because”. Sure it’s nice to stay in a University after the undergrad degree is done, but why pursue it unless you know you need that advanced degree!  Have a plan, have a career goal, and if a MSc or PhD is part of that plan, pursue graduate school.

In contrast, if you don’t have a plan, or a specific career in mind, perhaps graduate school is the *perfect* place to develop your research skills in an exciting, and familiar environment. Graduate school is a perfect transition to many, many careers, so if there is nothing else on your horizons, keep on trucking along at a University! If you are a curious person, and independent thinker, it’s an ideal learning environment.

I suspect many people fall somewhere in the middle (I think that was the case for me).  I always felt I might eventually like a career at a University, and since I seemed to like research, and be good at it, pursuing graduate school was a natural progression. So, even if the motivations for doing graduate school aren’t always based on a clear career path, those motivations can still be more than enough to give it a try.

I’ll finish by expanding that last point: “give it a try” does not mean “stick with it even when it’s not working”.  It’s important to know when to quit if grad school is not for you. It’s an awfully difficult and frustrating process if it’s not going well. Give it a try if it floats your boat, or it’s what you need. However, also know when to quit.

 

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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!