Rethinking guild classifications for insect herbivores

This is the start a (somewhat) regular series of blog posts highlighting some of my favourite research papers in the discipline of Arthropod ecology – I’ll call this category “must-read research papers”.  These posts will force me to look critically at some of the great research papers I have read in the past little while, figure out the ‘take home messages’ from these papers, and articulate this message.  I also hope these posts can inspire others to think about the best papers within their discipline and to share their opinions and ideas to a broad audience.  That is what science communication is all about! 

Typical herbivory by a “leaf chewing” insect

For the first in this series, I wanted to highlight a paper by Novotny (and fifteen other co-authors) published in 2010 in the Journal of Animal Ecology.  This work is titled “Guild-specific patterns of species richness and host specialization in plant–herbivore food webs from a tropical forest.”   This paper was discussed in my Insect Diversity class last autumn (co-taught with Terry Wheeler), and was used as an example of assumptions we make when considering what it means to be a herbivore.    From my biassed perspective (working mostly in north-eastern deciduous forests and the Arctic), when I think about herbivores, I automatically classify herbivores into a few pretty obvious categories: leaf chewers, leaf miners, gall-makers, and a suite of ‘piercing-sucking’-type herbivores.  My off-the-cuff estimate of the number of herbivore guilds would be much less than a dozen.

Novotny et al.’s paper really shook up my view of what it means to be a herbivore.  Using their considerable data and expertise from work in Papua New Guinea, the authors refine plant-herbivore food webs and, quite simply, explode the concept.    The authors classified insect herbivores by their main mode of feeding (chewing, sucking), developmental stages (larvae, adult), where they feed (internally, externally), and by the plant part which is fed upon (leaves, flowers, fruits, xylem, phloem, etc).    Their system resulted in 72 classifications – which they reduced down to more manageable 24 – still over double what my initial estimate was.  Their system certainly includes the classic guilds (e.g., leaf chewers) but also included some wonderfully detailed interactions that are easily overlooked (especially by someone who studies spiders…).  For example, fruit chewers, flower chewers, and xylem suckers.   As an aside, and for some eye candy, here’s a nice photo of a caterpillar from The Bug Geek (reproduced here, with permission)

A cryptic caterpillar, (c) C. Ernst

The authors then took their new and detailed classification system and completed a food web analysis for their tropical system in Papua New Guinea, focusing on 11 main guilds.  Their resulting 11 food-web diagrams are a lovely depiction of multivariate data in 2-dimensions, as they show the frequency with which each host plant is consumed by herbivores, the herbivore abundance and the frequency of each interaction – and they present this for 9 standardized plant species, for each of the 11 guilds.   Their research depicts “6818 feeding links between 224 plant species and 1490 herbivore species drawn from 11 distinct feeding guilds”. WOW!  They also show that 251 species of herbivores are associated with each tree species within their study system.  There are clearly a lot of different ways for herbivores to make a living.

This paper represents a major undertaking, and it is a bit sobering to see the results and see that despite the efforts, relatively few ‘generalities’ exist – that is to say, there are examples of extreme host specificity, extreme generalist feeding, and everything in between.   Here’s a quote from that paper to illustrate that point:

“We documented a wide range of host specificity patterns among herbivorous guilds: host specificity measures spanned almost the full range of theoretically possible values from extreme trophic generalization to monophagy. These results demonstrate the importance of taxonomically and ecologically comprehensive studies, as no single guild can be designated as ecologically representative of all herbivores.”

Mealybugs: another type of herbivore. (c) C. Ernst, reproduced with permission

What’s the take-home message?  

For me, this is a strong paper that depicts effectively the complexity of plant-herbivore food-webs and illustrates (once again!) that diversity in tropical forests is stunning. More than that, the work shows this diversity from a functional, food-web perspective, and illustrates how guilds behave differently.   From a more practical perspective, this paper is forcing me to rethink how I view herbivores – i.e., they are more than leaf-chewing caterpillars and aphids.  They are also root-feeders, fruit chewers, flower chewers, and specialized xylem suckers.  Novotny et al. suggest researchers use their 24 guild system for classifying insect herbivores, and I agree – their classification system is still manageable, yet much more comprehensive than what many researchers use.

If the topic of food-webs, plant-insect interactions, and the biodiversity & ecology of tropical forests interests you, this is a must-read paper.

Reference:

Novotny, V., Miller, S., Baje, L., Balagawi, S., Basset, Y., Cizek, L., Craft, K., Dem, F., Drew, R., Hulcr, J., Leps, J., Lewis, O., Pokon, R., Stewart, A., Allan Samuelson, G., & Weiblen, G. (2010). Guild-specific patterns of species richness and host specialization in plant-herbivore food webs from a tropical forest Journal of Animal Ecology, 79 (6), 1193-1203 DOI: 10.1111/j.1365-2656.2010.01728.x

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On Ants and Elephants: Clash of the titans

Now and then you come across a research paper that changes your perspective, and offers you a view into ecological interactions that, at first glance, seem unbelievable.  Such was the case last week in my graduate class in Forest Entomology.  One of the students led a discussion of a paper titled “Defensive plant-ants stabilize megaherbivore-driven landscape change in an African savanna”.   It’s an elegant paper about the interactions between elephants, ants and trees.  It was published in Current Biology in 2010.

This is a plate from the paper showing a "grazed" tree

This is not a particularly new story – it was actually discussed on a number of blogs quite a while ago:

Here: http://blogs.scientificamerican.com/observations/2010/09/03/wee-ants-protect-african-savanna-trees-from-elephants/     …by the way, that journalist failed to spell the primary author’s name correctly.  Unacceptable…

…here, http://www.sciencedaily.com/releases/2010/09/100902121053.htm

And Conservation Magazine did a write-up on the research:

Here’s a quote from that article:   “Pitting ants against elephants doesn’t seem like a fair fight. But according to a study in Current Biology, these humble insects can act as mighty “bodyguards” that prevent elephants from munching trees on the African savanna

The take-home message from the research is something like this:

Elephants suppress tree cover in the Savanna, and their intense feeding behaviour can alter the landscape composition of trees.  However, some species of trees, on some soil types, have symbiotic relationships with ants (genera Crematogaster and Tetraponera).  Though a series of well-designed experiments (i.e., manipulative and observational), the authors (Jacob Goheen and Todd Palmer) show that the ants are able to effectively defend some trees from these mega-herbivores and thus are indirectly affecting the tree composition at a landscape scale.  It’s a story of ants, elephants, and the Savanna landscape.

For a visual, here’s a nice photo of Crematogaster ants from Florida (thanks to Alex Wild for permission to post his image here)

Crematogaster ants (C) Alex Wild

So, what makes it worth revisiting this paper, now, and why is this paper and topic particularly interesting?

Well, two things came up in the discussion last week that have prompted this post.

1) It’s “Clash of the Titans” NOT “David and Goliath”.  Some of the aforementioned posts seem to like the whole “little ant takes on those big elephants” angle.  I just don’t think that is an appropriate analogy.   To be fair, an individual ant is certainly small compared to an elephant (and the authors of the research paper are quoted along these lines), but in terms of overall biomass, ants rule.  For example, it is argued that ants make up 15-20% of terrestrial animal biomass!  Furthermore, globally, I would argue that ants play a much more important functional role in many ecosystems than most vertebrates (although perhaps a proportionately greater effect in tropical regions).  Don’t misunderstand – I love elephants as much as the next person… but they are not the Goliath in that article.   In this paper, the Goliath was always the ants, and Goliath wins.

2) Another interesting point came up in our discussion.  The story is fascinating, the science is strong, and to the broader community of biologists/ecologists, it was new.  However, to the local people that live with and observe these interactions everyday, it’s probably not surprising, nor is it likely anything new.  It’s one of those cases of a ‘stunning’ discovery that, when speaking with natural historians, and people that live in proximity of the study area, may not actually be ground-breaking.  Let me be clear: I am NOT saying this shouldn’t be published, nor am I criticizing the science of this paper.  Instead, I wish to merely point out that there’s a good chance that behind these types of studies are probably a group of people who may find it quite surprising that a bunch of scientists are getting excited about an everyday, common occurrence.  This is something to keep in mind as we work to publish our latest, newsworthy results.

Here are some more links:

One of the authors (T. Palmer) for this study writes science blogs for the Huffington Post: http://www.huffingtonpost.com/todd-palmer-and-rob-pringle

And if you like ants, go here and browse: http://www.alexanderwild.com/

How to review a scientific paper

Last week’s post focused on WHY it’s good to review papers.  This week, the focus is on HOW to review a paper.  By “paper” I mean a manuscript resulting from primary research, submitted to peer-reviewed scientific journal.  The ideas and opinions here are drawn from my own experience in the fields of ecology / entomology – not all the comments will apply to all fields.

Reviews of a research paper will vary tremendously depending on the experience and expertise of the individual, the research discipline, and depending on what people think a ‘review’ ought to be.  For example, reviewers sometimes approach a manuscript as if they were copy-editors, and spend a lot of time and energy fixing grammar, sentence structure, and other stylistic / editorial issues within a paper.   This is not a productive use of your time – these things can be done by (paid) copy-editors further along in the publication process.  Instead, a good review should (i) focus on the scientific quality, (ii) ensure that the overall paper delivers the research message appropriately, (iii) assess that the manuscript fits within the aims and scope of the journal, and (iv) confirm that the manuscript is aligned with the field of study.    Of course, a readable and clean paper makes this much easier (another reason authors should make sure their manuscripts are error-free, and readable, prior to submission!).

For most reviews, two reads of a paper are required.  My advice is to read a manuscript from start to finish, and then walk away for a day or so.  This lets the material settle and work away in mysterious ways, out of your conscious thought.  Upon return, do another read, only this time write down positive and negative comments about the paper, using the following list for guidance:

Big Picture: What is the conceptual framework, and is it a good one? Do the author’s make a convincing argument about the broader rationale behind their research? Do they use (recent and old) literature effectively?

Research Question: One of most important parts of a paper is the section dealing with the overall research question / hypothesis / prediction.  Think carefully about this section: it must be clear, concise, logical, and ‘testable’. Everything in the rest of the paper must relate directly to the objectives of the study.

Methods:  fundamentally, do they make sense?  Remember, the scientific method is about repeatability of an experiment: could you do the project using the described methods?  Are the methods up-to-date? Where might they lead to errors or biases?

Data management/analyses:  How were data managed after they were collected?  What was the overall data management and analysis strategy? What are the response variables measured and what is the unit of statistical replication?  What test(s) did the authors complete?  What assumptions do these tests require and did they do tests to ensure they did not violate the assumptions?  Are ‘controls’ required, and if so, what are they and how are they dealt with in a statistical framework?

Results: are the figures/tables presented in an effective manner?  Are they clear and relate directly to the research questions? Do they make sense in light of the data analysis strategy? What’s missing?  Is their supplementary information (is it accessible, elsewhere)?

Discussion:  a discussion section of a paper is meant to be somewhat speculative, but it should not wander uncontrollably from the data and results.  Does the discussion section suggest alternative explanations for patterns, or do the author’s merely use this part of their paper in an act of self-congratulation? Do the author’s point to some of the flaws in the study and offer ways to improve the experiment?  Do the author’s return to the overall (broad) conceptual framework and revisit this in a meaningful way?

Literature Cited:  did they miss important papers?  Are there any unusual trends? (e.g., too many citations of unpublished works or personal communications, too may citations of the author’s friends, ignored old literature, depended too heavily on old literature?)

Working through this list will help come up with the key issues with a manuscript.  In addition, it may be useful to think about some of the following broader points:

• Does the paper move the discipline forward in a new and exciting way or is the work largely confirmatory?

• Is the research driven by a ‘cool’ system, or a specific taxa, ecosystem or place, or is the research driven by a strong research question and the system/taxa/place are secondary?

• Does the research make linkages to larger social/economic/environmental issues?  Should it? Do the author’s use larger environmental issues or politics just to ‘look important’, or are the linkages necessary and meaningful?

• Is the work original or a re-hashing of someone else’s approach (perhaps in a different system or with a different model organism)?

• Is the work appropriate for the journal?

This last point is quite important – your review must be within the ‘context’ of the journal, and of your discipline.   You don’t want to review a natural history paper in a focused entomological journal in the same way that you would review a paper about theoretical mathematical models for a general ecological journal.   Always keep the journal’s audience in mind.

In theory, you should now be ready to write your review and submitting it to the journal.  Submitting your actual review typically involves three tasks.  For most journals, reviewers are asked to provide comments for the authors, confidential comments to the editor, and reviewers are typically asked to rate the manuscript.

The first task, and the one that takes the most time and energy, is to write all your  comments that will be forwarded to the authors.  Try to keep your comments and writing concise, and clear.   In general, a review of 1-2 pages (single-spaced) is a good goal – most reviews are much shorter than that, but if you follow the points discussed above, you will be providing a very helpful and high quality review, and it will take you more than a page to do so.

Always start your review with a quick one-paragraph summary of the work (this shows that you read it!).  You should then try to provide authors some positive feedback before delving into (constructive) criticisms.  Always keep the tone of your writing even-handed, and constructive.  Don’t be mean (this sure won’t help your scientific karma!).   I recommend first providing general ‘big picture’ criticisms, and then follow with a section of ‘specific comments’ – this can be where you can highlight those stylistic/editorial issues that have been uncovered.   In general, it is useful to provide a numbered list of your criticisms (you may even wish to use subheadings, e.g., taken from the list above) – this helps authors respond to your comments in a clear manner, and also assists the editorial board for the journal.

Without experience doing reviews, it is likely that a good review will take a long time to complete (i.e. > half a day).  However, it does get easier, and I believe that after practice, a good review can be completed within a couple of hours, provided you know the discipline well.

The review, as I have discussed it above, is really for the authors, and is to help the Editor(s) make a final decision about a manuscript.  In your comments to the authors, you must avoid making any statements about whether the paper should be published (or not) – this is not the job of a reviewer!  In fact, these kind of statements can place an editorial board in an awkward position if reviewers make claims about whether a paper is publishable – a journal may have to refuse (good) paper simply due to page constraints, or the fact that a paper may be a poor fit within a particular issue.  The Editors (and publishers) make all these final decisions, not you!

The second task is when you provide confidential comments to the editors, and this is a place where you can be more candid, and can certainly make your opinions known about whether the work is publishable.

The third and final task is where you get to score or rate the paper.  This should align with your actual review.  For example, it’s pretty bad form to be highly critical in written review and than rate the paper as ‘acceptable in its present form’.  Or, providing and short and positive review should not typically equate with a rejection!

The style of these scales vary tremendously, but most having wording something like this:

-Accept in its present form with no revisions

-Accept after minor revisions (re-review unnecessary)

-Accept after major revisions (after re-review)

-Reject but encourage re-submission in another form (e.g. short paper)

-Reject

If your review uncovers more than a couple of significant criticisms, it’s likely you will select Major revisions.  Minor revisions are typically more related to specific concerns with specific sections of the manuscript and minor revisions generally do not require authors to rework sections of their paper (e.g., new analyses, different presentations of results, rewriting a discussion).

Now you’re done.  Phew. Take a break until the next request comes in…

Review a paper, it’s worth it.

Although it takes precious time, it is important to review papers – it keeps the wheels of academia churning away, and without reviewers, the peer-review process is dead and peer-review is the cornerstone of scientific publishing.  However, the review process is typically anonymous so why would anyone review papers?  What’s the benefit to an individual?  Why not just cheat the system and publish papers without ever reviewing papers?  Here are six arguments about why all researchers should review papers.

[ an aside …. academic publishing is undergoing significant changes these days, and there are other models that may eventually replace the current peer-review system.  But all that is discussion for some future blog post! ]

1. Responsibility.   If you publish papers, it is your responsibility to review papers.  A constructive and high quality review improves your own work and you owe it to other authors to provide the same (or better!) service.

2. Learning.  You can learn a lot from reviewing papers, including new techniques and methods (e.g., analytical, field and laboratory methods). Reviewing papers keeps you up-to-date on the literature within your discipline.  I find it exceedingly difficult to keep on top of current literature, in part because of the proliferation of journals in recent years, and because life is busy. Reviewing papers in your discipline helps you understand what other scientists are reading and citing, and can often point you to literature you would have otherwise missed.  Reviewing papers can also show you what NOT to do with your own research!   I am often amazing and sometimes stunned at mistakes uncovered when reviewing papers, and this in turn allows for a more critical approach with the research coming from my own laboratory.

3. Benchmarking. Reviewing papers allows you to stay on top of current theories, hypotheses, and controversies within your discipline, which allows you to embrace a stronger conceptual framework for your own research.  This allows for a very current and often insightful benchmark for your own research.

4. Personalities.  Reviewing provides you with a nice window into the ‘personality’ of science and the ‘personalities’ in science.  It allows you to interact with editorial boards, and allows you to read what people in your discipline say to editors (i.e., in their cover letters), and can provide you important insights about the personalities of leading researchers in your field.  In the competitive and often political world of scientific publishing, such insights can be useful as you maneuver through the peer-review process and work on your own manuscripts.

5. Validation.  Being asked to review a paper means that someone out there values you and your work.  ‘They’ have decided that you are one of a select few researchers who has the skill set needed to evaluate a piece of primary research. Feeling valued comes far too infrequently yet is important for morale and overall well-being (read: take it when you can get it).

6. Scientific karma.  What goes around comes around.  Cliché, perhaps, but I believe firmly that you can do yourself a lot of good by reviewing papers.  It can be a small world, and important personalities in science will remember you if you do a high quality review.  Continually refusing to do reviews will also put you in a negative spotlight, and people will also remember this.   Being collegial, and being willing to share your expertise, is a responsibility, and in many ways, a gift.  Good things will happen if you help out your scientific community. As an anecdote, when I was gearing up for tenure at McGill, I provided a review for the journal Ecography.  My review was selected as being high quality, and valuable, and the editorial board of that journal sent me a mug, and a nice letter of thanks (yes, a REAL letter!).  I put a copy of that letter into my tenure dossier to illustrate that the broader scientific community recognizes the value of this kind of contribution.  I do not know if that letter made any real difference in the tenure process at my institution, but I’m quite sure that it didn’t hurt.

The journal Ecography

To finish with a couple of practical questions:

How much reviewing should you do?  This is a tricky question.  When starting out your career, I think reviewing at least as much as you publish is a good idea.  Later, and as your skills at reviewing become more efficient, I think it possible to review perhaps one paper per month.  That being said, when a review request comes along that is precisely in your area of expertise, do not refuse!

Is it OK to say no? If you are under tight time constraints, if the area of research is beyond your expertise, or if you have a clear conflict of interest that will interfere with your ability to provide an unbiased review, you can and certainly should refuse a invitation to review.  However, please do the editor(s) a favour and suggest other potential reviewers that you think would be qualified.

How do you go about reviewing a paper in a timely and efficient manner? That is discussion for a future blog post!

Now, go check that e-mail… you may have a review request waiting.