How to write a research article in ecology

I wrote this for my students last year. They are thoughts I have to constantly remind myself of in my own writing. They are far from universal. I hope they help.  Jeff Wesner (21 August 2017)

Readers and reviewers are desperate to learn new and exciting science. They are not desperate to tear your science apart (with few exceptions, who no one likes). Write for the first group, not for the second.

Readers and reviewers will always know less about your study than you do. Your writing should be crystal clear in its justification (i.e. why the study is done and who cares). That justification is obvious to you, but is not obvious to almost anyone else in the world. As a reviewer, I often get stuck in the first few paragraphs, wondering why I’m spending time on this paper.

Here’s a hypothetical example of a vague justification for research on subsidies:

Not crystal clear – “Subsidies are clearly important for ecosystems (cite), though not always and in every case. We need to better understand their effects under X conditions. We measured the effects of d on insects.”

How to fix it?  – Each of the above sentences would need its own paragraph. For example, you’ll need to convince most readers that subsidies are important (paragraph 1), why we need to see another study of them under X conditions (paragraph 2), what the importance of d is (paragraph 3), and what your hypotheses are (paragraph 4). Even though these things might seem clear to you and me, they won’t be to readers. This is the job of your introduction, to use four paragraphs that get a point across that makes sense to you in four sentences

Papers are single ideas

An individual paper is a single idea that takes 5000 words to get across. All words should be in service of this single idea. Though it pains me to write this, one way to think about it is to ask – If someone tweeted this paper, what would they say about it in 140 characters?

Loose goals for the structure of your paper:

Abstract – ~200-250 words

  • No detailed methods, No stats (e.g. p-values)
  • 1-2 sentences of background
  • 1-2 sentences on your approach (“To test these hypotheses, we measured the effects of X on Y in artificial ponds.”
  • 2-3 sentences of results
  • 1 sentence that summarizes the importance of the results

The abstract will always feel sparse to you, because you know all of the details behind the study, and all of the cool things left out. But the abstract is key. It’s an invitation to read more, not the final story. It’s your elevator pitch.

Introduction – 4 paragraphs.

First paragraph sets the scope. Don’t limit yourself. Write for all ecologists, not just someone interested in freshwater, or in plants, insects, or bacteria, but anyone interested in how the world works. That usually means you need to tie your study to a key concept in the broader field (energy flow, predation, food webs, pollution, biodiversity, co-evolution, etc.). Those are broad concepts that transcend ecosystem types, scales and organisms. Start there, then narrow down.  

Fourth paragraph is simply a description of what questions you asked that addressed the big ideas in the first paragraph. Sometimes more than four paragraphs are required, but rarely. Aim for 4 and add only if necessary.

Methods – variable, but it should be clear how each of your methods relates to the questions you promised in the introduction.

Results – variable, but they need to explicitly answer the questions you laid out in the introduction. This is the #1 reason that papers often get bad reviews or rejected. They set up some great question, but don’t answer it in the results in any explicit way (or have a fatal flaw in the methods). Don’t make readers search for the answer. Give it to them.

Great results sections can be as short as a single paragraph (~4 sentences). When papers report every single p-value they came across (or credible interval), it signals that they aren’t sure what they’re studying. Report everything, but think hard about what to put in the supplementary information versus the actual paper.

Discussion – 4 paragraphs (on average). Common pitfalls of discussions:

  • Simply rehashes the results in more flowery language
  • Doesn’t tie the results to the main questions in the introduction.
  • Repeatedly says things like “We found such and such. It was similar to what so and so found, but not similar to what so and so found. [next topic].” The problem here is that there is no context. What are we supposed to learn from these similarities and dissimilarities to others work?
  • Doesn’t state the most important results. Don’t leave those up to the reader to interpret. State them explicitly.

Discussions are hard work, and the hardest part is knowing how your results fit into previous knowledge, but also being explicit about what we’ve learned now as a result of your work. How did your study shed light on the contrasting results you mentioned?

Discussion approach to consider:

Start with the following sentence. “The most important finding of this study is….” That forces you to be confident in the importance of your work, but also sets the stage for the reader, who will really want to know why they’ve invested time in this paper. What do you want them to remember? They may disagree with what is most important in your work, but at least they know where you stand.

Writer’s block

  • Will not be fixed by staring
  • 1 – Take a walk
  • 2 – Sleep
  • 3 – Read, read, read. The most effective tonic for my own writer’s block is to read other papers; typically a seminal paper that inspired the work is best. It takes a lot of effort to shut down your mind and focus on someone else’s work for a bit. Go someplace quiet, commit 2 hours for the paper. Thoughts will come that help your writing. I promise.

Read your paper out loud. Does it sound as if someone would talk that way (scientifically speaking?). It should.

Don’t utilize “utilize”, just use “use”.

You will write lots of things over your career. Any single paper is like an idea in a conversation that spans decades. Get it out and into the conversation, then move on to the next topic.


You will get harsh reviews. They will not matter to your career. Everyone gets them and it hurts every time. Chances are that a) famous person X didn’t really review your paper, b) even if they did, they wouldn’t remember it when you’re talking to them at a meeting, and c) all reviewers are human and may have given a different opinion at a different time. In other words, harsh reviews can be harsh depending on the reviewer’s mood – did they just give good reviews to a few other papers? Maybe they felt they weren’t careful enough on a previous review. Maybe they just got a really bad review themselves. Maybe their mom just died. Maybe they have no time for this review they signed up for 5 weeks ago and for which they’re now getting harsh reminder emails from the editor so they spit out a review that is not as careful or nuanced as they intended. They’ll do better next time. Promise. Maybe they’re just terrible people (some are). Reviews are a snapshot of the quality of the work and also the mindset of the reviewer (and editor) at the time. I promise, the next journal will give completely different assessments.


For better advice: see here, and here

Eric Sazama’s first article is published! Wolbachia in aquatic insects.

Wolbachia is a fascinating critter. It’s a bacterial genus that infects lots of arthropods, and does all kinds of things to them that make great headlines, like killing males or making them eat brains. However, it’s commonness is disputed, particularly among insects that live in rivers and lakes (i.e. freshwater insects). So in this study, Eric Sazama answered the question, How many freshwater insect species are infected with Wolbachia? See the answer here, for free.

Poll for USD grad students

Brianna Henry is an NSF Graduate Research Fellow!

Congratulations to Brianna Henry! Brianna is an undergraduate at Clarion University of Pennsylvania who was just awarded an NSF GRFP fellowship to conduct research on herbicides and wetland ecosystem ecology. This award is highly competitive – only 12% of the 16,500 submitted proposals were funded. She will join our lab at USD this summer, and we’re excited to learn what she discovers!

Welcome to Eric Sazama!

Eric joined the lab in Fall 2014 to pursue his M.S. He’s developing a fascinating project that will ask how Wolbachia, a widespread endosymbiotic bacterium, is distributed within aquatic insects. He will then ask how infection by Wolbachia might alter the ability for insects to complete metamorphosis, a key process in linking aquatic-terrestrial food webs.

Habitat selection paper published in Ecology and Evolution

Wesner JS, Meyers P, Billman EJ, Belk MC. Habitat selection and consumption across a landscape of multiple predators. Ecology and Evolution.

We tested whether egg-laying female insects could detect differences in predator community composition. Because some predators are more lethal than others, the ability to differentiate predator risk when laying eggs can have large fitness consequences. To test this, we allowed insects to oviposit in tanks that contained a native dragonfly (Ophiogomphus sp.) or a non-native trout brown trout (Salmo trutta). Predators were housed in isolated outdoor tanks either alone (single species) or combined (both species together). Predators were also caged to avoid direct consumption during colonization.

Surprisingly, insect colonization (number of larval insects after 21 days) did not depend on whether predators were present or not, regardless of community composition. However, follow-up consumption trials suggested that laying eggs in predator pools had clear negative consequences for larvae, particularly in trout pools, which reduced larval survival by ~47%. Thus, egg-laying insects either did not (or could not) detect differences in larval habitat quality.

Second metamorphosis paper accepted to ES&T! UPDATED

Kraus, JM, DM Walters, JS Wesner, CA Stricker, TS Schmidt, and RE Zuellig. In press. Metamorphosis alters contaminant transfer and diet tracers in insects. Environmental Science and Technology (open access)

We’re on a roll with metamorphosis at ES&T. Johanna Kraus, a Mendenhall Fellow at the USGS, led the way on this very important paper. It shows differential contaminant loss as insects metamorphose from larvae to adult. Some contaminants are lost, while others are retained. Further, some stable isotope tracers, like N15, also change during metamorphosis. The results have broad application to contaminant transfer in food webs, and the interpretation of stable isotope studies.

This paper was chosen as an “Editor’s Choice” by the American Chemical Society.
USGS Press Release