How To PublishScientific Papers
(in ecology and related fields)
(in high-impact journals)
(when you already have results)
Rubén Darío Palacio, Ph.D.
Science Director Fundacion Ecotonos
A scientific paper communicates research findings clearly and concisely.
A highly cited paper on the fragmentation
of tropical forests (> 470 citations)
The whole paper was written around this figure.
“I contend that English, even before mathematics, is the cornerstone of all good science”
— Corey J.A. Bradshaw
To be a scientist you must know how to write your research findings for a scholarly journal.
Basic structure of a scientific paper (I): The “Hourglass” model
[Link] The 5 pivotal paragraphs in a paper
Basic structure of a scientific paper (II)
Kliewer MA. 2005. Writing It Up: A Step-by-Step Guide to Publication for Beginning Investigators. American Journal of Roentgenology 185:591–596. American Roentgen Ray Society.
Structure over structure (I)
Just like in this example for radiology, you can reverse engineer the entire structure of a typical paper in your field!
Structure over structure (II)
Stick to the topic-body-conclusion scheme for each of your paragraphs
Determine the main message (central contribution) of your paper and select the results and methods supporting it. Then go for the discussion and introduction.
Montagnes et al. (2022) Finding your scientific story by writing backwards. https://doi.org/10.1007/s42995-021-00120-z
10 steps to writing a scientific paper(that I use myself)
1. Select figures and results.
2. Write the methods and results.
3. Write an outline for the introduction and discussion.
4. Write the last paragraph of the discussion.
5. Write the first paragraph of the discussion.
6. Write the last paragraph of the introduction.
7. Write the first paragraph of the introduction.
8. Write the abstract and craft the title.
9. Write a complete first draft.
10. Edit the paper until ready for submission.
Step ZERO is the most important: Determine the main message of the paper.
It started with the figures!
Figure 3 - Palacio et al 2020.
Plotted in Excel.
Figure 4 - Palacio et al. 2020
Plotted in Veusz – https://veusz.github.io
For the figures use any software you know!
Palacio & Clark (manuscript in preparation)
The last paragraph is
Bullet points for main ideas...
Follow this link to see a complete draft of a manuscript.
Follow this link to see a manuscript formatted for submission to a journal.
The Abstract (I)
How would you craft a title to explain animal locomotion in The Tortoise and The Hare?
The title should incorporate the main message of your paper. It is also a selling point to engage readers and get citations. Make it accessible yet accurate.
Figure 1. Doubleday and Connell (2017)
© Tullio Rossi
Peterson TC, Kleppner SR, Botham CM. 2018. Ten simple rules for scientists: Improving your writing productivity. PLOS Computational Biology 14:e1006379.
The KEY to staying motivated is to structure your writing!
Commit to a schedule. Create a timetable. Divide it into sessions and small chunks.
Dealing with Authorship (I)
McNutt et al. 2018 https://doi.org/10.1073/pnas.1715374115
Dealing with Authorship (II)
Authorship is complicated (read the above paper). It might not even be under your full control. Many researchers have had problems with authorship.
It is crucial to have a conversation of authorship for every research project with the potential people involved.
Also, get a sense of the role of First, Last, and Corresponding Author. E.g., Duffy (2017) https://doi.org/10.1002/ece3.3435
The Peer-review process
Response to reviewers (I)
Include the reviewer’s comments in full (I use blue color) and then respond. Note that I add the lines in the text that have changed, but also include them in the text.
Response to reviewers (II)
Always address each of the reviewer’s comments in full. If there are three reviewers, pay attention to all of them.
The editor’s will almost never accept your manuscript unless the reviewer’s are happy - which means you at least made an effort to improve your manuscript based on their feedback.
I was the unhappy reviewer!
The cover letter is your opportunity to explain to the editors why they should publish your work.
Be patient! Peer-review is slow.
When papers get accepted most journals will have an early view with citable DOI
(Digital Object Identifier)
You have your manuscript (the bull). After peer-review and depending on the journal, your manuscript will look different than you anticipated — while keeping the essence of your bull.
Expect peer-review to transform your manuscript
Rule 4: Brains Are Not Enough, You Also Need Courage
Rule 7: Believe and Doubt Your Hypothesis at the Same Time
Rule 8: Work on the Important Problems in Your Field
(you must know why your work is important)
Rule 9: Be Committed to Your Problem
This applies to getting published!
Drop modesty, Ask Yourself:What do I need to publish in a high impact journal?
We published this paper without budget and no PI (Principal Investigator). None of us had an extensive publication record.However…We knew we were working on an important problem.We were aiming to publish in a good journal.
Follow this link if you want to know more (in Spanish)
Rule 1: Read many papers, and learn from both the good and the bad work of others.
Rule 2: The more objective you can be about your work, the better that work will ultimately become.
Rule 3: Good editors and reviewers will be objective about your work.
Rule 5: Learn to live with rejection.
Rule 9: Decide early on where to try to publish your paper.
Google Scholar Top Publications
Read papers from the top journals in the world!
Top Conservation Biology Journals
And read papers from the top journals in your field!
“The diamond model has been successful in Latin America-based journals (95% of OA journals) following the emergence of large publicly-supported platforms, such as SciELO and Redalyc, and much less successful in other parts of the World.”
Get to know the Open Access publishing models
Another great journal (in Spanish): Ecología Austral (Q2)http://ojs.ecologiaaustral.com.ar/index.php/Ecologia_Austral
Platinum/Diamond OA Journals in ecology and evolution (shared by Ángela P. Cuervo-Robayo):
Q1 Diamond Access Journal:
Note: The diamond model is the ideal but most journals charge authors for open access to readers.
Tip: Many journals offer waivers (full or partial). Check for them in the journal’s website. I have gotten waivers, you can too! Example: https://www.springernature.com/gp/open-research/policies/journal-policies/apc-waiver-countries
Look for the waiver section! You might be eligible if your institution does not have funds for publishing.
Also choose journals that people in your field are reading!
Biotropica is Q3, but is highly regarded among tropical biologists. In this way you can get more citations.
My paper has been cited over 65 times (Up until May 2022)
Cited in several chapters of book “Ecological networks in the Tropics”. Key reference in frugivory review paper (Messeder et al. 2021)
Be aware of predatory journals!
Living with rejection (I): Not novel enough
Living with Rejection (II): Scope is too narrow
"You must keep sending work out; never let a manuscript do nothing but eat its head off in a drawer. You send that work out again & again, while you're working on another one. If you have talent, you will receive some measure of success - but only if you persist.”
― Isaac Asimov
Keep on the work! The results will come.
Want help publishing your next manuscript?
Rubén Darío Palacio, Ph.D.
Science Director Fundación Ecotonos
Contact me for editing services, or writing and publishing guidance: