This post is part of our blog series The Unwritten Curriculum. Previous posts include How to Apply for Grad School in Ecology and Evolution, Demystifying the Qualifying Exams, Paths to Ecology - Part I, and The Grad Student Life. Our goal is to help those considering graduate school in ecology and evolution to see how it all works, from our own experience. This post is by third-year Stanford Biology PhD student Lisa Couper and fifth-year Stanford Emmett Interdisciplinary Program in Environment and Resources PhD student Marissa Childs.
Getting ready to submit your first paper? Congrats! How does this process work? Do you just email a word doc of your paper to a journal with the subject line “here it is”? Not exactly. In submitting our first papers, we -- graduate students Marissa Childs and Lisa Couper -- were surprised by what was required and how long the process took. For context, we have primarily submitted to ecology, biology, infectious disease, and general interest journals. In the Q&A style blog post below, we try to shed some light on what to expect when submitting your first paper.
Q: What is involved in submitting a paper?
Tl;dr: your paper (“manuscript”), (usually) a cover letter, author information, and names of suggested reviewers
Your paper (“manuscript”). This usually consists of a pdf, word doc, or LaTeX doc that includes a title page, abstract, main text, figures, tables, references, and (sometimes) supplemental information. Typically the manuscript will be double-spaced, with line and page numbers, and figures/ tables at the end of the document. The exact formatting will vary based on the journal to which you’re submitting (more on that later) but often for the initial submission, the format isn’t super important. However, the length of manuscripts and the number of figures and tables you can include differ depending on the journal, so you’ll often need to know where you want to submit well in advance of completing the manuscript.
Cover letter (not required by all journals). Cover letters are a roughly one page letter to the editor where you explain why your manuscript is important, timely, interesting, relevant; how it would contribute to the field; and how it would be a good fit for the journal. These help the editor decide whether to send the manuscript out for review. They are not read by the reviewers. Typically the cover letter is something you either upload as a word doc/pdf or copy into a box in the submission portal.
Author information. You’ll need some information about all the authors on the manuscript. Depending on this journal, this may include emails, institutional affiliations (i.e., their University/ department), physical addresses, and ORCID ID (a unique ID for all researchers that links their identity to their publications to eliminate any confusion around people with the same names). These will usually be included on the manuscript title page or uploaded in boxes in the submission portal.
Reviewer suggestions. Journals will typically ask you to suggest 3-6 people who could peer review your work. This is often optional, but may be in your best interest as it can speed up the process and give you some say in who sees your manuscript. These will be people who are experts in the topic of your paper, but are not directly connected to the work or the authors. For example, you can’t suggest a postdoc in your lab, even if they weren’t on the paper as this poses a conflict of interest. Similarly, a professor couldn’t suggest someone who they frequently collaborate with, even if they weren’t authors on that particular paper. Similarly, you may also be required to suggest a handling editor. You can also sometimes provide names of “opposed reviewers” -- people who you do not want to review the manuscript (e.g., because they have a history of providing unfair reviews), but this is less common to do and should be done sparingly. In addition to suggested reviewers, some journals ask you to identify an editor at the journal who can best handle your submission. The editor names will be listed somewhere on the website and, as with the suggested reviewers, you may have to do some digging to figure out whose specialty most closely aligns with the topic of your manuscript.
The above are the main components, but some smaller or less common components of submitting a paper include:
Information about data/code availability. You may be asked to include a statement about the availability of the data and code required to reproduce the results in the paper either in the manuscript itself or as additional information provided when you’re submitting. This may involve uploading data to a public repository such as Dryad prior to submission. Many journals now require that you submit code used for all analyses, so be prepared to clean up your code and make it available to the journal or on a repository like GitHub.
Preprints. Many journals now ask if the paper is currently posted on a pre-print server (e.g., bioRxiv or Authorea) and/or offer to post it as a preprint on their server. Most journals now allow (some strongly encourage) papers to be uploaded as preprints prior to publication in a journal (more on this below)
Key words. Some journals ask you to provide 3-6 key words for the manuscript. These may include species names, central themes/concepts (e.g, thermal ecology, dilution effect) and/or a key method used in the paper (e.g., RNAseq, structural equation model). Depending on the journal, you may be asked to list these on the title page of the manuscript, or enter it in a box in the submission portal.
Q: How much time will this take?
Tl;dr forever.
As you can see from the above list, there are a lot of components involved in submission. Beyond writing and formatting your manuscript for submission, preparing the cover letter, list of suggested reviewers, etc. can take at least a few hours, but it can take substantially longer if you’re required to upload data/code/protocols. Even with all of this prepared beforehand, moving through the journal submission portal (i.e., uploading your files, filling out the questions, checking and re-checking (triple checking??) the proof (the compiled version of your manuscript generated during submission) can itself take a few hours. This isn’t meant to discourage you though! It is just a heads up to budget some extra time for this process. You will get faster at it as you submit more papers.
Q: How much does it cost?
Tl;dr It could be $0. It could be $5000.
You should not be charged any fee to submit your paper. However, there may be a cost to publish your paper if it is accepted for publication, depending on which type of access you choose. Under the traditional/non-open access model, authors typically aren’t charged to publish (though some journals do require page charges or charges for color figures), but readers must pay a subscription fee to access the article/journal (e.g., through libraries). However, under the open access model, the article is free to readers but researchers pay a publishing fee after acceptance. This fee will vary based on the journal, and sometimes the number of color images/pages, but can range from several hundred to several thousand dollars. You’ll probably want to discuss access options with your PI beforehand as some research funding requires open access publishing, and regardless, your PI may have budgeted funds to cover publishing costs. Some journals also have fee waivers if you do not have funding to cover publication fees (especially society journals, if you are a member of the society).
Q: When will I hear back?
Tl;dr A couple days (although that's usually bad news) to a few months. You can usually check your manuscript status online (although this status may be cryptic).
This part can take a while, and depends on whether your manuscript is sent out for review. After you submit your manuscript, it will often first go through a technical check to make sure it adheres to the requirements for that journal and article type (e.g., is your manuscript double-spaced, does it exceed the word count or page limit, etc.). If there are any issues here (not super common, but can happen), you may hear back from the journal within a couple days. Assuming no issues here, your manuscript will typically go to a handling editor who decides whether to send it out for peer review. The handling editor may reject the manuscript at this point (a “desk rejection”), in which case, you’d typically hear from them a few days to a few weeks after you submitted. If the editor decides to send it out for review, they have to contact and secure reviewers who can take a few weeks to review the manuscript and send it back. After receiving the reviewer comments, the editor then has to make a decision: reject the manuscript outright, suggest major revisions (sometimes confusingly communicated as “reject and resubmit”), or suggest minor revisions. The editor will contact you via email to deliver this decision. If you are asked to revise and resubmit, you’ll sometimes get a deadline by which you have to get the revisions back to the journal in order to get the same reviewers. In short, this whole process can take weeks to months (sometimes over a year!), but you can typically see your manuscripts status in the submission portal. If you don’t hear back for a long time and your manuscript status is not changing, you can also reach out to the journals’ editorial office to politely ask for an update.
Q: What do I do while waiting to hear back?
If you haven’t already, you could consider uploading your manuscript to a pre-print server like bioRxiv. After about a day (for your manuscript to undergo a basic screening), anyone will be able to find and read your work! We won’t cover all the arguments for and against pre-prints here, but we’ve personally found some benefits of posting pre-prints include a) you can begin gathering community feedback on your work right away, b) it can boost your morale to know your work is out there in some capacity, and c) you can list the pre-print on your CV so people can actually read it (much better than just listing it on your CV as ‘submitted’).
During this time you’ll also want to stay on top of the literature related to your manuscript so you can incorporate any new findings and references in your next version. I (Lisa) typically start a google doc where I list any new, relevant papers that came out after submission and the additions or changes I’d like to make based on the new information.
Post-submission is also a great time to return to all those side projects and other tasks you may have let fall by the wayside as you prepared to submit your paper! Since the manuscript is out of your hands for a while, you can turn your attention elsewhere for a few days/weeks/months!
Q: What happens when I hear back?
This depends on the decision. If you get a revise and resubmit, you revise! Reviews can be (emotionally, mentally, technically, (physically?!)) difficult and sometimes it’s worth reading them and sitting on them for a while before you start the revision process, but it’s helpful to think of the reviewers as trying to improve the work. You can read this https://eos.org/editors-vox/stuff-my-reviewers-say to help you feel better about the reviews you get. Also this https://shitmyreviewerssay.tumblr.com/
If you get a rejection, you find another journal and start again. Some great papers just take a while to find the right journal for them. If you get reviews with your rejection, it’s worth trying to incorporate their feedback into the version you submit to the next journal. Some rejections within a family of journals may offer the option to resubmit the manuscript to another journal within the family. For example, if you receive a rejection from Ecology, you may be offered the option to resubmit to Ecosphere since these are both ESA family journals (other ESA journals include Ecological Monographs, Ecological Applications, and Frontiers in Ecology and the Environment). This does not guarantee that your manuscript would get into the next journal (or that the suggested journal is necessarily the best fit for your work), but it can speed up the submission process since you typically won’t need to reformat the manuscript or enter all the submission information again.
