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Writing and Publishing Scientific Papers

Gábor L. Lövei

Part III. Publishing the paper

20. How to Submit a Manuscript

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1Once you believe the manuscript is ready to be sent, it is still worth being careful. Now, your natural desire is to see your work published as soon as possible; however, from this point, the manuscript will have to be handled by several people before publication and, therefore, extra care on your side will speed things up.

Electronic Submission

2Many journals, and most of the journals published in developed countries, require that you submit your manuscript electronically. This takes time — sometimes a lot of time. Prepare your manuscript carefully. Several journals provide you with a checklist (see Box 14 for an example) — it is a good idea to save one of those and use it, even when the target journal does not have one. Once all the parts are together, you should first register as a user on the journal website. Do this with thorough attention, checking all the questions or options, as well as what you authorise the website to use your data for.

Box 14. Pre-submission checklist
1. Is the manuscript complete? Does it contain all the necessary parts, arranged in the necessary order?
2. Are all word limits observed? There can be limits by number of words or even number of spaces on the total article, title words, abstract, highlights, key words, and the running title.
3. Is the summary well structured, informative?
4. Are the necessary structural requirements observed? These can include primary-secondary-tertiary headings, placements, numbering, etc.
5. Does the numbering of figures and tables correspond to the sequence of being mentioned in the text? Did you indicate the desired position of all figures and tables?
6. Are all listed references cited in text and all that are cited in text have the full bibliographic reference listed?
7. Are bibliographic details correct and in the appropriate format?

3Once you have registered and chosen a password, you should log in, and start the submission process. The process is step-by-step, and largely self-explanatory. Usually, all steps are obligatory. During electronic submission, the submitting author must do most of the clerical work that used to be done by the journal personnel. The submission process is tedious, often non-intuitive, and always takes a lot of time. Additionally, it depends on the speed of your Internet connection. The publisher wants you to believe that this system will allow you to track the path of your manuscript — but it is not actually much help. The editorial team will not want to hear from impatient authors immediately post-submission: “Leave us in peace, we are working on your manuscript”. The author, preferably, would like a daily update on her manuscript. Here the editor’s interest prevails — for months, all you may see is that your manuscript is “in review”.

4When submitting (unless the journal requires otherwise), combine your manuscript into one file. The figures do not have to be in their finest resolution, especially if this necessitates the use of different programs and file types — it is much easier if everything is together. You can attach figures to a Word document and, if possible, do so. When naming the file, include the corresponding author’s name.

5During the submission process, you should normally enter all the authors with their affiliations, the title, abstract, keywords, length of your manuscript, suggested and non-preferred reviewers, and various other bits of information that are sometimes not easy to link with your actual manuscript. Finally, you upload the manuscript itself, which will be converted to a pdf file. You will have to open and approve this. Only then will the manuscript be finally submitted. It is a good idea to save a copy of this pdf file.

6Do not forget about the accompanying letter. This can sometimes be added as a separate file — but, even if not, there will be space to send a message to the editor.

The Accompanying Letter

7Never send anything without an accompanying letter. This is not only a matter of courtesy; it is in your, the author’s, best interest to attach a cover letter, as it can speed up the handling of your manuscript. Editorial offices often resemble organised mayhem; they may handle several journals, and sometimes receive hundreds of manuscripts per day. Some are first submissions, others are annotated manuscripts, sent back by reviewers, still others are revised versions, or final manuscripts, sent by authors. The accompanying letter helps the office to handle your manuscript more effectively — and this means processing it more speedily.

8In the accompanying letter (see a sample in Box 15), state the following:

  • What is being submitted? Is your work a new submission, a revised manuscript, or a final version?
  • For which journal? Offices may run many journals and, from the title, it may not be obvious which one your work has been submitted for. You cannot ask the office to decide where your manuscript could fit; you have to make that decision (see Chapter 4).
  • Declare if any part of the work has previously been published and, if so, which parts and where? If it was presented as a talk, or a poster at a conference, it is also worth mentioning. An abstract in a conference volume is not a publication, but may be worth a mention. Be careful with Internet publishing — while many journals allow pre-publication in an open manuscript depository (such as BioRxiv:​), others even if you put the manuscript on your personal website, consider it published, and will not touch it.
  • Indicate the name and address of the corresponding author. Even if this is already noted on the manuscript, redundancy here is acceptable, even welcome. The editor does not then have to look up the address from the manuscript. Also, indicate if the corresponding author will have a different address during the next 6-8 months, even if temporarily. This will help the editor to get in touch with the corresponding author without delay. Do not go overboard — there is no need to let the editor know when, and where, you are going on holiday for 2 weeks. However, if you will be away from your workplace for more than a month, it is worth letting the editorial office know this, and give the temporary address. Even if they cannot reach you, at least they will know the reason for your lack of reply.
  • You should also state the co-authors’ agreement. This declaration will have to be repeated when the paper is accepted and the copyright form is signed. Nevertheless, it is also required here.
  • State the uniqueness of the work, indicating that this manuscript contains new, unpublished results.
  • State that the work is not under consideration elsewhere. You cannot send the same work to more than one journal at any one time.
  • Finally, in one or two paragraphs, argue for the merits of the manuscript. Journals have become so overloaded that the first decision is often made by the editor, who, after a quick scan of the paper, decides whether the manuscript should go out to reviewers, or be rejected without review. Assist the editor by pointing out the major new findings in your manuscript, and provide reasons why it should be considered for detailed review. This summary should not contain sentences “cut and pasted” from your manuscript — rephrase them.

Box 15. A sample manuscript submission letter
The Editor
Global Ecology & Biogeography
17 May 2008
Dear Editor
Re.: Submission of a MS
Enclosed please find a manuscript by Magura et al. “Urbanisation decreases the diversity of forest specialists but not overall diversity in ground beetles (Carabidae)”. We would be grateful if this could be considered for publication in the journal “Global Ecology and Biogeography”.
This work reports results obtained in the international Globenet Project. The Globenet Project, started in 2000, is an attempt to find out whether urbanisation has a general impact on invertebrates in geographically different locations. The individual sub-projects have a common setup and methodology, creating the necessary pre-conditions for a synthesis that has not yet been done. In this manuscript we attempted to examine one general hypothesis: that urbanisation would be detrimental to biodiversity. We believe the specific new aspects of our work are the following:
1.) We analysed patterns of diversity by using diversity ordering by the Renyi diversity index, which is not commonly used in ecology, although it has recently been recommended by Southwood & Henderson (Ecological methods, 2000) as a preferred way to compare diversity trends. We demonstrated that even by this synthetic measure, diversity does not decrease as urbanisation intensifies.
2.) As a new approach, we separately analysed the forest-associated species. If only the sub-assemblage containing species linked to the original habitat (forest) is considered, the diversity ordering indicated a decrease along the urbanisation gradient.
3.) Finally, we found that while urbanisation has a documented homogenising influence on the flora and fauna of cities, this does not seem to happen in ground beetles.
We believe that the results briefly summarised above reveal so far hidden effects of urbanisation on carabid assemblages, contradict some accepted wisdom, and represent an advance in the understanding of the effect of urbanisation on biodiversity. We believe that Global Ecology & Biogeography is a suitable forum for this research.
This is a first submission, containing unpublished information, and is not under consideration elsewhere. All co-authors have read and agreed to the content of the manuscript.
Please address all correspondence to me at the address indicated on the manuscript. Thank you in advance for your editorial assistance.
Sincerely yours
Submitting author

Submitting by Mail

9Today, electronic submission is the usual practice, although a few journals still operate “on paper”. To these journals, you have to submit your manuscript by mail. Your manuscript will be ten or more pages, and you are routinely requested to send three or four copies. This makes it a rather bulky shipment. If it is in a flimsy envelope, this may tear; parts of the manuscript can get damaged, arrive in battered condition, or lost; all this may slow the handling and publication process. If you do have to submit paper copies of your manuscript, use a strong envelope, possibly a padded one, and make sure the edges are strong enough or protected by extra tape. You can even use duct tape to strengthen the sides and corners — this is where a bulky envelope will be most easily damaged. Carefully separate the different copies — but do not staple unless the journal specifically requires you to do so.

10Send the manuscript by air mail (where required) and pay the appropriate postage charges. Mail services often downgrade mail with inappropriate postage and your manuscript may spend weeks or months, instead of days, in transport.

11Keep a hard copy for yourself. This will be your insurance against computer crashes and other unforeseen complications. This will also be the proof of the existence of the work — in many cases, electronic copies are not accepted as proof.

12Check that you have the required number of full copies. It is probable that different parts of your manuscript (for example, the text and figures) will be created using different programs and, thus, it is not always sufficient to print X copies of the same document. Be meticulous. Many journals provide help by offering a pre-submission check-sheet — use these.


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