Molecular Ecology

Author Guidelines

General Information
Molecular Ecology publishes papers that use molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. We discourage papers that are primarily descriptive and relevant only to the taxon being studied. Studies may employ neutral markers for inference about ecological and evolutionary processes, or examine ecologically important genes and their products directly. Molecular Ecology concentrates on primary research articles (i.e. Original Articles) but operates a flexible policy regarding other submissions, including Reviews, Meta-analyses, Opinions and Comments. We also publish articles on technical methods, computer programs and genomic resource development in our companion journal, Molecular Ecology Resources. We typically provide an editorial decision on new submissions within 4 to 8 weeks, and papers usually appear in print 6 to 10 weeks after receipt of the final manuscript.

Editorial Office
Managing Editor Dr Tim Vines and Dr Jen Gow
email: managing.editor@molecol.com

Molecular Ecology Editorial Office
6270 University Blvd
Vancouver, BC
V6T 1Z4
Canada
email: editorial.office@molecol.com
fax: ++ 1 604 822 8982

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Article Types
Molecular Ecology will consider several types of articles. Papers in all categories may, where appropriate, present Supporting Information for online publication.

Original Articles
Our principal function is to publish primary research papers. Such papers are reports of research projects that are complete to the extent that they yield valuable insights into topics within our coverage. About 90% of all papers we publish are in this category. Original Articles generally contain a Title Page, an Abstract (<250 words), Introduction, Materials and Methods, Results, Discussion, brief Acknowledgements, References, Data Accessibility, Author Contributions, Figure Legends, Tables and Figures, in this order. Original Articles have a limit of 8000 words per paper for all text (including title, abstract, keywords, references and table/figure legends), although exceptions may be granted in some cases. We generally prefer that they have separate Results and Discussion, but we will consider manuscripts where these sections have been combined.

'From the Cover' Papers
Our 'From the Cover' section contains papers of exceptional interest to a wide audience that address significant questions in ecology, evolution, behaviour or conservation. We will consider papers previously reviewed by other high impact journals, with the added innovation that we will utilize all documents associated with the previous review process. The use of these review materials does not guarantee acceptance or that the manuscript will not receive external review. However, papers with largely positive reviews from leading general science journals will receive immediate consideration for publication and may not require additional review. If the authors hope to avoid additional review, they need to revise the manuscript according to reviewers' comments and submit a cover letter describing these changes and explaining why their paper would be appropriate for publication as a Cover article in Molecular Ecology. Upon receipt, Senior Editor Bob Wayne will immediately review submissions for content and impact. Submissions that do not meet stringent standards will be returned at that stage without review, or they will be invited for resubmission as regular full papers.

From the Cover manuscripts must be brief and focused (4000 words or fewer) with up to five display items (tables and figures). Two colour figures will be published in print free of charge. Accepted articles will be highlighted on the cover and in the table of contents, and will frequently be featured in commentaries and press alerts.

NB We appreciate that authors of From the Cover papers are looking for rapid publication, and hence we will consider initial submissions that are not in standard Molecular Ecology format e.g., manuscripts in Nature, PNAS or Science format are welcome. Please note that articles deemed suitable for publication will need to be changed to Molecular Ecology format prior to final acceptance.

Opinions
We will occasionally publish articles presenting points of view that are relevant and potentially controversial as a means of encouraging debate. Such manuscripts may present speculative and provocative viewpoints, although they must be conditioned by the normal standards of scientific objectivity, and they will be subject to peer review. Opinion Articles should not present new data, and should be fewer than 6000 words for all text (including title, abstract, keywords, references and table/figure legends).

Comments
Comments on published papers, principally those published in Molecular Ecology, will be considered by the editors and published after consultation or peer review. Such manuscripts should be as brief as possible. A rebuttal by the original author(s) may also be solicited and published alongside the Comment.

Invited Reviews and Meta-analyses
The editors regularly invite review or meta-analysis articles from individuals who have major contributions to make to the field of molecular ecology. Authors may use boxes to provide additional information separate from the main text; the article should contain no more than five boxes, with each no more than 2000 words. All colour figures in these articles are published in print free of charge. We will consider unsolicited review or meta-analysis papers, but authors wishing to present such manuscripts should contact the Reviews Editor (Louis Bernatchez) in advance.

N.B. Molecular Ecology does not accept Short Communications for publication.

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Journal Policies
Policy on Data Archiving
Molecular Ecology expects that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, Gene Expression Omnibus, TreeBASE, Dryad, the Knowledge Network for Biocomplexity, your own institutional or funder repository, or as Supporting Information on the Molecular Ecology web site. Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future. Authors may elect to have the data publicly available at time of publication, or, if the technology of the archive allows, may opt to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information such as human subject data or the location of endangered species.

Authors are expected to archive the data supporting their results and conclusions along with sufficient details so that a third party can interpret them correctly. As discussed by Whitlock et al. (2010), this will likely "require a short additional text document, with details specifying the meaning of each column in the data set. The preparation of such shareable data sets will be easiest if these files are prepared as part of the data analysis phase of the preparation of the paper, rather than after acceptance of a manuscript." For additional guidelines on data deposition best practice, please visit http://datadryad.org/depositing.

Lastly, the utility of archived data is greatly enhanced when the scripts and input files used in the analyses are also made available. Given that scripts may be a mix of proprietary and freely available code, their deposition is not compulsory, but we nonetheless strongly encourage authors to make these scripts available whenever possible.

To enable readers to locate archived data from Molecular Ecology papers, we require that authors include a ‘Data Accessibility’ section after the references (see below for details). This section must be present at initial submission.

Policy on Conflicts of Interest
Authors are required to disclose any possible conflict of interest at the manuscript submission stage; these include financial conflicts (for example patent ownership, stock ownership, consultancies or speaker's fees). When appropriate, a conflict of interest statement will be included in the published manuscript under a separate heading.

Policy Regarding Number of Loci, Populations and Individuals
We have been reluctant to formulate guidelines regarding the minimum number of loci, populations and individuals needed for publication in Molecular Ecology, largely because such guidelines would depend on the question being addressed, the kind of molecular markers employed, the geographic range of the focal taxa and so forth. Likewise, the guidelines would have to be modified on a yearly basis as standards of the field continue to rise. Thus, our main criterion is that sampling strategies and marker choices should be designed to best address the question motivating the study. However, for phylogeographic studies, we recommend that authors base their inferences on multiple loci: our editors and reviewers often question the reliability of inferences based on a single locus and such manuscripts are unlikely to be sent out for review.

Policy on Data Analysis Best Practice
Molecular Ecology expects that statistical and molecular tools used in submitted papers should meet a high standard of rigour. All analytical approaches have inherent limitations, and authors should therefore attempt to identify the limitations of their chosen approach and corroborate their interpretations when possible.

Policy on the Use of RAPD/ISSR Markers
The appropriateness of RAPD or ISSR markers for population genetic inference is increasingly questioned by our reviewers and editors because of concerns about reproducibility, dominance, and homology. Given these worries, and the ready availability of other kinds of markers that do not suffer from all of these problems, studies based primarily on RAPD/ISSR rarely pass the scrutiny of peer review in Molecular Ecology. Of course, there may be situations in which these markers are appropriate, such as in genetic mapping studies or in searches for diagnostic markers for a given species or trait. These latter kinds of studies will continue to be reviewed by the journal.

Compliance with International Conventions and Regulations
We strongly recommend that papers submitted to Molecular Ecology comply with the Convention on Biological Diversity and the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CBD and CITES). Within the CBD, we ask that authors follow the Access to Benefit Sharing (ABS) guidelines, and give credit and equal access to benefits to countries, academic institutions and scientists that participated in the collection and analysis of data. Under the CITES convention, we request that authors observe the need for permits for the import and export of specimens that fall under CITES guidelines.

Compliance with Laws on Animal Experimentation
We expect that papers submitted to Molecular Ecology comply with the ARRIVE guidelines for the use of animals in research, see: http://www.nc3rs.org.uk/ARRIVE

Policy on Reporting Stable Isotope Data
For papers using stable isotopes, we recommend that authors follow the guidelines developed by the IUPAC Commission for Isotope Abundances and Atomic Weights; see http://onlinelibrary.wiley.com/doi/10.1002/rcm.5129/full for more details.

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Guidelines for Manuscript Submission
Molecular Ecology accepts manuscripts via Scholar One Manuscripts, an online submission system. This system streamlines the submission process and ensures all papers are processed quickly and efficiently. If an author cannot submit the MS using the electronic procedures outlined below, they should contact the Managing Editor to ascertain whether or not an exception can be made.

Molecular Ecology employs a plagiarism detection system. By submitting your manuscript you accept that it may be screened for plagiarism against previously published works.

Submission Procedure
To submit your article, first create an account on Scholar One Manuscripts. This can be done at http://mc.manuscriptcentral.com/mec.

Access the 'Author Centre', click on the 'submit new manuscript' link, and follow the instructions to submit your manuscript. The procedure consists of seven simple steps, which you are guided through by our online system. The help function is always available at the top right of the page for any questions you might have. If you have any questions that cannot be addressed by the online help, please direct them to the Editorial Office.

Preparing Manuscripts for Submission
Cover Letter
A brief message containing any relevant information you wish to convey to the Subject Editor or Managing Editor. If the MS is a resubmission of a previous manuscript, details of the changes made should be placed in the 'response to reviewers' box in step 1 of the resubmission process. Authors submitting manuscripts rejected by other journals are encouraged to state that all comments on previous versions have been taken into account. Authors should also use this space to explain their choice of preferred or non-preferred reviewers and editors.

Response to reviewers
If your paper is a resubmission, please prepare a detailed response to the previous set of editor and reviewer comments. The manuscript submission system typically removes text highlighting, bold type or text colours, so the most robust approach is to copy the decision letter and insert your responses beneath each comment, starting your text with “>>>”. Uploading a copy of the manuscript with changes tracked also assists with the review process, particularly for papers given a ‘reconsider after revision’ or an ‘accept, minor revisions’ decision.

Manuscript File
For initial submission, the main text of the manuscript can be in Microsoft Word with tables and figures either embedded in the document or uploaded as separate files. Manuscripts can also be submitted as a single PDF file containing the text, tables and figures. In either case, please ensure that continuous line numbers are included and that figures are sufficiently high quality for review; manuscripts failing to include either of these will be returned to you. Please upload Supporting Information separately.

If your MS has been prepared in LaTeX, please ensure that you upload all additional files required to read your document, as well as providing a PDF proof for our typesetters to use as a reference. Please use the LaTeX ‘article’ class, and do not add coding to ‘force’ line breaks or the positioning of ‘floats’, as this coding will need to be removed in the conversion of the file to XML. Authors can upload their LaTeX and EPS (figure) source files to ScholarOne Manuscripts, designating them 'LaTeX support files'. These will be used for typesetting purposes and must be re-uploaded with each version of a paper. A single .zip file containing all source files should also be uploaded. The accompanying PDF should be designated as the 'main document' during the file submission stage.

Keep the file as small as possible to facilitate information transmission (max 50 MB). Do not use any form of compression or zipping, excepting with LaTeX support files as outlined above, as these can interfere with our uploading process.

Format
To facilitate viewing on screen, please format your manuscript with 2.5 cm side margins, 3 cm top and bottom margins, and clear paragraph delimitations. All manuscripts must be double-spaced with page numbers and continuous line numbers.

Text
The Title page should contain: 1. Title; 2. Author’s names with initials; 3. Full postal address(es); 4. Four to six keywords for indexing purposes; 5. Name, address, fax number and electronic mail address of corresponding author, to whom proofs will be sent; 6. Running title of no more than 45 characters, including spaces.

Please see the guidelines for specific article types above for further additional layout information.

Tables and Figures
Tables and figures should appear after the main text. Table captions should be integral with and appear above the data tables. Footnotes for tables should be given below the table. Figure legends should not appear with their respective figure but should be grouped after the references. In the full-text online edition of the journal, figure legends may be truncated in abbreviated links to the full screen version. Therefore, the first 100 characters of any legend should inform the reader of key aspects of the figure.

Preparation of Figures
Almost all figures submitted to Molecular Ecology should be vector graphics - these are clear at all magnifications and look good both in print and online. Graphs should always be saved directly as .eps or .pdf files from a professional graphics program (e.g., R) and never as .jpg, .tif or any other pixel-based format. Maps should be made using vector graphics in e.g., Adobe Illustrator. The output of scientific software programs should also be saved directly as vector graphics whenever possible. Photographic images can be in a pixel-based format, but please ensure that these are saved as .tif files with at least 300 dpi, or (failing that) a .jpg with no compression. Failure to follow these guidelines may result in your paper having blurred, illegible or otherwise low-quality figures.

Please also ensure that figures are prepared such that, after reduction to fit across one column, two-thirds page width, or two columns (80 mm, 112 mm, or 169 mm, respectively) as required, all lettering and symbols will be clear and easy to read, i.e. no axes labels should be too large or too small.Further details are available at http://authorservices.wiley.com/bauthor/illustration.asp.

Figures published in Molecular Ecology will appear in colour in the online version of the article, at no cost to authors. It is journal policy that authors pay the full cost for any print reproduction of colour artwork. This cost is £150 for the first colour figure and £50 per additional figure (see Final MS Preparation). In the ‘Colour Online Only’ option, figures have the colour saturation of the original version reduced to zero for print. As a result, we recommend authors consider paying for colour printing if their figures and captions do not convey the same information in greyscale as they do in colour. More information on making figures that are legible in colour online and greyscale in print can be found at http://www.molecularecologist.com/figure-guidelines/.

The corresponding author is responsible for obtaining written permission to reproduce material 'in print and other media' from the publisher of the original source, and for supplying Wiley with that permission.

Acknowledgements
These should briefly give credit to other people who have made a contribution to the study. Please ensure that all relevant grant numbers are listed.

References
Please see a recent issue of the journal for reference formats.

Data Accessibility
To enable readers to locate archived data from Molecular Ecology papers, we require that authors include a 'Data Accessibility' section after the references. This should list the database and the respective accession numbers for all data from the manuscript that has been made publicly available. An example is below, and more details can be found at http://www.molecularecologist.com/data-archiving-the-nitty-gritty/.

"Data Accessibility:
- DNA sequences: Genbank accessions F234391-F234402; NCBI SRA: SRX0110215
- Final DNA sequence assembly uploaded as online supplemental material
- Climate data and MaxEnt input files: Dryad doi:10.5521/dryad.12311
- Sampling locations, morphological data and microsatellite genotypes: Dryad doi:10.5521/dryad.12311”

A Data Accessibility section must be present in your manuscript at initial submission, and should list where each dataset will be archived. There is no need to include accession numbers or DOI’s at initial submission, but manuscripts lacking a Data Accessibility section will not be passed through to an editor. Please note that reviewers will be asked to comment on the completeness of this section.

If you have any questions about the formatting or content of this section please contact the Managing Editor.

Author Contributions
Authors should include a brief Author Contributions statement at the end of the paper in which they describe their specific contributions to the published work. Contributions could include, for example, designed research, performed research, contributed new reagents or analytical tools, analyzed data, wrote the paper, etc. An author may have multiple contributions, and multiple authors may have contributed to the same component of the study.

NB The mandatory Author Contributions Box replaces the optional Author Information Box.

Supporting Information
Supporting Information gives authors the opportunity to present data in different formats than traditional print media. Large datasets can be submitted as separate files for on-line publication as Supporting Information. Please note that Supporting Information should be uploaded in a separate file and given the file designation 'Supporting Information for online publication'. For more information on preparing Supporting Information, please see: http://authorservices.wiley.com/bauthor/suppmat.asp

Cover Images
We are always looking for suitable images for the cover of Molecular Ecology. Cover images can be photographs of organisms or habitats; other possibilities are montages of photographs and/or diagrams, maps or data. If you have any candidate photographs that you would like to be considered for the cover please send the image and a brief, informative caption and photo credit (max. 100 words) to editorial.office@molecol.com. Please provide a cover image copyright release form when submitting a cover image suggestion. If your image is not selected, your form and image will not be used for any other purpose.

Related Manuscripts
Reviewers and Editors often ask to see unpublished manuscripts (i.e. 'in press', 'in review' or 'submitted') that appear to be related to the submitted paper. As obtaining these during the review process adds unnecessary delays, we request that these related manuscripts are uploaded as 'supplemental files for review only' at the submission stage.

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Notes for Accepted Manuscripts
The following items must be provided before your paper can be published:

1. A completed Copyright Transfer Agreement.

This form can be uploaded at submission, during the revision process, during the First Look stage after acceptance, or e-mailed to the Editorial Office. Please note: for contributor-owned manuscripts, rather than collecting individual signatures, it is acceptable for one author to sign on the Contributor line, and write “On behalf of all authors” on the co-contributor line. We recommend the signing author obtain written (e.g., emailed) permission from all co-authors for their own records.

2. A Colour Work Agreement for manuscripts where one or more figures will appear in colour in print.

Authors will be sent a notification e-mail containing the mailing address of the appropriate Production Editor when the Editorial Office approves the final files of an accepted manuscript. We ask that authors promptly post/courier the completed hard copy* of the Colour Work Agreement Form (including payment information) to the Production Office once the mailing address has been provided. Manuscripts where all colour figures will appear in greyscale in print do not require a Colour Work form.

*Because of changes to UK law, credit card information must be transmitted and stored physically, rather than virtually. This means the publisher cannot accept photocopied, scanned, or otherwise electronic versions of the Colour Work form. Colour Work forms are not processed or collected by the Editorial Office.

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Publishing Information

Exclusivity and Copyright
Manuscripts must be submitted exclusively to Molecular Ecology and we will only consider them for publication on the understanding that they have not been, nor will be, published elsewhere. If accepted, the copyright to papers is assigned to the journal. A statement confirming that all authors give formal consent to publication should accompany manuscripts in the covering letter. Permission to use published material elsewhere will be granted on request.

Copyright Transfer Agreement
Authors will be required to sign a Copyright Transfer Agreement (CTA) for all papers accepted for publication. Signature of the CTA is a condition of publication, and papers will not be passed to the publisher for production unless a signed form has been received. Please note that signature of the Copyright Transfer Agreement does not affect ownership of copyright in the material. (Government employees need to complete the Author Warranty sections, although copyright in such cases does not need to be assigned). After submission, authors will retain the right to publish their paper in various medium/circumstances (please see the CTA form for further details). Correspondence to the journal is accepted on the understanding that the contributing author licences the publisher to publish the letter as part of the journal or separately from it, in the exercise of any subsidiary rights relating to the journal and its contents. Please download the CTA form here, and further information can be obtained from http://authorservices.wiley.com/bauthor/faqs_copyright.asp#1.20

OnlineOpen
OnlineOpen is a pay-to-publish service from Wiley-Blackwell that offers authors whose papers are accepted for publication the opportunity to pay up-front for their manuscript to become open access (i.e., free for all to view and download) via Wiley Online Library. Each Online Open article will be subject to a one-off fee of US$3000 to be met by or on behalf of the author in advance of publication. Upon online publication, the article (both full-text and PDF versions) will be available to all for viewing and download free of charge. For the full list of terms and conditions, see http://wileyonlinelibrary.com/onlineopen#OnlineOpen_Terms. Any authors wishing to send their paper OnlineOpen will be required to complete the payment form available from our website at: https://onlinelibrary.wiley.com/onlineOpenOrder (Please note this form is for use with OnlineOpen material ONLY.)

Prior to acceptance, there is no requirement to inform the Editorial Office that you intend to publish your paper OnlineOpen if you do not wish to. All OnlineOpen articles are treated in the same way as any other article. They go through the journal's standard peer-review process and will be accepted or rejected based on their own merit.

Early View
Molecular Ecology is covered by Wiley-Blackwell's Early View service. Early View articles are complete full-text articles published online in advance of their publication in a printed issue. Articles are therefore available as soon as they are ready, rather than having to wait for the next scheduled print issue. Early View articles are complete and final. They have been fully reviewed, revised and edited for publication, and the authors' final corrections have been incorporated. Because they are in final form, no changes can be made after online publication. The nature of Early View articles means that they do not yet have volume, issue or page numbers, so Early View articles cannot be cited in the traditional way. They are therefore given a Digital Object Identifier (DOI), which allows the article to be cited and tracked before it is allocated to an issue. After print publication, the DOI remains valid and can continue to be used to cite and access the article. More information about DOIs can be found at: http://www.doi.org/faq.html.

NIH-funded authors and Molecular Ecology
From April 2008, the NIH is mandating grant-holders to deposit their published papers in PubMed Central within 12 months of publication. Molecular Ecology complies with the NIH mandate in allowing authors to post the accepted version of their article i.e., the version incorporating any amendments made during peer review, 12 months after publication (please see http://www.wiley.com/go/nihmandate). In doing so authors will be meeting the terms of their grant (http://publicaccess.nih.gov/FAQ.htm#general). Please tick the box at the end of the CTA form.

As an alternative, NIH-funded authors may use the Online Open service (http://authorservices.wiley.com/bauthor/onlineopen.asp). This service grants free and immediate availability of the article on publication, and deposition of the final PDF version with PubMed Central. 

Wiley-Blackwell Author Services
Wiley-Blackwell Author Services enables authors to track their article - once it has been accepted - through the production process to publication online and in print. Authors can check the status of their articles online and choose to receive automated e-mails at key stages of production so they don't need to contact the Production Editor to check on progress. Visit http://authorservices.wiley.com/bauthor for more details on online production tracking and for other resources including FAQs and tips on article preparation, submission and more.

Proofs
Authors will be sent an e-mail alerting them that PDF proofs are available to download from our secure designated author website. Therefore, the corresponding author should supply their email address when they submit their manuscript. It is the author's responsibility to check their proof carefully for any required changes. Corrections must be returned to the Production Editor within 3 days of receipt; fax should be used to facilitate communication and minor corrections can be advised by e-mail ensuring that journal title, paper reference number and corresponding author's name are given in the body of the message.

Authors should note that proof corrections should be marked as clearly as possible, and should be kept to a minimum. If the editors consider that significant changes have been introduced at the proof stage, the right is reserved either to levy the costs to authors, or to request resubmission of the manuscript. The corresponding author will be sent a form with their proofs to enable copies of offprints to be ordered.

Offprints
Free access to the final PDF offprint of your article will be available via Author Services only. Please therefore sign up for Author Services if you would like to access your article PDF offprint and enjoy the many other benefits the service offers.

Paper offprints of the printed published article may be purchased if ordered via the method stipulated on the instructions that will accompany the proofs. Printed offprints are posted to the correspondence address given for the paper unless a different address is specified when ordered. Note that it is not uncommon for printed offprints to take up to eight weeks to arrive after publication of the journal. For order enquiries please e-mail: offprint@cosprinters.com.

Referrals to the Open Access Journal Ecology and Evolution
Molecular Ecology works together with Wiley’s Open Access Journal, Ecology and Evolution, to enable rapid publication of quality research that we are unable to accept for publication. Authors will be offered the option of having the paper, along with any related reviews, automatically transferred for consideration by the Editor of Ecology and Evolution. Authors will not need to reformat or rewrite their manuscript at this stage, and publication decisions will be made a short time after the transfer takes place. Once the referral is made, the manuscript will be held in a secure Wiley FTP site that is not accessed until authors request to transfer their manuscript. The Editor of Ecology and Evolution will accept submissions that report well-conducted research that reaches the standard acceptable for publication. Accepted papers can be published rapidly, typically within 15 days of acceptance. Ecology and Evolution is a Wiley Open Access journal and article publication fees apply. For more information please go to www.ecolevol.org/info or contact the Editorial Office at ecoevo@wiley.com at any time with any questions.