Author information pack
The Journal of Molecular Biology provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide functional and mechanistic insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions.
In addition to research Communications and Articles, the journal welcomes submission of Methods Notes Databases/ Web Servers, Brevia, Perspectives and Reviews
Research areas include but are not limited to:
- DNA replication, repair and recombination, gene expression, epigenetics and chromatin structure and function,RNA processing, functions of non coding RNAs, transcription
- Structure, chemistry, processing and function of biologically important macromolecules and complexes
- Biomolecular interactions, systems biology
- Computational biology
- Translation, protein folding, processing and degradation
- Sorting, spatiotemporal organization, trafficking, signal transduction and intracellular signaling
- Membrane processes, cell surface proteins and cell-cell interactions
- Molecular basis of disease
- Methodological advances, both experimental and theoretical, including databases
The Journal aims to publish novel and significant research in the general areas of molecular genetics and structural biology. Acceptance of papers for publication in the Journal is at the discretion of the Editors. All manuscripts are reviewed initially by the Editorial Board and only those papers that meet the scientific and editorial standards of the Journal will be sent for outside review. Authors should indicate a suitable Editor to whom the paper could be allocated. However, the Journal reserves the right to reallocate manuscripts to the most appropriate Editor.
Many acceptable papers require minor revision or condensation. It is in the mutual interest of both the authors and the journal that amended manuscripts are returned promptly. A paper requiring major revision will retain its original date of receipt only if it is received by the Editor within 60 days of the date of return to the author. Extensions to the 60 days limit may be granted at the discretion of the Editor. Papers requiring minor revision must be returned to the Editor within 30 days.As soon as the paper has been reviewed, the corresponding author will receive a decision letter from the Editor. Revised manuscripts and correspondence concerning such manuscripts should be addressed to the Editor at the address indicated on the decision letter.
The Journal of Molecular Biology discourages authors from submitting multiple manuscripts on closely related topics. Submission of two or more related manuscripts intended for simultaneous publication will be permitted only under exceptional circumstances. Authors wishing to submit related manuscripts must obtain prior permission from the Editors.
The Board will editorially reject papers, without outside review, if in their opinion the paper falls outside the scope of papers normally published by JMB, if the paper lacks originality, or if the paper fails to meet expected technical standards. The following specific points are brought to the attention of authors:
(b) Methodology papers. Papers that deal only with new methods and do not contain important new results discovered by means of these methods will be accepted only when the general applicability and interest of the method are immediately obvious and clearly documented in the manuscript. Improvements on existing methods will in general be viewed as appropriate to more specialized journals unless it can be shown that they lead to important new insights that were not accessible with current technologies.(c) Sequences. Papers describing new members of a gene family will not ordinarily be accepted unless they contain results of particular importance for studies of evolution or of the function of the gene. In general, papers describing the cloning and sequencing of new genes will be acceptable only if there is experimental evidence for the function of the gene.
(d) Structural studies. Communications describing preliminary crystallographic data (crystallization conditions and diffraction pattern and space group) will not, in general, be accepted. Papers of this type will be considered only if, in the judgment of the Editorial Board, they contain results of exceptional interest and importance. Low-resolution structural studies will be acceptable only if they have clear biological implications and exhibit features of special interest. Papers describing structures of mutant proteins are appropriate if the mutations have been successfully designed to provide new insights into structural principles or biological function. Similar criteria apply to structures of proteins from variant species. In the particular case of unliganded antibody Fab fragments, papers would not normally be acceptable unless they provide novel structural or biological insight.(e) Modeled structures. Papers describing modeled structures will in general be considered only if they provide novel and important biological insights. The reliability of the model must be clearly documented, including evidence that the expected accuracy level of the model is consistent with the application that is described. This could be based, for example, on the known success rate of the modeling procedure at specified levels of sequence identity, or the application of model validation procedures. Validation of the model through experimental tests is always desirable.
(f) Theory and computer simulation. Papers reporting theoretical studies should have direct applicability to experimental work in a field normally represented in papers published in JMB or should address issues of current interest to the broader biological community. As a general rule, all theory papers should deal directly with experimental data; the papers should provide predictions that are testable experimentally or provide an interpretation of experimental observations. Papers describing computer simulations are generally acceptable only if they provide new insights of high biological significance or lead to novel interpretations of experimental data. As is the case for modeled structures, evidence must be provided that the accuracy level of the method is consistent with the application that is described. This might involve, for example, control simulations on systems that have been well-characterized experimentally.
(g) Database papers. Papers describing biological or molecular databases will be considered if they report important new results discovered by means of that database, or if the database permits novel integration of biological information that will be of general applicability and lead to important new insights. The biological principles used in the construction of the database must be clearly documented in the paper.(h) Preprints. Authors are required to disclose in their cover letter if their manuscript has been previously posted on a preprint server.
Sharing of reagents and data
To allow others to build on work published in JMB, the Editors strongly encourage authors to share reagents (e.g., cloned DNAs; antibodies; bacterial, animal, or plant cells; viruses), data, algorithms, computer codes, and detailed scientific protocols with their colleagues in the scientific community. Authors are also encouraged to deposit as much of their data as possible in publicly accessible databases to facilitate the free exchange of scientific information.
Papers dealing with amino acid sequences of proteins or with nucleotide sequences must carry a statement that the data have been deposited with an appropriate data bank, e.g., the European Molecular Biology Laboratory (EMBL) or GenBank Data Libraries. The data base accession number must be given at the end of the Materials and Methods section of the manuscript under the separate heading 'Accession numbers'. For example: Coordinates and structure factors have been deposited in the Protein Data Bank with accession number 2XYZ. Lengthy nucleotide sequences will be published only if, in the judgement of the Editorial Board, these results are of general interest and importance.
For papers describing structures of biological macromolecules, the atomic coordinates and the related experimental data (structure factor amplitudes/intensities and/or NMR restraints) must be deposited at a member site of the Worldwide Protein Data Bank (http://www.wwpdb.org): RCSB PDB (http://www.pdb.org), MSD-EBI (http://www.ebi.ac.uk/pdbe/), PDBj (http://www.pdbj.org), or BMRB (http://www.bmrb.wisc.edu). Manuscripts must carry a statement that coordinates and structure factors (or NMR restraints) have been deposited in the Protein Data Bank. The accession number(s) must be cited in the manuscript at the end of the Materials and Methods section. Authors must agree to release the atomic coordinates and experimental data immediately upon publication. Small angle scattering (Small angle X-ray and neutron scattering (SAXS and SANS)) data and structural models must be deposited at SASBDB (https://www.sasbdb.org/) prior to submission. The database accession numbers must be cited in the manuscript and authors must agree to release the experimental data and structural models immediately upon publication.
It is increasingly common for coordinates to be deposited in the Protein Data Bank without an associated publication. Before submission to JMB, authors are expected to search the Protein Data Bank for related structures using one or more alignment programs and report the outcome. Prior deposition of related coordinates, without an associated publication, does not necessarily preclude publication in JMB. The primary criteria for publication of a structure in JMB are that it provides novel structural insights or important new functional and biological insights that are likely to be of general interest.You can enrich your online articles by providing 3D molecular models (optional) in PDB, PSE or MOL/MOL2 format, which will be visualized using the interactive viewer embedded within the article. Using the viewer, it will be possible to zoom into the model, rotate and pan the model, and change display settings. Submitted models will also be available for downloading from your online article on ScienceDirect. Each molecular model will have to be uploaded to the online submission system separately, via the ″3D molecular models″ submission category. For more information see: www.elsevier.com/3DMolecularModels.
NMR assignment data must be deposited in the BioMagResBank (BMRB; http://www.bmrb.wisc.edu). The accession number(s) must be cited in the manuscript at the end of the Materials and Methods section. Tables listing resonance assignments will not be published in the Journal but may be deposited as Supplemental data that will be actively linked to the online version of the paper. Supplemental data must be included with the manuscript submitted for review (see below for full instructions)
In keeping with NIH guidelines, the Journal considers it to be good practice for cultured cell lines to be authenticated. A description of the methods used to authenticate cells should be included in the Materials and Methods section. Authors are expected to check that cell lines used in their experiments are free from mycoplasma infections.
Types of paper
The Journal of Molecular Biology will publish full Articles, Communications, Reviews, Perspectives, Brevia, Methods Notes, Databases/ Web Servers..
Communications are brief papers that make a specific well-documented point. In general, a Communication should include no more than four figures and tables. The text will be continuous, with technical and methodological detail printed in the legend to the tables and figures.Reviews are scholarly and balanced accounts of progress in fields of interest to the general reader. Reviews should be no longer than 12 printed pages and with no more than 12 figures and tables. Authorship is normally by invitation: an Editor should be consulted in advance by anyone wishing to submit an unsolicited Review.
Perspectives are brief reviews that present a sharply focused view of a rapidly advancing area of research. Authorship is normally by invitation: the Editor-in-Chief or Scientific Editor should be consulted in advance by anyone wishing to submit an unsolicited Perspective.Brevia are brief notes that report a specific well-documented result. Brevia are limited to a single page, including references and captions, and contain only one figure or table. Details of methods must be provided as Supplemental Material.
Methods Notes report novel methods of immediate and general interest and applicability. Methods Notes are limited to 5 pages, including references and captions, with a maximum of 3 displayed items (figures or tables). Additional details required to implement the new method must be provided as Supplemental Material. Preliminary enquiries about the suitability of a submission to this section are encouraged.Databases and web servers are descriptions of new or updated databases and web servers of broad interest to the general readership of the journal. The database/server must be freely available to the academic community. The journal has set some limits on the length of the database/server articles. The journal requires that database/server articles should have less than 5000 words including title, abstract, legends, acknowledgements and references, a maximum of 3 displayed items (figures or tables) that in total will occupy less than one and a half (1 1/2) printed pages, and less than 50 references. Additional details required to implement the new method must be provided as Supplemental Material. Normally, the title of the paper will start with the database/server name. If the requirement to start with a name is not appropriate, please consult with the journal. On submission, the authors must in their covering letter identify any previous publications reporting this (or a closely-related) database/server and explain why this paper presents a substantial advance. Related databases/servers must be reported and referenced in the article. Preliminary enquiries about the suitability of a submission to this section are encouraged.
Contact details for submission
Please submit your manuscript for the Journal of Molecular Biology via the web site at http://ees.elsevier.com/jmb. If you are unable to provide an electronic version of your paper, please contact the Editorial Office prior to submission (email: firstname.lastname@example.org). All correspondence regarding manuscripts should be sent to email@example.com.
- DNA replication, repair and recombination, gene expression, epigenetics and chromatin structure and function, RNA processing, functions of non coding RNAs, transcription
- Structure, chemistry, processing and function of biologically important macromolecules and complexes
- Biomolecular interactions, systems biology
- Computational biology
- Translation, protein folding, processing and degradation
- Sorting, spatiotemporal organization, trafficking, signal transduction and intracellular signalling
- Membrane processes, cell surface proteins and cell-cell interactions
- Methodological advances, both experimental and theoretical, including databases
Authors are asked to suggest 6 expert referees. Where appropriate, authors should suggest 2 to 3 referees who are expert in the methodology as well as 2 to 3 referees who are expert on the biological system. Authors should avoid suggesting as referees people who, within the past 3 years, they have had a collaborative relationship, have mentored, or have been mentored by.In rare instances, authors may also request that conflicted individuals be excluded from the review process. However, the editors reserve the right to choose as referees individuals who in their opinion are best qualified to review the paper.
A PDF file comprising all text and figures is acceptable for initial submission. When submitting a revised manuscript, separate electronic files are required. Each manuscript is to be accompanied by an electronic cover letter outlining the basic findings of the paper and their significance. PDFs of all related manuscripts under consideration for publication must also be included with the submitted manuscript.
Ethics in publishing
Please see our information pages on Ethics in publishing and Ethical guidelines for journal publication.
All authors must disclose any financial and personal relationships with other people or organizations that could inappropriately influence (bias) their work. Examples of potential conflicts of interest include employment, consultancies, stock ownership, honoraria, paid expert testimony, patent applications/registrations, and grants or other funding. Authors must disclose any interests in two places: 1. A summary declaration of interest statement in the title page file (if double-blind) or the manuscript file (if single-blind). If there are no interests to declare then please state this: 'Declarations of interest: none'. This summary statement will be ultimately published if the article is accepted. 2. Detailed disclosures as part of a separate Declaration of Interest form, which forms part of the journal's official records. It is important for potential interests to be declared in both places and that the information matches. More information.
Submission declaration and verification
Submission of an article implies that the work described has not been published previously (except in the form of an abstract or as part of a published lecture or academic thesis or as an electronic preprint, see 'Multiple, redundant or concurrent publication' section of our ethics policy for more information), that it is not under consideration for publication elsewhere, that its publication is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out, and that, if accepted, it will not be published elsewhere in the same form, in English or in any other language, including electronically without the written consent of the copyright-holder. To verify originality, your article may be checked by the originality detection service Crossref Similarity Check.
All authors should have made substantial contributions to all of the following: (1) the conception and design of the study, or acquisition of data, or analysis and interpretation of data, (2) drafting the article or revising it critically for important intellectual content, (3) final approval of the version to be submitted.
Changes to authorship
Authors are expected to consider carefully the list and order of authors before submitting their manuscript and provide the definitive list of authors at the time of the original submission. Any addition, deletion or rearrangement of author names in the authorship list should be made only before the manuscript has been accepted and only if approved by the journal Editor. To request such a change, the Editor must receive the following from the corresponding author: (a) the reason for the change in author list and (b) written confirmation (e-mail, letter) from all authors that they agree with the addition, removal or rearrangement. In the case of addition or removal of authors, this includes confirmation from the author being added or removed.
Only in exceptional circumstances will the Editor consider the addition, deletion or rearrangement of authors after the manuscript has been accepted. While the Editor considers the request, publication of the manuscript will be suspended. If the manuscript has already been published in an online issue, any requests approved by the Editor will result in a corrigendum.
Upon acceptance of an article, authors will be asked to complete a 'Journal Publishing Agreement' (see more information on this). An e-mail will be sent to the corresponding author confirming receipt of the manuscript together with a 'Journal Publishing Agreement' form or a link to the online version of this agreement.
Subscribers may reproduce tables of contents or prepare lists of articles including abstracts for internal circulation within their institutions. Permission of the Publisher is required for resale or distribution outside the institution and for all other derivative works, including compilations and translations. If excerpts from other copyrighted works are included, the author(s) must obtain written permission from the copyright owners and credit the source(s) in the article. Elsevier has preprinted forms for use by authors in these cases.For open access articles: Upon acceptance of an article, authors will be asked to complete an 'Exclusive License Agreement' (more information). Permitted third party reuse of open access articles is determined by the author's choice of user license.
As an author you (or your employer or institution) have certain rights to reuse your work. More information.
Find out how you can share your research published in Elsevier journals.
Funding body agreements and policies
Elsevier has established a number of agreements with funding bodies which allow authors to comply with their funder's open access policies. Some funding bodies will reimburse the author for the Open Access Publication Fee. Details of existing agreements are available online.
This journal offers authors a choice in publishing their research:
• Articles are made available to subscribers as well as developing countries and patient groups through our universal access programs.
• No open access publication fee payable by authors.
• Articles are freely available to both subscribers and the wider public with permitted reuse.
• An open access publication fee is payable by authors or on their behalf, e.g. by their research funder or institution.
For open access articles, permitted third party (re)use is defined by the following Creative Commons user licenses:Creative Commons Attribution (CC BY)
Lets others distribute and copy the article, create extracts, abstracts, and other revised versions, adaptations or derivative works of or from an article (such as a translation), include in a collective work (such as an anthology), text or data mine the article, even for commercial purposes, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article, and do not modify the article in such a way as to damage the author's honor or reputation.
Creative Commons Attribution-NonCommercial-NoDerivs (CC BY-NC-ND)
For non-commercial purposes, lets others distribute and copy the article, and to include in a collective work (such as an anthology), as long as they credit the author(s) and provided they do not alter or modify the article.
The open access publication fee for this journal is USD 2350, excluding taxes. Learn more about Elsevier's pricing policy: https://www.elsevier.com/openaccesspricing.
Authors can share their research in a variety of different ways and Elsevier has a number of green open access options available. We recommend authors see our green open access page for further information. Authors can also self-archive their manuscripts immediately and enable public access from their institution's repository after an embargo period. This is the version that has been accepted for publication and which typically includes author-incorporated changes suggested during submission, peer review and in editor-author communications. Embargo period: For subscription articles, an appropriate amount of time is needed for journals to deliver value to subscribing customers before an article becomes freely available to the public. This is the embargo period and it begins from the date the article is formally published online in its final and fully citable form. Find out more.
This journal has an embargo period of 12 months.
Elsevier Researcher Academy
Researcher Academy is a free e-learning platform designed to support early and mid-career researchers throughout their research journey. The "Learn" environment at Researcher Academy offers several interactive modules, webinars, downloadable guides and resources to guide you through the process of writing for research and going through peer review. Feel free to use these free resources to improve your submission and navigate the publication process with ease.
Please write your text in good English (American or British usage is accepted, but not a mixture of these). Authors who feel their English language manuscript may require editing to eliminate possible grammatical or spelling errors and to conform to correct scientific English may wish to use the English Language Editing service available from Elsevier's WebShop.
Our online submission system guides you stepwise through the process of entering your article details and uploading your files. The system converts your article files to a single PDF file used in the peer-review process. Editable files (e.g., Word, LaTeX) are required to typeset your article for final publication. All correspondence, including notification of the Editor's decision and requests for revision, is sent by e-mail.
This journal operates a single blind review process. All contributions will be initially assessed by the editor for suitability for the journal. Papers deemed suitable are then typically sent to a minimum of two independent expert reviewers to assess the scientific quality of the paper. The Editor is responsible for the final decision regarding acceptance or rejection of articles. The Editor's decision is final. More information on types of peer review.
It is important that the file be saved in the native format of the word processor used. The text should be in single-column format. Keep the layout of the text as simple as possible. Most formatting codes will be removed and replaced on processing the article. In particular, do not use the word processor's options to justify text or to hyphenate words. However, do use bold face, italics, subscripts, superscripts etc. When preparing tables, if you are using a table grid, use only one grid for each individual table and not a grid for each row. If no grid is used, use tabs, not spaces, to align columns. The electronic text should be prepared in a way very similar to that of conventional manuscripts (see also the Guide to Publishing with Elsevier). Note that source files of figures, tables and text graphics will be required whether or not you embed your figures in the text. See also the section on Electronic artwork.
To avoid unnecessary errors you are strongly advised to use the 'spell-check' and 'grammar-check' functions of your word processor.
Manuscripts should be submitted as a word processing file, with one inch margins and double spaced lines.
The conventions used in current issues of the Journal for headings, references etc. should be used in preparing manuscripts. Articles, Methods Notes and Databases/ Web Servers are divided into sections in the following order: Introduction; Results; Discussion; Materials and Methods. Other section headings (e.g., Theory, Results and Discussion) may be used if this improves the clarity of presentation. Communications should not be divided into sections but should include topic headings where appropriate.
Essential title page information
•Title. The title should convey the concept and the importance of the paper to non-specialist readers. Titles may occupy no more than three lines of type. Each line should contain no more than 50 characters, including spaces. Titles are often used in information-retrieval systems. Avoid abbreviations and formulae where possible.
•Author names and affiliations. Where the family name may be ambiguous (e.g., a double name), please indicate this clearly. Present the authors' affiliation addresses (where the actual work was done) below the names. Indicate all affiliations with a lower-case superscript letter immediately after the author's name and in front of the appropriate address. Provide the full postal address of each affiliation, including the country name, and, if available, the e-mail address of each author.
•Corresponding author. Clearly indicate who will handle correspondence at all stages of refereeing and publication, also post-publication. Ensure that telephone and fax numbers (with country and area code) are provided in addition to the e-mail address and the complete postal address.
•Present/permanent address. If an author has moved since the work described in the article was done, or was visiting at the time, a "Present address" (or "Permanent address") may be indicated as a footnote to that author's name. The address at which the author actually did the work must be retained as the main, affiliation address. Superscript Arabic numerals are used for such footnotes.
The abstract must be concise (limit of 250 words) and factual. It should convey the concept and the importance of the paper to non-specialist readers. The abstract should state briefly the background of the question, the principal results and conclude on a clear description of the conceptual advance and significance of the work. Detailed descriptions of the study or of the findings should not be included in the abstract. An abstract is required for all papers; the abstract for Brevia should be limited to 100 words whereas the abstract of Methods Notes, Databases and Servers should be limited to 150 words.
A Graphical abstract is required for this journal and should summarize the contents of the article in a concise, pictorial form designed to capture the attention of a wide readership online. Authors must provide images that clearly represent the work described in the article. A Graphical abstract should as much as possible provide a visual indication of the context of the results depicted and should contain simple labels. Specifications: the maximum size of the image should be 200 x 500 pixels with a minimum resolution of 300 dpi, using Arial font with a size of 10-16 points; Preferred file types: TIFF, EPS, PDF or MS Office files. Preparation Guidelines: a Graphical Abstract should be one image and should not contain multiple panels; visualize one process or make one point clear; for ease of browsing, images should have a clear start and end, preferably 'reading' from top to bottom or left to right. No additional text, outline or synopsis should be included. Any text or label must be part of the image file. Graphical abstracts should be submitted as a separate file in the online submission system. Graphical Abstracts can be uploaded in EES by selecting "Graphical Abstract" from the drop-down list when uploading files.
Highlights are required for this journal. Specifications: include 3 to 5 bullet points (max. 85 characters per bullet point including spaces); only the core results of the paper should be covered. The first bullet point should state the background or context of the question. One to three bullet points should describe the principal results. The last bullet point should conclude on a clear description of the conceptual advance and significance of the work. Highlights should be submitted as a separate file in EES by selecting 'Highlights' from the drop-down list when uploading files. Highlights will be displayed in online search result lists, the contents List and in the online article, but will not appear in the article PDF file or print.
Authors should supply five keywords after the Abstract. Keywords should not be words from the title.
Define non-standard abbreviations in a footnote to be placed on the first page of the article. Abbreviations that are unavoidable in the abstract must be defined at their first mention there, as well as in the footnote. Ensure consistency of abbreviations throughout the article.
State the objectives of the work and provide an adequate background, avoiding a detailed literature survey or a summary of the results.
Results should be clear and concise.
This should explore the significance of the results of the work, not repeat them. A combined Results and Discussion section is often appropriate. Avoid extensive citations and discussion of published literature.
Materials and methods
Provide sufficient detail to allow the work to be reproduced. Methods already published should be indicated by a reference: only relevant modifications should be described.
Accession numbers must be cited immediately following the Materials and Methods section. Accession numbers are unique identifiers in bioinformatics allocated to nucleotide and protein sequences to allow tracking of different versions of that sequence record and the associated sequence in a data repository [e.g., databases at the National Center for Biotechnical Information (NCBI) at the National Library of Medicine ('GenBank') and the Worldwide Protein Data Bank]. There are different types of accession numbers in use based on the type of sequence cited, each of which uses a different coding. Authors should explicitly mention the type of accession number together with the actual number, bearing in mind that an error in a letter or number can result in a dead link in the online version of the article. Please use the following format: accession number type ID: xxxx (e.g., MMDB ID: 12345; PDB ID: 1TUP). Note that in the final version of the electronic copy, accession numbers will be linked to the appropriate database, enabling readers to go directly to that source from the article.
For each and every accession number cited in an article, authors should type the accession number in bold, underlined text. Letters in the accession number should always be capitalised.Example 1: "GenBank accession nos. AI631510, AI631511, AI632198 , and BF223228 , a B-cell tumor from a chronic lymphatic leukemia (GenBank accession no. BE675048 , and a T-cell lymphoma (GenBank accession no. AA361117 )".
Please supply, as a separate list, the definitions of field-specific terms used in your article.
Collate acknowledgements in a separate section at the end of the article before the references and do not, therefore, include them on the title page, as a footnote to the title or otherwise. List here those individuals who provided help during the research (e.g., providing language help, writing assistance or proof reading the article, etc.).
Footnotes should be used sparingly. Designate them throughout the article, using an asterisk (*). Many wordprocessors build footnotes into the text, and this feature may be used. Should this not be the case, indicate the position of footnotes in the text and present the footnotes themselves separately at the end of the article. Do not include footnotes in the Reference list.
• Make sure you use uniform lettering and sizing of your original artwork.
• Embed the used fonts if the application provides that option.
• Aim to use the following fonts in your illustrations: Arial, Courier, Times New Roman, Symbol, or use fonts that look similar.
• Number the illustrations according to their sequence in the text.
• Use a logical naming convention for your artwork files.
• Size the illustrations close to the desired dimensions of the published version.
• Provide captions next to each illustration.
A detailed guide on electronic artwork is available on our website:
You are urged to visit this site; some excerpts from the detailed information are given here.
If your electronic artwork is created in a Microsoft Office application (Word, PowerPoint, Excel) then please supply 'as is' in the native document format.
Regardless of the application used other than Microsoft Office, when your electronic artwork is finalized, please 'Save as' or convert the images to one of the following formats (note the resolution requirements for line drawings, halftones, and line/halftone combinations given below):
EPS (or PDF): Vector drawings, embed all used fonts.
TIFF (or JPEG): Color or grayscale photographs (halftones), keep to a minimum of 300 dpi.
TIFF (or JPEG): Bitmapped (pure black & white pixels) line drawings, keep to a minimum of 1000 dpi.
TIFF (or JPEG): Combinations bitmapped line/half-tone (color or grayscale), keep to a minimum of 500 dpi.
Please do not:
• Supply files that are optimized for screen use (e.g., GIF, BMP, PICT, WPG); these typically have a low number of pixels and limited set of colors;
• Supply files that are too low in resolution;
• Submit graphics that are disproportionately large for the content.
Composite figures. In general, no more than four sections should appear in a single figure. If more than four sections are required, it is better to create several separate figures. Label individual sections in composite figures clearly with lower case letters, using (a), (b), (c).
Please make sure that artwork files are in an acceptable format (TIFF, EPS or MS Office files) and with the correct resolution. If, together with your accepted article, you submit usable color figures then Elsevier will ensure, at no additional charge, that these figures will appear in color on the Web (e.g., ScienceDirect and other sites) in addition to color reproduction in print. For further information on the preparation of electronic artwork, please see http://www.elsevier.com/artworkinstructions.
Ensure that each illustration has a caption. Supply captions next to each figure. A caption should comprise a brief title (not on the figure itself) and a description of the illustration. Keep text in the illustrations themselves to a minimum but explain all symbols and abbreviations used.
Please submit tables as editable text and not as images. Tables can be placed either next to the relevant text in the article, or on separate page(s) at the end. Number tables consecutively in accordance with their appearance in the text and place any table notes below the table body. Be sparing in the use of tables and ensure that the data presented in them do not duplicate results described elsewhere in the article. Please avoid using vertical rules and shading in table cells.
Citation in text
Please ensure that every reference cited in the text is also present in the reference list (and vice versa). Unpublished results and personal communications are not recommended in the reference list, but may be mentioned in the text. If these references are included in the reference list they should follow the standard reference style of the journal and should include a substitution of the publication date with either "Unpublished results" or "Personal communication". Citation of a reference as "in press" implies that the item has been accepted for publication and a copy of the title page of the relevant article must be submitted.
As a minimum, the full URL should be given. Any further information, if known (DOI, author names, dates, reference to a source publication, etc.), should also be given. Reference to material which is available on the Internet but has not been published elsewhere should be made in the text only and should not be included in the reference list.
This journal encourages you to cite underlying or relevant datasets in your manuscript by citing them in your text and including a data reference in your Reference List. Data references should include the following elements: author name(s), dataset title, data repository, version (where available), year, and global persistent identifier. Add [dataset] immediately before the reference so we can properly identify it as a data reference. The [dataset] identifier will not appear in your published article.
Most Elsevier journals have their reference template available in many of the most popular reference management software products. These include all products that support Citation Style Language styles, such as Mendeley and Zotero, as well as EndNote. Using the word processor plug-ins from these products, authors only need to select the appropriate journal template when preparing their article, after which citations and bibliographies will be automatically formatted in the journal's style. If no template is yet available for this journal, please follow the format of the sample references and citations as shown in this Guide.
Users of Mendeley Desktop can easily install the reference style for this journal by clicking the following link:
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For the scientific journal, see Molecular Ecology.
Molecular ecology is a field of evolutionary biology that is concerned with applying molecular population genetics, molecular phylogenetics, and more recently genomics to traditional ecological questions (e.g., species diagnosis, conservation and assessment of biodiversity, species-area relationships, and many questions in behavioral ecology). It is virtually synonymous with the field of "Ecological Genetics" as pioneered by Theodosius Dobzhansky, E. B. Ford, Godfrey M. Hewitt and others. These fields are united in their attempt to study genetic-based questions "out in the field" as opposed to the laboratory. Molecular ecology is related to the field of Conservation genetics.
Methods frequently include using microsatellites to determine gene flow and hybridization between populations. The development of molecular ecology is also closely related to the use of DNA microarrays, which allows for the simultaneous analysis of the expression of thousands of different genes. Quantitative PCR may also be used to analyze gene expression as a result of changes in environmental conditions or different response by differently adapted individuals.
Molecular ecological techniques have recently been used to study in situ questions of bacterial diversity. This stems from the fact that many microorganisms are not easily obtainable as cultured strains in the laboratory, which would allow for identification and characterisation. It also stems from the development of PCR technique, which allows for rapid amplification of genetic material.
The amplification of DNA from environmental samples using general of group-specific primers leads to a mix of genetic material that has to be sorted out before sequencing and identification. The classic technique to achieve this is through cloning, which involves incorporating the amplified DNA fragments into bacterial plasmids. Techniques such as temperature gradient gel electrophoresis, allow for a faster result. More recently, the advent of relatively low-cost, next-generation DNA sequencing technologies, such as 454 and Illumina platforms, has allowed exploration of bacterial ecology in relation to continental-scale environmental gradients such as pH that was not feasible with traditional technology.
Exploration of fungal diversity in situ has also benefited from next-generation DNA sequencing technologies. The use of high-throughput sequencing techniques has been widely adopted by the fungal ecology community since the first publication of their use in the field in 2009. Similar to exploration of bacterial diversity, these techniques have allowed high-resolution studies of fundamental questions in fungal ecology such as phylogeography, fungal diversity in forest soils, stratification of fungal communities in soil horizons, and fungal succession on decomposing plant litter.
The majority of fungal ecology research leveraging next-generation sequencing approaches involves sequencing of PCRamplicons of conserved regions of DNA (i.e. marker genes) to identify and describe the distribution of taxonomic groups in the fungal community in question, though more recent research has focused on sequencing functional gene amplicons (e.g. Baldrian et al. 2012). The locus of choice for description of the taxonomic structure of fungal communities has traditionally been the internal transcribed spacer (ITS) region of ribosomal RNA genes  due to its utility in identifying fungi to genus or species taxonomic levels, and its high representation in public sequence databases. A second widely used locus (e.g. Amend et al. 2010, Weber et al. 2013), the D1-D3 region of 28S ribosomal RNA genes, may not allow the low taxonomic level classification of the ITS, but demonstrates superior performance in sequence alignment and phylogenetics. In addition, the D1-D3 region may be a better candidate for sequencing with Illumina sequencing technologies. Porras-Alfaro et al. showed that the accuracy of classification of either ITS or D1-D3 region sequences was largely based on the sequence composition and quality of databases used for comparison, and poor-quality sequences and sequence misidentification in public databases is a major concern. The construction of sequence databases that have broad representation across fungi, and that are curated by taxonomic experts is a critical next step.
Next-generation sequencing technologies generate large amounts of data, and analysis of fungal marker-gene data is an active area of research. Two primary areas of concern are methods for clustering sequences into operational taxonomic units by sequence similarity, and quality control of sequence data. Currently there is no consensus on preferred methods for clustering, and clustering and sequence processing methods can have a significant impact on results, especially for the variable-length ITS region. In addition, fungal species vary in intra-specific sequence similarity of the ITS region. Recent research has been devoted to development of flexible clustering protocols that allow sequence similarity thresholds to vary by taxonomic groups, which are supported by well-annotated sequences in public sequence databases.
In recent years, molecular data and analyses have been able to supplement traditional approaches of behavioral ecology, the study of animal behavior in relation to its ecology and evolutionary history. One behavior that molecular data has helped scientists better understand is extra-pair fertilizations (EPFs), also known as extra-pair copulations (EPCs). These are mating events that occur outside of a social bond, like monogamy and are hard to observe. Molecular data has been key to understanding the prevalence of and the individuals participating in EPFs.
While most bird species are socially monogamous, molecular data has revealed that less than 25% of these species are genetically monogamous. EPFs complicate matters, especially for male individuals, because it does not make sense for an individual to care for offspring that are not their own. Studies have found that males will adjust their parental care in response to changes in their paternity. Other studies have shown that in socially monogamous species, some individuals will employ an alternative strategy to be reproductively successful since a social bond does not always equal reproductive success.
It appears that EPFs in some species is driven by the good genes hypothesis (295). In red-back shrikes (Lanius collurio) extra-pair males had significantly longer tarsi than within-pair males, and all of the extra-pair offspring were males, supporting the prediction that females will bias their clutch towards males when they mate with an "attractive" male. In house wrens (Troglodytes aedon), extra-pair offspring were also found to be male-biased compared to within-offspring.
Without molecular ecology, identifying individuals that participate in EPFs and the offspring that result from EPFs would be impossible.
Isolation by distance
Isolation by distance (IBD), like reproductive isolation, is the effect of physical barriers to populations that limit migration and lower gene flow. The shorter the distance between populations the more likely individuals are to disperse and mate and thus, increase gene flow. The use of molecular data, specifically allele frequencies of individuals among populations in relation to their geographic distance help to explain concepts such as, sex-biased dispersal, speciation, and landscape genetics.
The Mantel test is an assessment that compares genetic distance with geographic distance and is most appropriate because it doesn't assume that the comparisons are independent of each other. There are three main factors that influence the chances of finding a correlation of IBD, which include sample size, metabolism, and taxa. For example, based on the meta-analysis, ectotherms are more likely than endotherms to display greater IBD.
Metapopulation theory dictates that a metapopulation consists of spatially distinct populations that interact with one another on some level and move through a cycle of extinctions and recolonizations (i.e. through dispersal). The most common metapopulation model is the extinction-recolonization model which explains systems in which spatially distinct populations undergo stochastic changes in population sizes which may lead to extinction at the population level. Once this has occurred, dispersing individuals from other populations will immigrate and "rescue" the population at that site. Other metapopulation models include the source-sink model (island-mainland model) where one (or multiple) large central population(s) produces disperses to smaller satellite populations that have a population growth rate of less than one and could not persist without the influx from the main population.
Metapopulation structure and the repeated extinctions and recolonizations can significantly affect a population's genetic structure. Recolonization by a few dispersers leads to population bottlenecks which will reduce the effective population size (Ne), accelerate genetic drift, and deplete genetic variation. However, dispersal between populations in the metapopulation can reverse or halt these processes over the long term. Therefore, in order for individual sub-populations to remain healthy, they must either have a large population size or have a relatively high rate of dispersal with other subpopulations. Molecular ecology focuses on using tests to determine the rates of dispersal between populations and can use molecular clocks to determine when historic bottlenecks occurred. As habitat becomes more fragmented, dispersal between populations will become increasingly rare. Therefore, subpopulations that may have historically been preserved by a metapopulation structure may start to decline. Using mitochondrial or nuclear markers to monitor dispersal coupled with population Fst values and allelic richness can provide insight into how well a population is performing and how it will perform into the future.
The molecular clock hypothesis states that DNA sequences roughly evolve at the same rate and because of this the dissimilarity between two sequences can be used to tell how long ago they diverged from one another. The first step in of using a molecular clock is it must be calibrated based on the approximate time the two lineages being study diverged. The sources usually used to calibrate the molecular clocks are fossils or known geological events in the past. After calibrating the clock the next step is to calculate divergence time by dividing the estimated time since the sequences diverged by the amount of sequence divergence. The resulting number is the estimated rate at which molecular evolution is occurring. The most widely cited molecular clock is a ‘universal’ mtDNA clock of approximately 2 per cent sequence divergence every million years. Although it is referred to as a universal clock, this idea of "universal" clock is not really possible considering rates of evolution differ within DNA regions. Another drawback to using molecular clocks is that they ideally need to be calibrated from an independent source of data other than the molecular data. This poses a big problem for taxa that don’t fossilize or preserve well because its almost impossible to calibrate their molecular clocks. Despite these inconveniences, the molecular clock hypothesis is still used today, and has been successful in dating events happening as long ago as 65 million years such as the emergence of ancestral mammals.
Mate choice hypotheses
The concept of mate choice explains how organisms select their mates based on two main methods; The Good Genes Hypothesis and Genetic Compatibility. The Good Genes Hypothesis, also referred to as the sexy son hypothesis, suggests that the females will choose a male that produce an offspring that will have increased fitness advantages and genetic viability. Therefore, the mates that are more 'attractive" are more likely to be chosen for mating and pass on their genes to the next generation. In species which exhibit polyandry the females will search out for the most suitable males and re-mate until they have found the best sperm to fertilize their eggs. Genetic compatibility is where mates are choosing their partner based on the compatibility of their genotypes. The mate which is doing the selecting must know their own genotype as well as the genotypes of potential mates in order to select the appropriate partner. Genetic compatibility in most instances is limited to specific traits, such as the major histocompatibility complex in mammals, because of complex genetic interactions. This behavior is potentially seen in humans. A study looking at women's choice in men based on body odors concluded that the scent of the odors were influenced by the MHC and that they impact for mate choice in human populations.
Sex-biased dispersal, or the tendency of one sex to disperse between populations more frequently than the other, is a common behavior studied by researchers. Three major hypotheses currently exist to help explain sex-biased dispersal. The resource-competition hypothesis infers that the more philopatric sex (the sex more likely to remain at its natal grounds) benefits during reproduction simply by having familiarity with natal ground resources. A second proposal for sex-biased dispersal is the local mate competition hypothesis, which introduces the idea that individuals encounter less mate competition with relatives the farther from their natal grounds they disperse. And the inbreeding avoidance hypothesis suggests individuals disperse to decrease inbreeding.
Studying these hypotheses can be arduous since it is nearly impossible to keep track of every individual and their whereabouts within and between populations. To combat this time-consuming method, scientists have recruited several molecular ecology techniques in order to study sex-biased dispersal. One method is the comparison of differences between nuclear and mitochondrial markers among populations. Markers showing higher levels of differentiation indicate the more philopatric sex; that is, the more a sex remains at natal grounds, the more their markers will take on a unique I.D, due to lack of gene flow with respect to that marker. Researchers can also quantify male-male and female-female pair relatedness within populations to understand which sex is more likely to disperse. Pairs with values consistently lower in one sex indicate the dispersing sex. This is because there is more gene flow in the dispersing sex and their markers are less similar than individuals of the same sex in the same population, which produces a low relatedness value. FST values are also used to understand dispersing behaviors by calculating an FST value for each sex. The sex that disperses more displays a lower FST value, which measures levels of inbreeding between the subpopulation and the total population. Additionally, assignment tests can be utilized to quantify the number of individuals of a certain sex dispersing to other populations. A more mathematical approach to quantifying sex-biased dispersal on the molecular level is the use of spatial autocorrelation. This correlation analyzes the relationship between geographic distance and spatial distance. A correlation coefficient, or r value, is calculated and the plot of r against distance provides an indication of individuals more related to or less related to one another than expected.
Quantitative trait loci
A quantitative trait locus (QTL) refers to a suite of genes that controls a quantitative trait. A quantitative trait is one that is influenced by several different genes as opposed to just one or two. QTLs are analyzed using Qst. Qst looks at the relatedness of the traits in focus. In the case of QTLs, clines are analyzed by Qst. A cline (biology) is a change in allele frequency across a geographical distance. This change in allele frequency causes a series of intermediate varying phenotypes that when associated with certain environmental conditions can indicate selection. This selection causes local adaptation, but high gene flow is still expected to be present along the cline.
For example, barn owls in Europe exhibit a cline in reference to their plumage coloration. Their feathers range in coloration from white to reddish-brown across the geological range of the southwest to the northeast. This study sought to find if this phenotypic variation was due to selection by calculating the Qst values across the owl populations. Because high gene flow was still anticipated along this cline, selection was only expected to act upon the QTLs that incur locally adaptive phenotypic traits. This can be determined by comparing the Qst values to Fst (fixation index) values. If both of these values are similar and Fst is based on neutral markers then it can be assumed that the QTLs were based on neutral markers (markers not under selection or locally adapted) as well. However, in the case of the barn owls the Qst value was much higher than the Fst value. This means that high gene flow was present allowing the neutral markers to be similar, indicated by the low Fst value. But, local adaptation due to selection was present as well, in the form of varying plumage coloration since the Qst value was high, indicating differences in these non-neutral loci. In other words, this cline of plumage coloration has some sort of adaptive value to the birds.
Fixation indices are used when determining the level of genetic differentiation between sub-populations within a total population. FST is the script used to represent this index when using the formula:
In this equation, HT represents the expected heterozygosity of the total population and HS is the expected heterozygosity of a sub-populations. Both measures of heterozygosity are measured at one loci. In the equation, heterozygosity values expected from the total population are compared to observed heterozygosity values of the sub-populations within this total population. Larger FST values imply that the level of genetic differentiation between sub-populations within a total population is more significant. The level of differentiation is the result of a balance between gene flow amongst sub-populations (decreasing differentiation) and genetic drift within these sub-populations (increasing differentiation); however, some molecular ecologists note that it cannot be assumed that these factors are at equilibrium. FST can also be viewed as a way of comparing the amount of inbreeding within sub-populations to the amount of inbreeding for the total population and is sometimes referred to as an inbreeding coefficient. In these cases, higher FST values typically imply higher amounts of inbreeding within the sub-populations. Other factors such as selection pressures may also have an impact on FST values.
FST values are accompanied by several analog equations (FIS, GST, etc.).These additional measures are interpreted in a similar manner to FST values; however, they are adjusted to accompany other factors that FST may not, such as accounting for multiple loci.
Inbreeding depression is the reduced fitness and survival of offspring from closely related parents. Inbreeding is commonly seen in small populations because of the greater chance of mating with a relative due to limited mate choice. Inbreeding, especially in small populations, is more likely to result in higher rates of genetic drift, which leads to higher rates of homozygosity at all loci in the population and decreased heterozygosity. The rate of inbreeding is based on decreased heterozygosity. In other words, the rate at which heterozygosity is lost from a population due to genetic drift is equal to the rate of accumulating inbreeding in a population. In the absence of migration, inbreeding will accumulate at a rate that is inversely proportional to the size of the population.
There are two ways in which inbreeding depression can occur. The first of these is through dominance, where beneficial alleles are usually dominant and harmful alleles are usually recessive. The increased homozygosity resulting from inbreeding means that harmful alleles are more likely to be expressed as homozygotes, and the deleterious effects cannot be masked by the beneficial dominant allele. The second method through which inbreeding depression occurs is through overdominance, or heterozygote advantage. Individuals that are heterozygous at a particular locus have a higher fitness than homozygotes at that locus. Inbreeding leads to decreased heterozygosity, and therefore decreased fitness.
Deleterious alleles can be scrubbed by natural selection from inbred populations through genetic purging. As homozygosity increases, less fit individuals will be selected against and thus those harmful alleles will be lost from the population.
Outbreeding depression is the reduced biological fitness in the offspring of distantly related parents. The decline in fitness due to outbreeding is attributed to a breakup of coadapted gene complexes or favorable epistatic relationships. Unlike inbreeding depression, outbreeding depression places emphasis on interactions between loci rather than within them.
Risks of outbreeding depression increase with increased distance between populations. If outbreeding is limited and the population is large enough selective pressure acting on each generation may be able to restore fitness. Selection acts on out bred generations using increased diversity to adapt to the environment. This may result in greater fitness among offspring than the original parental type.
Conservation units are classifications often used in conservation biology, conservation genetics, and molecular ecology in order to separate and group different species or populations based on genetic variance and significance for protection. Two of the most common types of conservation units are:
- Management Units (MU): Management units are populations that have very low levels of gene flow and can therefore be genetically differentiated from other populations.
- Evolutionarily significant units (ESU): Evolutionarily significant units are populations that show enough genetic differentiation to warrant their management as distinct units.
Conservation units are often identified using both neutral and non-neutral genetic markers, with each having its own advantages. Using neutral markers during unit identification can provide unbiased assumptions of genetic drift and time since reproductive isolation within and among species and populations, while using non-neutral markers can provide more accurate estimations of adaptive evolutionary divergence, which can help determine the potential for a conservation unit to adapt within a certain habitat.
Because of conservation units, populations and species that have high or differing levels of genetic variation are can be distinguished in order to manage each individually, which can ultimately differ based on a number of factors. In one instance, Atlantic salmon located within the Bay of Fundy were given evolutionary significance based on the differences in genetic sequences found among different populations. This detection of evolutionary significance can allow each population of salmon to receive customized conservation and protection based on their adaptive uniqueness in response to geographic location.
Phylogenies are the evolutionary history of an organism, also known as Phylogeography. A Phylogenetic tree is an tree that shows evolutionary relationships between different species based on similarities/differences among genetic or physical traits. Phylogenies embrace aspects of both time (evolutionary relationships) and space (geographic distribution). Typically phylogeny trees include tips, which represent groups of descendent species, and nodes, which represent the common ancestors of those descendants. If two descendants split from the same node, they are called Sister groups. They also may include an outgroup, a species outside of the group of interest. The trees depict clades, which is a group of organisms that include an ancestor and all descendants of that ancestor. The maximum parsimony tree is the simplest tree that has the minimum number of steps possible.
Phylogenies confer important historical processes that shape current distributions of genes and species. When two species become isolated from each other they retain some of the same ancestral alleles also known as allele sharing. Alleles can be shared because of lineage sorting and hybridization. Lineage sorting is driven by genetic drift and must occur before alleles become species specific. Some of these alleles over time will simply be lost, or they may proliferate. Hybridization leads to introgression of alleles from one species to another.
Species concepts are the subject of debate in the field of molecular ecology. Since the beginning of taxonomy, scientists have wanted to standardize and perfect the way species are defined. There are many species concepts that dictate how ecologists determine a good species. The most commonly used concept is the biological species concept which defines a species as groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups (Mayr, 1942). This concept is not always useful, particularly when it comes to hybrids. Other species concepts include phylogenetic species concept which describes a species as the smallest identifiable monophyletic group of organisms within which there is a parental pattern of ancestry and descent. This concept defines species on the identifiable. It would also suggest that until two identifiable groups actually produce offspring, they remain separate species. In 1999, John Avise and Glenn Johns suggested a standardized method for defining species based on past speciation and measuring biological classifications as time dependent. Their method used temporal banding to make genus, family and order based on how many tens of millions of years ago the speciation event that resulted in each species took place.
Landscape genetics is a rapidly emerging interdisciplinary field within molecular ecology. Landscape genetics relates genetics to landscape characteristics, such as land-cover use (forests, agriculture, roads, etc.), presence of barriers and corridors, rivers, elevation, etc. Landscape genetics is used to answer how landscape affects dispersal and gene flow.
Barriers are any landscape features that prevents dispersal. Barriers for terrestrial species can include mountains, rivers, roads, and unsuitable terrain, such as agriculture fields. Barriers for aquatic species can include islands or dams. Barriers are species specific; for example a river is a barrier to a field mouse, while a hawk can fly over a river. Corridors are areas over which dispersal is possible. Corridors are stretches of suitable habitat and can also be man-made, such as overpasses over roads and fish ladders on dams.
Geographic data used for landscape genetics can include data collected by radars in planes, land satellite data, marine data collected by NOAA, as well as any other ecological data. In landscape genetics researchers often use different analyses to attempt to determine the best way for a species to travel from point A to point B. Least cost path analysis uses geographic data to determine the most efficient path from one point to another. Circuit scape analysis predicts all the possible paths and the probability of each path's use between point A and point B. These analyses are used to determine the route a dispersing individual is likely to travel.
Landscape genetics is becoming an increasingly important tool in wildlife conservation efforts. It is being used to determine how habitat loss and fragmentation affects the movement of species. It is also used to determine which species need to be managed and whether to manage subpopulations the same or differently according to their gene flow.
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