INSTRUCTIONS FOR AUTHORS

ALL MANUSCRIPTS MUST:

• conform to the guidelines in the Council of Science Editors Style Manual (7th ed., 2006) Council of Science Editors Style Manual and to the style conventions described here
• be concise.
  Long articles attract more page charges; consider presenting large tables, sequence alignments, etc., as online supplements.
• use American English spelling and grammar
• be organized in the sequence described below
• be double-spaced for both initial and revised manuscript submission
• have 25-mm (1-in) page margins
• use a font no smaller than 12-point Times Roman
• use correct diacritics for non-English words
• include accession numbers for GENBank and other public databases for all newly-reported sequences and structural coordinates
• acknowledge funding sources in the acknowledgments
• be submitted as a .doc, LaTeX, TeX, .rtf, .ps or .pdf file
• include text, tables, and figure legends in a single file
  Tables should be listed at the end of the manuscript with the caption and number at the top of each table. Figure captions (but not figures themselves) should be listed after the tables at the end of the paper
• include figures as separate files
• Please note that upon initial submission only a complete (text, tables, figure legends, and figures) .pdf document is required

KEEP FORMATTING SIMPLE:

• avoid hyphenation, justification, linked and embedded objects and images, and other advanced word processing features, as they have to be removed during typesetting
• avoid nonstandard fonts (Symbol, Times/Times New Roman, Helvetica/Arial, Courier/Courier new, Computer Modern, and mathematical or symbol fonts are acceptable)
• be consistent in representing symbols
• distinguish similar-looking symbols (e.g., letter x, multiplication sign, and Greek chi; minus sign, hyphen, and dash)
• do not approximate characters by creating your own symbols (e.g., superscript o for degree symbol)
• do not approximate formatting (e.g., linebreak + tab for hanging indent)
• do not use underlining to indicate italics or in plus-minus signs

For useful information on preparing your figures for publication, please visit Sheridan's Web site.

Figures must:

• be numbered consecutively following the sequence in which they are mentioned in the text
• include scale bars where appropriate. These should not be placed in the legend
• be the size intended for publication. Maximum single column width = 8.2 cm/3.25 inches; 2 columns = 16.9 cm/6.75 inches; depth = 24 cm/9.25 inches
• have uniform lettering style
• not include sequences and alignments that exceed one journal page. Larger alignments must be submitted as online Supplementary Material at the MBE Web site and their availability indicated in print in the Supplementary Materials section.

Programs suitable for creating production-ready graphics files include the latest versions of:

* Preferred

• Adobe Photoshop (latest version)*
• Adobe Illustrator (latest version)*
• Canvas (version 7 or later)
• Corel Draw (version 7 or later)
• Macromedia FreeHand (version 8 or later)

Electronic versions of figures must:

• use Adobe Postscript fonts, NOT TrueType or system "bitmap" fonts
• be converted to grayscale or bitmap mode if originally in color but to be reproduced in black and white
• have any unnecessary white space cropped from around the outside of the image if the file is a TIFF file. Be careful not to crop any of the intended image
• each be saved in a separate file. If a figure has multiple parts (e.g., Fig. 1A, Fig. 1B) all parts should be saved into one file
• be submitted for publication at resolutions of 600 dots per inch for line figures and 300 dots per inch for half tones
• always use the latest version of the software program available. Files from older versions often lose integrity when opened in newer versions
• Figures must be submitted as .tif, .eps, .ppt, .xls, .doc, .pdf, .gif, or .jpg files. Contact the Editorial Office if you are not able to provide figures in one of the acceptable formats.

Files created using Microsoft PowerPoint are not suitable for production. If you are not able to provide figures in one of the above formats please contact the Editorial Office.

Color figures must:

• be in CMYK mode NOT RGB mode
• be saved at a resolution of at least 300 dots per inch.
• be paid for.
  Color figures will incur a charge of $450 per figure. Charges for color figures cannot be waived, nor will page charges be waived for manuscripts that include color figures. Figures can be published in black and white (normal page charges apply) in the article, with a color version published as supplementary material permanently linked to the online journal. There is no cost for publishing online supplementary material
• be submitted correctly. If you ticked the color charge approval box in Manuscript Central, the online submission site for the journal, you will incur color figure charges

All files must be given names that include BOTH the manuscript handling number AND the corresponding author's name. The manuscript submission system automatically allocates manuscript numbers of the form MBE-03-0058, where 03 is the year of submission and 0058 the manuscript number. Files pertaining to ms MBE-03-0058 submitted by author Chen should therefore be named Chen03-0058.pdf; Chen03-0058.rtf; Chen03-0058.eps; Chen03-0058.html, etc.

Sequence alignments can also be deposited at EMBL-ALIGN.

Authors will be notified of receipt of their manuscript by the online submission system. The Editor, Marcy Uyenoyama, is responsible for the peer review process and for deciding whether the manuscript should be accepted, returned for revision, or rejected. The corresponding author will be able to view the stage of processing of the manuscript at the submission system Web site. Authors will receive a final decision e-mail message from the Editor. If, at any time, you are dissatisfied with any aspect of the handling of your manuscript, or if you have any suggestions that might improve our performance, please contact the Editor.

Following review, resubmit revised manuscripts online. These must be submitted as .doc, .rtf, TeX, or LaTeX (for text), .tif or .eps files (for illustrations), and as listed above under Preparation of Supplementary Material (for supplementary materials). These are the files that will be used for production of the final printed and electronic files of your paper. This .pdf is the file that will appear on the Advance Access page. The .pdf must contain every part of the paper including tables, figures, and figure captions. It should not contain supplementary material files or file captions, but should reference such files within the text. Note that for production purposes tables must be double-spaced, each beginning on a new page, and that figure legends should be grouped together starting on a new page and should also be double spaced.

It is a condition of publication that authors grant an exclusive license to Oxford University Press. This ensures that requests from third parties to reproduce articles are handled efficiently and consistently and will also allow the article to be disseminated as widely as possible. As part of the license agreement, authors may use their own material in other publications, provided that the journal is acknowledged as the original place of publication and Oxford University Press is acknowledged as the publisher. The copyright license form is available here and should be signed and submitted immediately upon acceptance.

As an integral part of the online submission process, Corresponding authors are required to confirm whether they or their co-authors have any conflicts of interest to declare, and to provide details of these. If the Corresponding author is unable to confirm this information on behalf of all co-authors, the authors in question will then be required to submit a completed Conflict of Interest form to the Editorial Office. It is the Corresponding author’s responsibility to ensure that all authors adhere to this policy.

If the manuscript is published, Conflict of Interest information will be communicated in a statement in the published paper.

For information about this journal's policy, please visit our Author Self-Archiving policy page.

MBE authors have the option, at an additional charge, to make their paper freely available online immediately upon publication, under the Oxford Open initiative. After your manuscript is accepted, as part of the mandatory licence form required of all corresponding authors, you will be asked to indicate whether or not you wish to pay to have your paper made freely available immediately. If you do not select the Open Access option, your paper will be published with standard subscription-based access and you will not be charged.

Permission to reproduce copyright material, for print and online publication in perpetuity, must be cleared and if necessary paid for by the author; this includes applications and payments to DACS, ARS, and similar licensing agencies where appropriate. Evidence in writing that such permissions have been secured from the rights-holder must be made available to the editors. It is also the author's responsibility to include acknowledgements as stipulated by the particular institutions. Oxford Journals can offer information and documentation to assist authors in securing print and online permissions: please see the Guidelines for Authors section. Information on permissions contacts for a number of main galleries and museums can also be provided. Should you require copies of this, please contact the editorial office of the journal in question or the Oxford Journals Rights department.

• Abbreviations and symbols should follow the International System of Units (SI)
• Nonstandard abbreviations must be defined at first occurrence, in both abstract and main text
• Species must be identified by italicized scientific binomens. Generic names that are also common names should not be italicized unless they form part of a binomen (thus an investigation may involve Drosophila melanogaster or D. melanogaster, but a comparison would be made between Drosophila and human genes). Binomen abbreviations of the form "Gsp" (Genus, species) as, for example, "Hsa" for Homo sapiens may be used in tables and figures
• Genetic loci must be italicized and must follow the established rules of genetic nomenclature that have been established for the various organisms (e.g. HUGO Nomenclature Committee, the International Immunogenetics Database, Mouse Nomenclature Guidelines, or Mendel-GFDb (plants)
• The International Union of Pure and Applied Chemistry and the International Union of Biochemistry and Molecular Biology rules of nomenclature must be followed for amino acids, peptides, proteins, enzymes, nucleic acids, polynucleotides, carbohydrates, and lipids
• Mathematical equations must be presented with correct spacing between characters. Characters in equations and their counterparts in the text will be set in italics unless the author specifies otherwise the first time a character appears. Equations must be numbered sequentially, in Arabic numerals in parentheses, on the right-hand side of the page
• Statistical inferences, including those used for phylogenetic estimation, must be soundly based. Where appropriate, the assumptions underlying statistical inferences should be made explicit and sources of error should be clearly identified
• The IUBMB single-letter code for nucleotide bases including ambiguity is as follows: A = adenine; C = cytosine; G = guanine; T = thymine; U = uracil; R = A/G (purine); Y = C/T (pyrimidine); M = A/C; W = A/T; S = C/G; K = G/T; B = C/G/T (not A); D = A/G/T (not C); H = A/C/T (not G); V = A/C/G (not T); and N = X = A/C/G/T (any or unknown). For ambiguous nucleotides, T and U are equivalent
• Effective interdisciplinary communication requires that the precise meaning of words be understood in both disciplines. The following conventions should generally be followed
  1. When aligned sequences are compared, differences, not changes, may be observed. Changes can only be inferred, and a single difference may result from multiple changes.
  2. The word "invariant" has two common but different meanings, invariable and unvaried. Either can be used, but the meaning must be clear.
  3. A mutation generally occurs in a single individual and gives rise to an allele. If an allele achieves some frequency in a population it can be referred to as a polymorphism (not a "common [or rare] mutation"). If it has become fixed in a population it may be referred to as a substitution.
  4. If two molecules are alike in some degree, they are similar. If it is inferred from their similarity that they have a common ancestor, then they are homologous, but if their similarity was acquired by convergence, they are analogous. When homology arises via a gene duplication (all or part), it is paralogy; when it arises via speciation, it is orthology; when it arises by horizontal gene transfer, it is xenology.
  5. The phrase "insertions and/or deletions" may be reduced to "indels."
  6. Gaps are introduced into sequences to increase their similarity rather than to optimize similarity, unless an algorithm is employed that guarantees an optimized result according to the way similarity is defined (e.g., as maximum matches).
  7. Similarity should not be asserted to be significant unless accompanied by a probability statement and its method of determination.