Supplemental material 1: Journal archiving policies

BMC Evolutionary Biology - http://www.biomedcentral.com/bmcevolbiol/about

Data and materials release
Submission of a manuscript to BMC Evolutionary Biology implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes. Nucleic acid sequences, protein sequences, and atomic coordinates should be deposited in an appropriate database in time for the accession number to be included in the published article. In computational studies where the sequence information is unacceptable for inclusion in databases because of lack of experimental validation, the sequences must be published as an additional file with the article.
Any 'in press' articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.

Biological Journal of the Linnean Society - http://www.wiley.com/bw/journal.asp?ref=0024-4066

Data archiving
Data that is integral to the paper must be made available in such a way as to enable readers to replicate, verify and build upon the conclusions published in the paper. Any restriction on the availability of this data must be disclosed at the time of submission. Data may be included as part of the main article where practical. We recommend that data for which public repositories are widely used, and are accessible to all, should be deposited in such a repository prior to publication. The appropriate linking details and identifier(s) should then be included in the publication and where possible the repository, to facilitate linking between the journal article and the data. If such a repository does not exist, data should be included as supporting information to the published paper or authors should agree to make their data available upon reasonable request.

Journal of Heredity - http://www.oxfordjournals.org/our_journals/jhered/for_authors/msprep_submission.html#4. 

DATA ARCHIVING POLICY
The primary data underlying the conclusions of an article are critical to the verifiability and transparency of the scientific enterprise, and should be preserved in usable form for decades in the future. For this reason, Journal of Heredity requires that newly reported nucleotide or amino acid sequences, and structural coordinates, be submitted to appropriate public databases (e.g., GenBank; the EMBL Nucleotide Sequence Database; DNA Database of Japan; the Protein Data Bank ; and Swiss-Prot). Accession numbers must be included in the final version of the manuscript. For other forms of data (e.g., microsatellite genotypes, linkage maps, images), the Journal endorses the principles of the Joint Data Archiving Policy (JDAP) in encouraging all authors to archive primary datasets in an appropriate public archive, such as Dryad, TreeBASE, or the Knowledge Network for Biocomplexity. Authors are encouraged to make data publicly available at time of publication or, if the technology of the archive allows, opt to embargo access to the data for a period up to a year after publication.

The American Genetic Association also recognizes the vast investment of individual researchers in generating and curating large datasets. Consequently, we recommend that this investment be respected in secondary analyses or meta-analyses in a gracious collaborative spirit.

PLoS One - http://www.plosone.org/static/policies.action

7. Sharing of Materials, Methods, and Data
Publication is conditional upon the agreement of the authors to make freely available any materials and information described in their publication that may be reasonably requested by others for the purpose of academic, non-commercial research.

Availability of data and materials. PLoS is committed to ensuring the availability of data and materials that underpin any articles published in PLoS journals. PLoS's ideal is to make all data relevant to a given article and all readily replaceable materials immediately available without restrictions (while not compromising confidentiality in the context of human-subject research).

We appreciate, however, that this ideal is not yet the norm in all fields. We are therefore collaborating with a number of subject-specific initiatives in order to develop relevant policies. In the meantime, authors must comply with current best practice in their discipline for the sharing of data through databases: for example, deposition of microarray data in ArrayExpress or GEO; deposition of gene sequences in GenBank, EMBL or DDBJ; and deposition of ecological data in Dryad. We encourage all authors to comply with available field-specific standards for the preparation and recording of data; for more information, see below (section 8, Reporting Guidelines for Specific Study Designs).

Failure to comply with this policy will be taken into account when publication decisions are made. PLoS journal editors encourage researchers to contact them if they encounter difficulties in obtaining data or materials from articles published in PLoS journals. PLoS reserves the right to post corrections on articles, to contact authors' institutions and funders, and in extreme cases to withdraw publication, if restrictions on access to data or materials come to light after publication of a PLoS journal article.
Data for which public repositories have been established should be deposited before publication, and the appropriate accession numbers or digital object identifiers (DOIs) published with the paper.

If an appropriate repository does not exist, data should be provided in an open access institutional repository, a general data repository such as Dryad, or as Supporting Information files with the published paper. If none of these options is practical, data should be made freely available upon request.

The conclusions of a study must not depend solely on the analysis of proprietary data. If proprietary data were used to reach a conclusion, and the authors are unwilling or unable to make these data public, then the paper must include an analysis of public data that validates the conclusions so that others can reproduce the analysis and build on the findings. Any restrictions on the availability or use of datasets might be judged to diminish the significance of a paper and may therefore influence the decision about whether a paper should be published. These policies have been developed in accordance with the principles established in Sharing Publication-Related Data and Materials (National Academies Press, 2003).
Software. PLoS supports the development of open source software and believes that, for submissions in which software is the central part of the paper, adherence to appropriate open source standards will ensure that the submission conforms to (1) our requirements that methods be described in sufficient detail that another researcher can reproduce the experiments described, (2) our aim to promote openness in research, and (3) our intention that all work published in PLoS journals can be built upon by future researchers. Therefore, if new software or a new algorithm is central to a PLoS paper, the authors must confirm that the software conforms to the Open Source Definition, have deposited the following three items in an open software archive, and included in the submission as Supporting Information:

•	The associated source code of the software described by the paper. This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (see http://www.opensource.org/licenses/alphabetical for a full list). Dependency on commercial software such as Mathematica and MATLAB does not preclude a paper from consideration, although complete open source solutions are preferred.
•	Documentation for running and installing the software. For end-user applications, instructions for installing and using the software are prerequisite; for software libraries, instructions for using the application program interface are prerequisite.
•	A test dataset with associated control parameter settings. Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies — for example, a database dump.

Acceptable archives should provide a public repository of the described software. The code should be easy to locate and download without the requirement for creating user accounts, logging in or otherwise registering personal details. The repository must have been in existence for over five years or be hosting more than 1,000 projects. Examples of such archives are: SourceForge, Bioinformatics.Org, Open Bioinformatics Foundation (O|B|F), Google Code, BerliOS Developer, Savannah, GitHub and the Codehaus. Authors should provide a direct link to the deposited software from within the paper.

Deposition with the journal and in an open source archive ensures that the original source associated with the paper is available as well as any enhancements made after the paper is published. An article can be considered for publication if it covers a well-established project that has been providing an open source code repository for an extended amount of time. A condition of acceptance is that the software can be run by reviewers accessing the public software and that the results presented in the paper are reproducible. The software need run on only one hardware-software platform in common use by the readership (including MATLAB), although it must run without dependencies on proprietary or otherwise unobtainable ancillary software. Articles describing software that requires access to databases and other resources whose persistence is not guaranteed (e.g. individual laboratory databases without funding support) will not be considered. In addition, the results described in the paper must be reproducible when peer reviewers, editors, or readers run the software on the deposited dataset and with the provided control parameters.
When the software or algorithm is not central to the paper, we nevertheless encourage authors to make all relevant materials freely available.

Journal of Evolutionary Biology - http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1420-9101/homepage/ForAuthors.html

Data sharing
The Journal of Evolutionary Biology requires, as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, TreeBASE, Dryad, the Knowledge Network for Biocomplexity or other suitable long-term and stable public repositories. 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. Longer embargoes or exceptions to depositing data may be granted at the discretion of the Editor-in-Chief, especially for sensitive information such as human subject data or the location of endangered species. All accepted papers should provide accession numbers or DOI for data underlying the work that have been deposited, so that these can appear in the final accepted article.

Evolution - http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1558-5646/homepage/ForAuthors.html

Data archiving. As a condition for publication, Evolution requires that data used in the paper are archived. DNA sequence data must be submitted to GenBank and phylogenetic data to TreeBASE. Other types of data must be deposited in an appropriate public archive such as Dryad, the NCEAS Data Repository, or as supplementary online material associated with the paper published in Evolution. The data should be given with sufficient detail that, together with the contents of the paper, they allow each result in the published paper to be recreated. 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-in-Chief, especially for sensitive information such as the location of endangered species. Authors must state their intention to archive their data when they submit their manuscript and must confirm that this has been done before the manuscript is sent to press. If a repository is to be cited, the citation should include the sequence name and accession number, if available. The basic format for citing electronic resources is: Author's Last Name, First initial. Title of data package (e.g., Data from “Article name”). Data Repository Name, Data identifier (or DOI), address/URL. Please include on your title page the location of your data or where you intend to archive your data.

Heredity (4.56) - http://mts-hdy.nature.com/cgi-bin/main.plex?form_type=display_auth_instructions#datapolicy

DATA POLICY

Heredity subscribes to the Joint Data Archiving Policy agreed by several leading journals (see Butlin 2010 for further background information). For manuscripts submitted after 1 March 2011, archiving of the primary data on which the study is based is mandatory. We strongly believe that the free availability of data to other research scientists is beneficial to the development of our field of study and that electronic archiving now makes this goal attainable. The data archived should be sufficient for another scientist to repeat your analyses or conduct new analyses of their own. For a population genetic survey, for example, this would mean archiving genotypes of individuals but not raw data such as sequencer spectrograms or gel photographs. Similarly, for a QTL analysis individual genotypes and phenotypes would be archived.

Authors are strongly encouraged to follow established minimum guidelines for the reporting of biological data, wherever appropriate. Guidelines for many relevant data types are available from MIBBI: Minimum Information for Biological and Biomedical Investigations (www.mibbi.org). Advice on good practice in data archiving is provided by Whitlock (2011).

DNA sequences published in Heredity must be deposited in a publicly available database, usually EMBL/GenBank/DDBJ, and accession numbers must be included in the final version of the manuscript. Where public databases exist for other data types, such as microarray data (see www.ebi.ac.uk/Databases/microarray.html, for example), they must be used and the relevant reference should be included in the manuscript. Where no public database exists, authors must submit their data to the Dryad data repository (www.datadryad.org). On acceptance of an Original Article, the corresponding author will automatically receive an email with details of the steps necessary for submission to Dryad.

Dryad can accept data of any type. The data should be formatted for use in a relevant, readily available software package, ideally one which allows data export in a variety of formats (such as CREATE for population genetic data:https://bcrc.bio.umass.edu/pedigreesoftware/node/2). It is the corresponding author’s responsibility to ensure that sufficient metadata (such as sample locations, individual identities etc.) are provided to allow easy repetition of analyses presented in the manuscript. We recognise that some information may be sensitive (such as identities of subjects or locations of endangered species). Such information can excluded from the submission provided that this does not prejudice re-analysis of the data.

Original Articles must contain a section entitled ‘Data Archiving’ which specifies where the data used in the paper can be accessed. See the section under Format of Papers for details. Authors will be asked about data archiving during the manuscript submission process but data archiving is not mandatory until the paper has been accepted for publication. At that stage, the corresponding author will be asked to confirm that all relevant data have been appropriately archived and the manuscript will not be published until this confirmation, and relevant accession numbers or other data identifiers, have been received.

Where a paper describes new simulations or analytical methods, Heredity requires authors to make any relevant software publicly available wherever possible. The Dryad repository can accept code. We recognise that software may utilise proprietary code which the authors are not free to distribute and in such cases the requirement to submit code may be waived. Authors should consult the Editorial Office if in doubt.

We recognise that, in some cases, authors may wish to restrict access to their data while they perform additional analyses. Where the relevant database supports the use of embargoes on data access, Heredity will allow an access restriction of up to one year from the date of publication of the article. In exceptional circumstances, longer embargoes may be possible, at the discretion of the Managing Editor.

Molecular Ecology (6.45) - http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-294X/homepage/ForAuthors.html

Policy on data archiving
NOTE: the policy below comes into force for papers submitted after 1st January 2011, but we hope that authors will comply in the interim. DNA sequence data from either Sanger or next generation sequencing should continue to be archived in a public data base and the accession numbers included in the manuscript.

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

*Whitlock MC, McPeek MA, Rausher MD, Rieseberg LR, Moore AJ (2010) Data archiving. American Naturalist, 175, 145-146.