1. Integrating manuscript processing with the Dryad Digital Repository A step-by-step overview March 2014 1datadryad.org

2. BASIC PROCESS – ARCHIVING AT ARTICLE ACCEPTANCE 2datadryad.org

3. Submit manuscript Author submits manuscript to journal 3datadryad.org

4. Peer review Acceptance notification Submit manuscript Journal sends… 1.notification to Dryad system of manuscript acceptance 2.request to author to deposit data to Dryad, including custom link for the manuscript Dryad creates provisional record for the manuscript, with authors, title, abstract, etc. 4datadryad.org

5. Journal Name: Molecular Ecology Journal Code: XXXX Print ISSN: 0962-1083 Online ISSN: 1365-294X Journal Admin Email: editorial.office@molecol.comeditorial.office@molecol.com Journal Editor: Tim Vines Journal Editor Email: managing.editor@molecol.commanaging.editor@molecol.com Article Status: accepted MS Reference Number: XXXXX MS Title: Contrasting pattern of natural variation in global Drosophila melanogaster populations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian Contact Author: Maria Nunes Contact Author Email: (removed) Contact Author Address 1: (removed) Contact Author Address 2: Contact Author Address 3: Contact Author City: (removed) Contact Author State: Contact Author Country: (removed) Contact Author ZIP/Postal Code: (removed) Keywords: Molecular Evolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey using neutral microsatellites and mitochondrial sequence variation jointly........ Sample email notice from integrated journal to Dryad, sent upon ms acceptance: 5datadryad.org Bolded fields are mandatory

6. Sample email from journal to author inviting data deposit, providing the custom Dryad link: Dear XXXXXXXXXXX, Congratulations again on the acceptance of your manuscript, XXXXXXXXXXXX We would like to encourage you to deposit the data underlying this article in the Dryad Data Repository, at http://datadryad.org. As you may recall, we ask all authors to agree to make data available. This is a way to achieve that. Advantages of depositing data in Dryad include: * Visibility: Making your data available online (and linking it back to the publication) provides a new pathway for others to learn about your work through topical searches. * Citability: all data packages and data files you deposit will receive persistent, resolvable Digital Object Identifiers (DOIs) that can be used in a citation as well as listed on your CV. * Workload reduction: if you receive individual requests for data, you can simply direct them to the items in Dryad. * Preservation: your data files will be permanently and safely archived in perpetuity. * Impact: you will garner citations through the reuse of your data, and you can monitor the use of your data through Dryad's usage statistics The link below will take you to the Dryad record for your article, so you won't have to re-enter its bibliographic information, and can upload your files directly. More information about depositing data in Dryad is available at datadryad.org/depositing. Please use the following link: EXAMPLE: http://datadryad.org/submit?journalID=NNNN&manu=XXXXX (where NNNN is replaced by journal ID and XXXXX is replaced with a real manuscript number) Once you deposit your data package, it receives a unique and stable DOI identifier, which is immediately sent back to you and to the journal for inclusion in the published article. Depositing your data in good time for this to happen is optimal; if the Dryad DOI doesn't appear in the final published article, that of course greatly weakens its connection to the underlying data. 6datadryad.org

7. Submit data Peer review Acceptance notification Submit manuscript Author submits data to Dryad, using the link sent by the journal. 7datadryad.org

8. Submit data Peer review Acceptance notification Curation Data DOI Production Submit manuscript Dryad curator… 1. reviews & approves the data files 2.notifies journal and author of DOI 8datadryad.org

9. Thank you for your recent submission to the Dryad repository titled "Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations". Your data package has been archived in Dryad and assigned a unique identifier, called a DOI. Including the data DOI in the published article will make readers aware that the data files are available, and enable their access and citation. The DOI may be presented as follows: Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.123abc Dryad links your data to your published article; it is up to authors and journals to link the published article to its supporting data. Please work with your journal’s editorial and production staff to ensure that the data DOI is included. Many journals specify a particular location for such links to data in repositories, or have a section for Data Accessibility. You can also provide your data DOI in the text, just before the References. If your article has already been published, use this DOI to refer others to your data. Please let us know if you have any questions or concerns. The Dryad Team Sample email notice from Dryad to author indicating data package DOI: 9datadryad.org

10. Weekly report to journal In the week since the last report (2013-06-14), Dryad has received the following. New notifications of accepted publications in this journal: 2 New deposits associated with publications in this journal: 2 Please find the data DOIs for new deposits below, for inclusion in the published articles. Layton EVA-2013-048-OA.R1 doi:10.5061/dryad.13j34 Smith-Rodel EVA-2013-104-OA doi:10.5061/dryad.m9st63 The DOI may be presented as below: Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.NNNN Dryad links the data files to the published articles; it is up to journals to link published articles to their supporting data. Journal staff and authors collaborate to ensure that data DOIs are included in the appropriate locations for the print and online versions of published articles. datadryad.org10

11. Submit data Peer review Acceptance notification Curation Data DOI Production Submit manuscript Article Publication Article Publication Data publicatio n Journal article is published with link to data DOI Dryad publishes data files with reference to article 11datadryad.org

12. Submit data Peer review Acceptance notification Curation Data DOI Production Submit manuscript Article Publication Article Publication Data publicatio n Curation After article publication, Dryad updates the article citation to include final bibliographic details 12datadryad.org

13. Submit data Peer review Acceptance notification Curation Data DOI Production Submit manuscript Article Publication Article Publication Data publicatio n Curation Journals are only responsible for the notification circled in red. 13datadryad.org

14. REVIEW WORKFLOW 14datadryad.org

15. Submit manuscript Author submits manuscript to journal 15datadryad.org

16. Manuscript metadata Submit manuscript Journal sends… 1.notification to Dryad of submitted manuscript 2.request to author to upload data to Dryad, including URL Dryad creates provisional record for the manuscript, with authors, title, abstract, etc. 16datadryad.org

17. Journal Name: Molecular Ecology Journal Code: XXXX Print ISSN: 0962-1083 Online ISSN: 1365-294X Journal Admin Email: editorial.office@molecol.comeditorial.office@molecol.com Journal Editor: Tim Vines Journal Editor Email: managing.editor@molecol.commanaging.editor@molecol.com Article Status: Submitted MS Reference Number: XXXXX MS Title: Contrasting pattern of natural variation in global Drosophila melanogaster populations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian Contact Author: Maria Nunes Contact Author Email: (removed) Contact Author Address 1: (removed) Contact Author Address 2: Contact Author Address 3: Contact Author City: (removed) Contact Author State: Contact Author Country: (removed) Contact Author ZIP/Postal Code: (removed) Keywords: Molecular Evolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey..................... First email notice from integrated journal to Dryad, sent at manuscript submission: 17datadryad.org Bolded fields are mandatory

18. Sample email from journal to author, inviting data deposit & providing the custom Dryad URL: Dear XXXXXXXXXXX, Thank you for submission of your manuscript, XXXXXXXXXXXX We would like to encourage you to deposit the data underlying this article in the Dryad Data Repository, http://datadryad.org. As you may recall, we ask all authors to agree to make data available. This is a way to achieve that. Advantages of depositing data in Dryad include: * Visibility: Making your data available online (and linking it back to the publication) provides a new pathway for others to learn about your work through topical searches. * Citability: all data packages and data files you deposit will receive persistent, resolvable Digital Object Identifiers (DOIs) that can be used in a citation as well as listed on your CV. * Workload reduction: if you receive individual requests for data, you can simply direct them to the items in Dryad. * Preservation: your data files will be permanently and safely archived in perpetuity. * Impact: you will garner citations through the reuse of your data, and you can monitor the use of your data through Dryad's usage statistics The link below will take you to the Dryad record for your article, so you won't have to re-enter its bibliographic information, and can upload your files directly. More information about depositing data in Dryad is available at http://www.datadryad.org/depositing. Please use the following link: EXAMPLE: http://datadryad.org/submit?journalID=NNNN&manu=XXXXX (where NNNN is replaced by journal ID and XXXXX is replaced with a real manuscript number) Once you deposit your data package, it receives a unique and stable DOI identifier, which is immediately sent back to you and to the journal for inclusion in the published article. Depositing your data in good time for this to happen, is optimal; if the Dryad DOI doesn't appear in the final published article, that of course greatly weakens its connection to the underlying data. 18datadryad.org

19. Submit data Submission notification Submit manuscript Author submits data to Dryad, using the link sent by the journal to the provisional record. 19datadryad.org

20. Submit data Submission notification Peer review Review passcode Submit manuscript Dryad sends review passcode to journal. 20datadryad.org

21. Dryad has received the following data package: Title: Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations Submitted by: Jane User (jane@someuniversity.edu)jane@someuniversity.edu) Data file(s): Microsatellite data Microsatellite Primers Dryad has assigned the following provisional DOI to the submission. This DOI may be included in the article manuscript. Although this DOI is not yet fully registered with the DOI system, it will be registered when the manuscript is accepted for publication. doi:10.5061/dryad.123abc Journal editors and anonymous peer reviewers may view the submission for review purposes using the following url: http://datadryad.org/submission-review?wfID=517&token=d8420534-3477-4986-9366-bb17856d818b Many thanks! The Dryad Team Sample email notice from Dryad with review passcode URL: 21datadryad.org

22. Submit data Submission notification Peer review Review passcode Acceptance notification Curation Data DOI Production Submit manuscript Dryad curator… 1. reviews & approves data files 2.notifies journal and author of DOI At article acceptance, journal… 1.notifies Dryad 2.includes Dryad DOI in article 22datadryad.org

23. Journal Name: Molecular Ecology Journal Code: XXXX Print ISSN: 0962-1083 Online ISSN: 1365-294X Journal Admin Email: editorial.office@molecol.comeditorial.office@molecol.com Journal Editor: Tim Vines Journal Editor Email: managing.editor@molecol.commanaging.editor@molecol.com Article Status: accepted MS Reference Number: XXXXX MS Title: Contrasting pattern of natural variation in global Drosophila melanogaster populations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian Contact Author: Maria Nunes Contact Author Email: (removed) Contact Author Address 1: (removed) Contact Author Address 2: Contact Author Address 3: Contact Author City: (removed) Contact Author State: Contact Author Country: (removed) Contact Author ZIP/Postal Code: (removed) Keywords: Molecular Evolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey using neutral microsatellites and mitochondrial sequence variation jointly........ Second email notice from integrated journal to Dryad, sent upon ms acceptance: 23datadryad.org Bolded fields are mandatory

24. Thank you for your recent submission to the Dryad repository titled "Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations". Your data package has been archived in Dryad and assigned a unique identifier, called a DOI. Including the data DOI in the published article will make readers aware that the data files are available, and enable their access and citation. The DOI may be presented as follows: Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.123abc Dryad links your data to your published article; it is up to authors and journals to link the published article to its supporting data. Please work with your journals editorial and production staff to ensure that the data DOI is included. Many journals specify a particular location for such links to data in repositories, or have a section on Data Accessibility. You can also provide your data DOI in the text, just before the References. If your article has already been published, use this DOI to refer others to your data. Please let us know if you have any questions or concerns. The Dryad Team Sample email notice from Dryad to author indicating data package DOI 24datadryad.org

25. Weekly report to journal In the week since the last report (2013-06-14), Dryad has received the following. New notifications of manuscripts in review: 9 New deposits of data in review: 0 New notifications of accepted publications in this journal: 4 New archived deposits associated with publications in this journal: 2 Please find the data DOIs for new deposits below, for inclusion in the published articles. Almira JRL-2013-002924.R1 doi:10.5061/dryad.jv45h Magnusson JRL-2013-002791.R2 doi:10.5061/dryad.58vg9 The DOI may be presented as below: Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.NNNN Dryad links the data files to the published articles; it is up to journals to link published articles to their supporting data. Journal staff and authors collaborate to ensure that data DOIs are included in the appropriate locations for the print and online versions of published articles datadryad.org25

26. Submit data Submission notification Peer review Review passcode Acceptance notification Curation Data DOI Production Article Publication Article Publication Data publicatio n Submit manuscript Journal article is published with Dryad data DOI Dryad publishes data files with link to article 26datadryad.org

27. Submit data Submission notification Peer review Review passcode Acceptance notification Curation Data DOI Production Curation Submit manuscript This may look complicated, but journals are only responsible for the two notifications circled in red, and the first is only required if the review workflow is used. 27datadryad.org Article Publication Article Publication Data publicatio n

28. DATA CITATION 28datadryad.org

29. Article: Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. PLoS ONE 6(3): e18011. doi:10.1371/journal.pone.0018011doi:10.1371/journal.pone.0018011 Dryad data package: Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.838410.5061/dryad.8384 Dryad cites the article and its DOI, and the article cites the data and the Dryad DOI. This establishes a permanent reciprocal linkage between the article and its data. 29datadryad.org

30. For more information… Complete documentation & examples are on the Dryad wiki: http://wiki.datadryad.org/Submission_Integration Contact the Dryad team: – Ryan Scherle admin@datadryad.org – Peggy Schaeffer pschaeffer@datadryad.org – Jamie Lamkin jlamkin@datadryad.org – journalsetup@datadryad.org 30datadryad.org