As a condition of publication, all data needed to recreate the results of a paper must be publicly accessible in usable format. We encourage authors to make their data and code available to reviewers upon first submission, and we require it for revisions and resubmissions.
- Dryad publishes a list of best practices (https://datadryad.org/stash/best_practices)
- The American Naturalist provides a checklist for authors preparing their data.
- (Word version of the Am Nat checklist)
- See also the Instructions for Authors for more detail
Archiving Data (Required)
Complete data deposition in a public data archive is a condition for publication in The American Naturalist (embargoes on data deposits are allowed). This is required only when a paper is resubmitted with revisions but can be included at the time of initial submission, if you wish. We recommend the Dryad repository for both data and code. There are no charges for Dryad during peer review. The American Society of Naturalists covers all the costs for publishing data in Dryad if a paper is accepted.
At the resubmission stage, data must be made available in a data repository to be checked by an editor before final acceptance. The data (and other repository files) are also made available to reviewers at this stage. If a paper is found to lack a complete and well-documented archive, the authors will be contacted. After publication, if the data archive is found to be insufficient to recreate the results of the study, the journal retains the right to publish an Editorial Expression of Concern noting the lack of complete data or to retract the paper.
Please deposit gene sequence data and original phylogenetic trees to GenBank or TreeBASE, respectively.
All accession numbers and DOIs for GenBank, TreeBASE, and Dryad must be included in accepted manuscripts before they go to Production.
Archiving Code for Analysis and Modelling (Required)
As part of our commitment to scientific reproducibility, The American Naturalist strongly encourages authors to provide any data analysis code (e.g., R or Python scripts or notebooks) used to generate statistical results, figures, and models. These may be provided as a single script or a separate script for each figure, table, or coherent set of analyses. This code should be included in a recommended repository or as a digital supplement to the submitted paper. The data repository should also contain all data files needed to run the code. This allows reviewers, editors, and readers, to check the statistical analysis if they so choose. All code should be clearly annotated to explain to a reader what each step in the code is intended to do and how it maps onto the contents of the manuscript (e.g., identifying figures by number). Include version numbers of all packages accessed by the code and the version of software (e.g., R or Python) used in the analysis.
Citing Published Data (Required)
When you use a data set, be sure to cite it in your article using the DataCite DOI and be sure the citation occurs in the Literature Cited section of your article as well as in the text. The data citation in the Literature Cited should include the name of the database, a record locator or descriptor, an access date, the URL, and the DOI if available.
Reporting and Archiving Sequence Data (Required)
DNA should be sequenced on both strands. The sequences of all PCR primers used should be clearly stated either in the text or in cited references. Variation inferred from cloned allelic sequences should consider polymerase error and in vitro recombination. All new nucleotide sequence data must be submitted to Genbank or EMBL.
Laboratory and Field Protocols (Optional)
The American Naturalist strongly encourages authors of empirical papers to deposit detailed laboratory and field protocols at protocols.io. Your protocol will be hidden from the public (except editors and reviewers with the DOI), until you select Publish on the protocols.io website. Upon publication, any protocols.io entries in the published paper will automatically become public. Write a step-by-step protocol with photographs, or links to videos, where relevant. When using commercial products, you should include the vendor and catalogue number. All details that you might record to train a new lab member on how to implement a given protocol, should be documented. This helps others replicate your methods, but also can serve as a resource for your own lab members and collaborators in the future.