• Adequate proof of this permission or a clear indication of how the access was allowed under local or international law must be provided at submission.
• If verbal permission was obtained then the name and authority of the person who gave it must be provided.

Camera Traps, Drones and Passive Acoustic Monitoring: Wildlife studies using recording devices to record still/video images and/or audio have the potential to capture human subjects. This has implications for privacy, and — in the event that illegal acts are captured — a duty on the part of the researcher to report them. There might also be issues of personal safety in the latter case. See https://doi.org/10.1002/2688-8319.12033 and https://doi.org/10.1111/csp2.374 for more information.

Ideally, this should have been considered by the authors and their ethics committee before the study was approved but we understand that this is not currently a widespread practice. While the field is reaching a consensus on this matter, we ask authors who are reporting data from such studies to explain how the ethical approval/field permit they obtained relate to these issues, or explain why this was not considered necessary.

Where the study uses mobile platforms such as uncrewed aerial vehicles (UAVs/drones) these must have been operated in accordance with all applicable regulations.

This policy is likely to adapt as the field develops.

• FORCE11 has developed a useful overview for reporting in the life sciences. Please review these recommendations before submitting. Recommendations cover the following areas: Sequence Molecule Identification, Reporting of Antibodies, Reporting of Model Organisms, Reporting of Cell Lines, Constructs, and Reporting of Knockdown Reagents.
• Large domain-specific datasets should be deposited in a public repository (e.g. GenBank, INSDC, China National Gene Bank (CNGBdb), Protein Data Bank, UK Stem Cell Bank, Addgene, PRIDE, Panorama, RIKEN Bioresource Centre, ProteomeXchange, NP-MRD, MassIVE, MassBank) and an accession number or access address provided in the published article. Additional databases may be found by consulting the BioSharing database, re3data.org, or the NIH Data Sharing Repositories list.
• If you are reporting an assembled gene/genome/peptide etc. then you must deposit the raw reads and the assembled sequence in the appropriate databases (e.g. NCBI archives).
• Authors are encouraged to extend the utility of their manuscripts with the inclusion of helpful meta-data so that published works can find connections to other works in the public domain. Journal manuscripts are often scanned by text-mining software that locates and extracts core data elements, like gene function. Adding standard ontology terms, such as the Gene Ontology or others from the OBO Foundry can enhance the recognition of your contribution and description. This will also make human curation of literature easier and more accurate. Depending on the details of the data being presented, this information may be requested by editors.
• Where suitable domain-specific repositories do not exist, authors may deposit in Dryad, Dataverse, the Open Science Framework, or an institutional repository and provide the access information with the manuscript. Alternately, authors may choose to deposit non-standard data (including figures, posters, rich media) on Figshare for example. In all cases, the DOI reference (where applicable) should be provided in the article.
• Any supporting data sets for which there are no suitable repositories may be made available as publishable Supplemental Information files by PeerJ.
• Data should be provided in an appropriate, machine-readable format. Note: formats such as PDF, Powerpoint, and images of tables etc. are not considered suitable for raw data sharing.
• Community norms should be followed when storing, archiving and cataloging experimental materials. Where appropriate, physical materials (e.g. type specimens, microbial isolates, mutant seed stock, voucher specimens, paleontological specimens, etc.) must be permanently deposited in recognized centers (e.g. culture collections, seed stock centers, herbaria, or recognized museums or institutions) and accession numbers provided at the time the manuscript is submitted.
• A non exhaustive list of repositories for physical materials such as cell lines or mutant strains includes the RIKEN Bioresource Centre; the Jackson Laboratory; the European Mouse Mutant Archive; the European Conditional Mouse Mutagenesis Program; the American Type Culture Collection; the Knockout Mouse Project; Addgene; the Mutant Mouse Regional Resource Centers.
• Where novel research compounds are used, their chemical identity must be disclosed. Rigorous evidence for both the purity and identity of the materials must be provided so that the reliability of the experimental results can be assessed.
• Publications using commercial antibodies should report the supplying company and code number for all antibodies used. We recommend reporting using the following format:
  The following antibodies were used: Mouse anti-protein A monoclonal antibody (company E, catalogue number #1000) was used for Western blotting with human cells, as validated in (figure X or reference Y or validation profile Z).
• In accordance with the principles in Sharing Publication-Related Data and Materials (National Academies Press, 2003), research using proprietary data must also evaluate a piece of comparable public data if the authors cannot or do not make the proprietary data available.
• For software papers, 'materials' are taken to mean the source code and/or relevant software components required to run the software and reproduce the reported results. The software should be open source, made available under an appropriate license, and deposited in an appropriate archive. Data used to validate a software tool is subject to the same sharing requirements as any data in PeerJ publications.

• PeerJ is committed to improving scholarly communications and as part of this commitment, authors must make materials, code, data, and associated protocols available at the time of submission for peer review and publication. The preferred way to meet this requirement is to publicly deposit as noted below. Cases of non-compliance will be investigated by PeerJ which reserves the right to act on the results of the investigation.

  • All code needed to reproduce the results of the submission, as well as all raw data, must be made available either:
    • In a repository such as GitHub/GitLab (in which case a DOI, available via Zenodo, is a requirement), OR
    • As a supplementary file, to be published alongside the article
  • GitHub repositories can be archived directly by Zenodo, which creates a DOI. GitLab repositories must be "released", downloaded as a .zip file and then uploaded to Zenodo to obtain a DOI. Other similar archival repositories (e.g. figshare, institutional repositories) may also be used.
  • Third-party code must be cited appropriately, with a DOI (referred) or Software Heritage ID provided where available. Authors should make all reasonable attempts to ensure that the unpublished third-party code can be found by subsequent readers, and encourage the code writer to preserve their project by obtaining a persistent identifier.
  • Data should be provided in an appropriate, machine-readable format. Note: formats such as PDF, Powerpoint, and images of tables etc. are not considered suitable for raw data sharing.
  • Any supporting datasets for which there are no suitable repositories may be made available as publishable Supplemental Information files by PeerJ.
• 3D scans/models should be uploaded to a repository such as MorphoSource and made public at or before acceptance.
  • Data should be reported on a per-scan/specimen basis - not simply a link to a project. Morphosource provides guidance on how to cite data and can assign a DOI to each scan. If you are using a different repository, please use the most granular citation you can.
  • Authors using MorphoSource to share data during the review process must allow access to a PeerJ "reviewer account" in order to share their private data with editors/reviewers.
  • Authors using MorphoSource to share data during the review process must allow anonymous reviewer access using a temporary access link to the individual media files , as appropriate.
  • At acceptance, authors must make the dataset public and provide the public DOIs for each scan.
  • Authors using a different repository must make arrangements to allow anonymous reviewer access if the data are not public at the time of submission.

Any potential restrictions on data, code or materials (for example: proprietary data, material limitations, or information relating to human subjects), including how other researchers might attempt replication without this data, must be disclosed at the time of submission. PeerJ reserves the right to refuse consideration of such articles.

Where data can only be made available with restrictions, you must provide clear instructions on how these may be accessed. Authors may not act as sole contacts for data access so these data must be submitted to a suitable third party such as a data protection or ethics committee at your institution.

We strongly recommend (and in some cases require) that authors adhere to the reporting standards which have been adopted by their field (or which apply to their study design).

All statistical results should be reported in full, including the test that was performed, the reason for choosing that test, the corresponding test statistic, sample size, degrees of freedom, the exact p-value expressed up to 2 decimal spaces unless 'p<0.001' or confidence interval, and effect sizes. Where multiple testing is performed, suitable corrections must be made.

Do not report inferential statistics such as p values or confidence intervals for known quantities such as baseline measurements. The spread of the data can be indicated by descriptive statistics such as standard deviation, or quantiles and ranges.

Where appropriate, we recommend that you overlay bar graphs with scatter plots showing individual data points, or use another method to show the distribution of the data, such as boxplots, violin plots, etc.

PeerJ will consider Stage 1 Registered Reports. In brief, Registered Reports separate the review of the research question and protocol from that of the results and discussion. The intention is that if the methodology is peer-reviewed before the work is even performed, that the resulting research article (i.e. Stage 2) will be much more robust and less susceptible to post hoc manipulation (e.g. p-hacking). Please see osf.io/8mpji/wiki/home for a detailed explanation of what a Registered Report is.

Please note that we do not consider Systematic Review protocols or laboratory protocols as Registered Reports.

Authors should use the template at osf.io/93znh when preparing their registered report and that reviewers use the criteria at royalsocietypublishing.org/rsos/registered-reports to assess:

• The scientific validity of the research question(s).
• The logic, rationale, and plausibility of the proposed hypotheses.
• The soundness and feasibility of the methodology and analysis pipeline (including statistical power analysis where applicable).
• Whether the clarity and degree of methodological detail would be sufficient to replicate exactly the proposed experimental procedures and analysis pipeline.
• Whether the authors provide a sufficiently clear and detailed description of the methods to prevent undisclosed flexibility in the experimental procedures or analysis pipeline.
• Whether the authors have considered sufficient outcome-neutral conditions (e.g. absence of floor or ceiling effects; positive controls; other quality checks) for ensuring that the results obtained are able to test the stated hypotheses.

Peer-review of a Registered Report happens as normal, and authors might still be requested to make revisions, etc. before Acceptance. However, it is expected that if a Registered Report is accepted, then assuming the authors follow that protocol, the research article which will then report on the results is effectively pre-approved for publication. This only applies to submissions by the original authors of the Registered Report.

Stage 1 Registered Reports and their subsequent Research Articles are typically published in the same journal but this is not a requirement. Any Research Article should still be submitted and peer-reviewed (and it is our hope that the same Academic Editor will handle both submissions), but if the protocol was followed correctly then the results should be publishable, even if they are negative or inconclusive.

PeerJ welcomes articles describing bioinformatics software tools. These articles should present new software tools (or significant new functionality in existing software) of particular relevance to the bioinformatics and/or computational biology communities. The described tools should provide new computational or analytical functionality for researchers.

The functionality of the software should, where appropriate, be validated using real-world biological data and/or compared to existing tools. If available as a package (e.g. Python, R, Matlab, Octave), it should be accompanied by a minimal script that downloads the data (if not included in the package), loads it, and performs the analysis to reproduce the results (tables, plots, visualizations etc.) in the manuscript. Documentation & comments must be clear and sufficient to allow a typical user to perform the analysis described in the article. Ideally, the tools should be usable in a workflow that encourages reproducible research practices.

The software must be released under an open source license (e.g. MIT, GPL) and be widely available (i.e. hosted in a public repository such as Github or Bitbucket, or an institutional repository). Use of a version control system (e.g. Git, Subversion etc.) is strongly encouraged, as is adherence to language-specific packaging practices where appropriate. We also recommend the inclusion of appropriate unit tests. The software must be free to noncommercial users, and must be accessible without requiring any personally identifiable information. Software and validation data sets must comply with PeerJ Data and Materials Sharing policies. Reliance on a proprietary software such as Matlab does not preclude the publication but in general, a fully open source method is to be preferred.

PeerJ welcomes Data Reports that describe new curated datasets or major extensions of an existing dataset of interest and value to the research community. The rationale for collecting the dataset and its utility beyond a single research paper must be clearly articulated. To the extent possible, submissions should follow the form of a research article with the methodology described in enough detail to allow replication and reproduction. Where relevant, materials, specimens, etc. should be deposited in a suitable public repository. The dataset must either be uploaded with the submission or linked to a publicly accessible repository with a DOI and be available under a free and open license. Data must be in a usable and accessible format and be accompanied by sufficient metadata to allow reuse (i.e. following FAIR principles). If the dataset is expected to be extended over time then details of the ongoing curation, inclusion/exclusion criteria, storage, and availability must be provided. PeerJ's usual requirements for ethical approval, consent, field permits, and so on apply. Descriptive statistics may be included but submissions that analyze the dataset to test hypotheses and reach conclusions should be submitted as Research Articles.

PeerJ welcomes Method Papers which describe new or significantly improved methods and protocols, or the adaptation or reuse of an existing method in a new domain. Simple descriptions of a protocol are not considered. Submissions must articulate the need for the method and be accompanied by any data used to (i) develop and (ii) validate the method. Any materials required to complete the method must also be available and described with enough detail to allow others to obtain them. The method should be compared to any existing methods, ideally by direct comparison using the same materials, or otherwise by citing appropriate literature. Advantages and disadvantages of the method as compared to the available alternatives must be described and, where possible, quantified. Improvements might include, but are not limited to reduced cost, improved accessibility, greater specificity/sensitivity, etc.

Articles which report on clinical trials must follow the WHO definition of a clinical trial.

In accordance with the ICMJE guidelines, all clinical trials initiated from July 1st 2005 must be registered in an approved registry listed by the WHO or the ICMJE. Unregistered or retrospectively registered trials will not be considered. Where participant recruitment began before trials were publicly registered, authors must a) register all related clinical trials and include the relevant information, in the Methods section, and b) explain the reason for failing to register before participant recruitment, in the Methods section. Registration must be completed before trial interventions or data analysis are begun.

Clinical trials must be reported according to the relevant reporting guidelines (CONSORT for randomized controlled trials and TREND for non-randomized trials).

Specifically, authors must provide a copy of the trial protocol and a completed CONSORT (or TREND) checklist as supplemental information (these documents will also be published with the manuscript, if accepted). The CONSORT flow diagram must also be included, preferably as Figure 1 of the manuscript. The manner of the informed consent should be discussed in the article, and if consent was written, an empty copy of the patient consent form should be provided as a Confidential Supplemental Information file.

Manuscripts that report on population genetics should include special justification for presenting data based on both limited genetic data (<10 microsatellites or a single, low variability mtDNA region) and/or small sample sizes (<100 individuals). PeerJ does not publish primer notes. Manuscripts that report the characterization of specific primers (such as microsatellites) should include substantial biological analyses, and address a biological question or hypothesis as the focus of the submission.

Manuscripts that report range extensions, life history information, or the description of new species or other taxa should address a biological question or hypothesis as the focus of the submission. Unless there are compelling mitigating circumstances, descriptions of new extant taxa should be based on the whole organism (rather than shells/fragments/organs alone) and be supported by multiple lines of evidence (e.g. morphology, genetics, etc.).

• We require all authors to comply with the 'Animal Research: Reporting In Vivo Experiments' ARRIVE 2.0 guidelines, developed by NC3Rs. A completed full (21-point) ARRIVE 2.0 checklist must be submitted as a supplemental file with any submission that describes an interventional study on regulated animals.
• Manuscripts describing studies of wildlife must show in their Methods section that they adhere to the ARROW guidelines.
• Research on non-human primates is subject to specific guidelines from the Weatherall (2006) report, The Use of Non-Human Primates in Research.

• where the animals were obtained
• animal care, feeding, housing, and enrichment
• what experimental interventions were carried out, including details of any analgesia given. If no analgesia, justify this decision.
• what outcomes were measured
• sampling techniques, including any anesthetic procedures. If no anesthesia was given, justify this decision
• details of euthanasia method(s) used. Please refer to the current edition of the AVMA Guidelines for the Euthanasia of Animals for acceptable methods.
• criteria for euthanizing animals prior to the planned end of the experiment and whether this was needed
• what happened to any surviving animals at the conclusion of the experiment
• for studies involving tumors in animal models, all tumor sizes must be reported and photographic evidence provided as a Figure or Supplemental file. The protocol must ensure that experimental animals are humanely euthanized if the tumor size reaches a maximum dimension of 20 mm in mice or 40 mm in rats, or the combined volume of tumors in a single animal reaches 2000 mm³ (mice) or 4000 mm³ (rats).

In order to increase discoverability, when naming a new species we recommend that the names are mentioned in the title (where feasible) and in the abstract of your article. If multiple new species are being named then it may not be practical to include all or any of them in the title due to space constraints.

- In the metadata, the globally unique identifier (GUID), currently a Life Science Identifier (LSID), should be listed with the new species name. For example:

Brachycephalus mariaeterezae sp. nov. urn:lsid:zoobank.org:act:74D8D85E-BE68-4A51-AF85-DC97C564D458

- Authors must use the following text in the Methods section:

"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Commission on Zoological Nomenclature (ICZN), and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix http://zoobank.org/. The LSID for this publication is: [INSERT HERE]. The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central SCIE and CLOCKSS."

- The globally unique identifier, currently a Life Science Identifier (LSID), should be listed under the new taxon name in the Results Section.

• At acceptance, the International Plant Names Index (IPNI, a database which deals only with seed plants, ferns & lycophytes) will be contacted by PeerJ editorial staff to provide the identifier. It should be noted that obtaining an LSID isn’t a requirement under the ICN, but it is a requirement of PeerJ.

-Assuming an LSID is obtained, authors will be made aware of them by PeerJ staff and must use the following text in the Methods section:

"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants (ICN), and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work which have been issued with identifiers by IPNI will eventually be made available to the Global Names Index. The IPNI LSIDs can be resolved and the associated information viewed through any standard web browser by appending the LSID contained in this publication to the prefix "http://ipni.org/". The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central SCIE, and CLOCKSS".

- An additional ICN publication requirement effective January 1, 2013: all manuscripts naming fungi must obtain the citation of an identifier issued by a recognized repository such as MycoBank or Index Fungorum and include it in the protologue (everything associated with a name at its valid publication). Life Science Identifiers (LSIDs) or Globally Unique Identifier are only required for fungi.

- In the Methods section, authors must include a sub-section called "Nomenclature" using the following wording (this example is for taxon names submitted to MycoBank; please substitute appropriately if the name was submitted to Index Fungorum):

"The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants, and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work have been submitted to MycoBank from where they will be made available to the Global Names Index. The unique MycoBank number can be resolved and the associated information viewed through any standard web browser by appending the MycoBank number contained in this publication to the prefix "http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=". The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central SCIE, and CLOCKSS."

- Authors of new names and new combinations must provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). Upload these certificates as Supplemental Files at submission.

- As required by the Bacteriological Code, the IJSEM publishes Validation Lists containing new names that were effectively published in any journal other than the IJSB/IJSEM. To complete validation of new names effectively published, authors should submit a covering letter and three reprints or photocopies or a PDF file of the published article(s) to the IJSEM Editorial Office.

- All new viral taxa must be approved by ICTV before any individual taxon (and its name) can be official. To create a new taxon, a proposal should be submitted to the ICTV using the procedures detailed in their FAQ.