template, example, and instructions on how to make an a priori phylogenetic protocol
For a detailed discussion of phylotocol, please see our preprint: https://peerj.com/preprints/26585/
The rationale for phylotocol is to provide general guidelines and a very generic template for researchers to document a priori planned phylogenetic analyses as well as changes to the original protocol through updated versioning. The concept is modeled after clinical trial protocols. The original template is modeled after the NIH clinical trial template available here: http://osp.od.nih.gov/wp-content/uploads/Protocol-Template-Version-1.0-040717.docx
It is intended that a phylotocol would be posted to a public repository like GitHub or FigShare immediately after it is completed, and that a DOI or link to the document would be provided in any publications that resulted from the proposed analyses. It can also be used as the basis of a preregistration (e.g., through the Open Science Framework http://help.osf.io/m/registrations/l/524205-register-your-project). It is highly recommended to post the phylotocol on a public site that will provide a timestamp.
A phylotocol adds transparency to the process of phylogenetic analysis. It allows readers of a phylogenetic study to understand the original rationale for a study. It forces any changes (e.g., removal of taxa, change in methods, etc.) to be accompanied by explicit justification. In this way, it helps reduce confirmation bias, and allows outsiders to assess the work rather than assume that the reported results were influenced by confirmation bias.
A phylotocol can be very helpful in planning a study. It helps trainees organize their work and provides an opportunity for mentees to provide feedback early in the study. It provides a clear set of tasks that can then be divided between collaborators. It can be helpful for assessing computational needs for the project. It can help establish expected timelines for completing particular tasks. It can also serve as the text of methods or extended methods in a publication.
Public comment is very important for the success of phylotocol. Please do not hesitate to post ideas, concerns, requests, etc. as an issue on this GitHub repository.
It is important to incorporate all sections of the template into your phylotocol and to do so in the same order. If a particular section is not applicable to your study, include it, but indicate that it is not applicable.
Example text is included to further aid in phylotocol writing and can be modified to suit the study or deleted. Within example text, a need for insertion of specific information is notated by <angle brackets>.
Version control is important to track phylotocol development, revisions, and amendments. With each revision, the version number and date located on the cover page and in the footer of each page should be updated. When making changes to a released phylotocol, the amendment history should be maintained (see Section 5 PHYLOTOCOL AMENDMENT HISTORY). All versions should be published with the study.
The following are repos with examples of phylotocol
- gene family analyses: https://github.com/josephryan/2018-Pastrana_etal_SpongeParaHoxAnalyses
- simulation analyses: https://github.com/josephryan/Hernandez_Ryan_2018_RecodingSim
- species phylogeny analyes: https://github.com/josephryan/Whelpley_et_al_2018_SeaCucumberPhylo
The following is an example of a preregistration that includes a phylotoocol
- simulation analyses: https://osf.io/aqv3y/register/565fb3678c5e4a66b5582f67
phylotocol is released under the GNU v3 license. See LICENSE for details.