Phylotocol: Promoting Transparency and Overcoming Bias in Phylogenetics

Area of Science:

• Evolutionary Biology
• Computational Biology
• Bioinformatics

Background:

• Scientific integrity relies on sound experimental design and objective methodology.
• Reproducibility and transparency are crucial for mitigating biases in scientific research.
• Phylogenetics, with its numerous analysis options and evolving methodologies, particularly benefits from enhanced research transparency.

Purpose of the Study:

• To introduce phylotocol, an a priori protocol-driven approach for phylogenetic research.
• To enhance transparency and accountability in phylogenetic study design.
• To foster a dialogue on best practices for transparent research in phylogenetics.

Main Methods:

• Development of phylotocol, a flexible and simple template for planning and documenting all analyses at the project's outset.
• Implementation of protocol-driven strategies to standardize research design in phylogenetics.
• Focus on reducing administrative burden while maintaining scientific creativity.

Main Results:

• Phylotocol increases transparency and accountability in phylogenetic research.
• Auxiliary benefits include improved study design, enhanced reproducibility, and better collaboration.
• The approach supports education and increases the likelihood of project completion.

Conclusions:

• Phylotocol offers a practical solution for increasing transparency in phylogenetics.
• Adoption of protocol-driven research can significantly improve the quality and reliability of phylogenetic studies.
• Encouraging dialogue and implementing transparent practices are vital for the future of the field.