Phylotocol: Promoting transparency and overcoming bias in phylogenetics

Research products that lack transparency and are influenced by confirmation bias lead to barriers that, when left unchecked, propagate throughout the scientific record and lead to wasted research effort. Phylogenetics is particularly vulnerable given its ever-evolving methodology and wide choice of options for conducting analyses. Great strides in transparency have been achieved in clinical research by the implementation of a priori protocols. Here we propose a similar approach—phylotocol—a straightforward, protocol-driven strategy tailored to the needs of phylogenetic studies. We provide a simple template and offer a flexible range of implementation frameworks, including preregistration options. Besides increasing transparency and accountability, phylotocol has the added benefits of improving study design and reproducibility, enhancing collaboration and education, and increasing the likelihood of project completion. The increased transparency afforded by wide adoption of an a priori system like phylotocol would have extensive benefits to science.