Meeting Abstract
Inferring relationships between genes, genomes, and species is essential for a fundamental understanding of biology. Current best practices in phylogenetics do not include any formalized a priori decision making, which makes the process susceptible to confirmation bias. In clinical trials, where the outcomes of a study can lead to decisions that put human lives at risk, biases have been explicitly controlled for and transparency ensured by requiring an a priori protocol that outlines objective(s), design, methodology, statistical considerations, and study organization. Here we introduce phylotocol, a version-controlled a priori methodological procedure for providing a publicly available protocol for phylogenetic analyses. We have implemented the process for several projects, and besides promoting transparency and accountability in our process, phylotocol has led to several unforeseen advantages including: (1) serving as a training tool for junior researchers, (2) increasing productivity, (3) facilitating collaboration, (4) promoting efficient computational resource allocation, and (5) providing a detailed outline for a subsequent manuscript. We are currently seeking feedback on the concept and on our phylotocol template, which is based on a clinical trial protocol from the National Institutes of Health. Phylotocol is an easy to implement process that promotes transparency, reduces the risk of confirmation bias and facilitates project organization. A widespread increase in transparency is an important step in phylogenetics that will greatly accelerate our understanding of the evolutionary history of life.
