Abstract
The integrity of science requires that the process be based on sound experimental design and objective methodology. Strategies that increase reproducibility and transparency in science protect this integrity by reducing conscious and unconscious biases. Given the large number of analysis options and the constant development of new methodologies in phylogenetics, this field is one that would particularly benefit from more transparent research design. Herein, we introduce phylotocol (fi lō ’ta kôl), an a priori protocol-driven approach in which all analyses are planned and documented at the start of a project. The phylotocol template is simple and the implementation options are flexible to reduce administrative burdens and allow researchers to adapt it to their needs without restricting scientific creativity. While the primary goal of phylotocol is to increase transparency and accountability, it has a number of auxiliary benefits including improving study design and reproducibility, enhancing collaboration and education, and increasing the likelihood of project completion. Our goal with this Point of View article is to encourage a dialog about transparency in phylogenetics and the best strategies to bring transparent research practices to our field.
Highlights
Inferring relationships between genes, genomes, and species is essential for a fundamental understanding of biology
Given the large number of analysis options and the constant development of new methodologies in phylogenetics, this field is one that would benefit from more transparent research design
While the primary goal of phylotocol is to increase transparency and accountability, it has a number of auxiliary benefits including improving study design and reproducibility, enhancing collaboration and education, and increasing the likelihood of project completion. Our goal with this Point of View article is to encourage a dialog about transparency in phylogenetics and the best strategies to bring transparent research practices to our field. [Accountability; confirmation bias; open science; phylogenetics; phylotocol; protocol; transparency.]
Summary
Genomes, and species is essential for a fundamental understanding of biology. Research plans are generally informal and rarely outlined in detail prior to the start of the project; rather, plans are often constructed gradually, with each step motivated by the results of the step before, an approach Gelman and Loken (2014) refer to as the “garden of forking paths.”. This strategy is problematic because the selection of some paths is more likely than the selection of others, if researchers make downstream methodological decisions consciously or, POINT OF VIEW more often, unconsciously, in response to results that conflict with expected outcomes. The biggest barrier to widespread adoption to preregistration is the administrative effort associated with its implementation, perceived restrictions on scientific creativity and exploratory analyses, and concerns that project ideas will be scooped
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