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      Phylotocol: Promoting Transparency and Overcoming Bias in Phylogenetics

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          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.

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          Most cited references37

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          The case for motivated reasoning.

          Ziva Kunda (1990)
          It is proposed that motivation may affect reasoning through reliance on a biased set of cognitive processes--that is, strategies for accessing, constructing, and evaluating beliefs. The motivation to be accurate enhances use of those beliefs and strategies that are considered most appropriate, whereas the motivation to arrive at particular conclusions enhances use of those that are considered most likely to yield the desired conclusion. There is considerable evidence that people are more likely to arrive at conclusions that they want to arrive at, but their ability to do so is constrained by their ability to construct seemingly reasonable justifications for these conclusions. These ideas can account for a wide variety of research concerned with motivated reasoning.
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            Confirmation bias: A ubiquitous phenomenon in many guises.

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              SCIENTIFIC STANDARDS. Promoting an open research culture.

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                Author and article information

                Contributors
                Role: Associate Editor
                Journal
                Syst Biol
                Syst. Biol
                sysbio
                Systematic Biology
                Oxford University Press
                1063-5157
                1076-836X
                July 2019
                31 December 2018
                31 December 2018
                : 68
                : 4
                : 672-678
                Affiliations
                [1 ]Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
                [2 ]Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
                Author notes
                Correspondence to be sent to: Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA; E-mail: joseph.ryan@ 123456whitney.ufl.edu .
                Article
                syy090
                10.1093/sysbio/syy090
                6568013
                30597106
                1a266cb4-ea52-4d3e-9235-1bc9494c7412
                © The Author(s) 2018. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 20 November 2018
                : 20 December 2018
                : 20 December 2018
                Page count
                Pages: 7
                Funding
                Funded by: National Science Foundation 10.13039/100000001
                Award ID: 1542597
                Categories
                Point of View

                Animal science & Zoology
                accountability,confirmation bias,open science,phylogenetics,phylotocol,protocol,transparency

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